Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format. Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png Could someone please show me how to fix this? Thank you.
And the table after I converted it to tabular format looks like this: On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui <buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
And the table after I converted it to tabular format looks like this: GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 - On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui <buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui <buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
Hi Minh, I found this previous discussion that is related to your problem. You can search our mailing list by using "site:http://lists.bx.psu.edu/pipermail/" in google. Please check if it's applicable to you and let us know! http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002551.html Thanks, Kanwei On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui <buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui <buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui <buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature "An error occurred running this job: sort: multi-character tab `$\t'" Even I already use Text Manipulation->Convert to convert my table to Tabs format. Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Kan, I read the discussion but they didnt come up with a solution. I need to test it more. Thank you, On Wed, Jul 28, 2010 at 4:05 PM, Kanwei Li <kanwei@gmail.com> wrote:
Hi Minh,
I found this previous discussion that is related to your problem. You can search our mailing list by using "site:http://lists.bx.psu.edu/pipermail/" in google. Please check if it's applicable to you and let us know!
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002551.html
Thanks,
Kanwei
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui <buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui <buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui <buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature "An error occurred running this job: sort: multi-character tab `$\t'" Even I already use Text Manipulation->Convert to convert my table to
Tabs
format. Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment. I suspect, there is an error in your big file? Hans On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort this table). If the big file have errors, it should give me some kind of errors when I Convert it. I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them. On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
Hi,
I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans,
This is interesting. I copied that table from Galaxy (I couldnt sort this table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote: Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote: And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
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I just had this exact issue. For me, the problem was caused by my default shell (different than login shell) being set to dash instead of bash. Dash doesn't respect the $'\t' trick, and so fails. The sorter.py script performs a system call (os.system(...)) which uses /bin/sh. On Ubuntu (me) and perhaps other distro's, /bin/sh is a symbolic link to dash. To see if this is your issue, do: $ ls -l /bin/sh If it points to dash, then either do: $ sudo dpkg-reconfigure dash # for debian-based systems like ubuntu then choose "No-- Don't install dash" OR $ sudo ln -s /bin/sh bash -- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587 On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort this table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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Hi Jacob, Guru I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. When I sort the table (c2) , it returns a table without sorting it. When I filter the table (c2=='Unmapped'), it returns an empty table. Screenshot: http://img514.imageshack.us/img514/6047/screenshotks.png My data after convertion looks like this: GIQPZ7U01A1A82-W3_11_11 Partial 99 95 chr3 17443613 17443685 - GIQPZ7U01BM124-W3_11_11 Partial 99 89 chr3 17443521 17443685 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 99 67 chr3 17443511 17443685 - GIQPZ7U01CB92X-W3_10_21 Partial 99 88 chr3 17443608 17443685 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Partial 96 95 chr3 17443615 17443685 - GIQPZ7U01CHEFR-W3_11_11 Partial 99 95 chr3 17443611 17443685 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 99 64 chr3 17443511 17443685 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 87 chr3 17443523 17443685 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 99 78 chr3 17443625 17443685 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 91 chr3 17443509 17443685 - GIQPZ7U01CGAG5-W3_10_21 Partial 99 88 chr3 17443521 17443685 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 98 79 chr3 17443608 17443685 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 98 78 chr3 17443608 17443685 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443685 ..... P.S: I am using Ubuntu. On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu>wrote:
I just had this exact issue. For me, the problem was caused by my default shell (different than login shell) being set to dash instead of bash. Dash doesn't respect the $'\t' trick, and so fails. The sorter.py script performs a system call (os.system(...)) which uses /bin/sh. On Ubuntu (me) and perhaps other distro's, /bin/sh is a symbolic link to dash.
To see if this is your issue, do: $ ls -l /bin/sh
If it points to dash, then either do: $ sudo dpkg-reconfigure dash # for debian-based systems like ubuntu then choose "No-- Don't install dash" OR $ sudo ln -s /bin/sh bash
-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort this table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3
17443511
17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155
GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155
GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155
On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote: - - -
GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
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Hi Minh, I'm unable to reproduce this behavior with the small dataset pasted in one of your earlier emails. Would you mind sending me your large dataset with 30008 lines, so that I can take a look at what might be going wrong? Thanks, Guru Galaxy team. On Aug 5, 2010, at 1:32 PM, Minh Bui wrote:
Hi Jacob, Guru
I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. When I sort the table (c2) , it returns a table without sorting it. When I filter the table (c2=='Unmapped'), it returns an empty table. Screenshot: http://img514.imageshack.us/img514/6047/screenshotks.png
My data after convertion looks like this: GIQPZ7U01A1A82-W3_11_11 Partial 99 95 chr3 17443613 17443685 - GIQPZ7U01BM124-W3_11_11 Partial 99 89 chr3 17443521 17443685 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 99 67 chr3 17443511 17443685 - GIQPZ7U01CB92X-W3_10_21 Partial 99 88 chr3 17443608 17443685 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Partial 96 95 chr3 17443615 17443685 - GIQPZ7U01CHEFR-W3_11_11 Partial 99 95 chr3 17443611 17443685 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 99 64 chr3 17443511 17443685 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 87 chr3 17443523 17443685 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 99 78 chr3 17443625 17443685 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 91 chr3 17443509 17443685 - GIQPZ7U01CGAG5-W3_10_21 Partial 99 88 chr3 17443521 17443685 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 98 79 chr3 17443608 17443685 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 98 78 chr3 17443608 17443685 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443685 .....
P.S: I am using Ubuntu.
On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu> wrote: I just had this exact issue. For me, the problem was caused by my default shell (different than login shell) being set to dash instead of bash. Dash doesn't respect the $'\t' trick, and so fails. The sorter.py script performs a system call (os.system(...)) which uses /bin/sh. On Ubuntu (me) and perhaps other distro's, /bin/sh is a symbolic link to dash.
To see if this is your issue, do: $ ls -l /bin/sh
If it points to dash, then either do: $ sudo dpkg-reconfigure dash # for debian-based systems like ubuntu then choose "No-- Don't install dash" OR $ sudo ln -s /bin/sh bash
-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort this table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format.
Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png
Could someone please show me how to fix this? Thank you.
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Hi Guru, I attached the original 454 GS Mapper in the email. Thank you for helping me. On Thu, Aug 5, 2010 at 2:01 PM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
Hi Minh,
I'm unable to reproduce this behavior with the small dataset pasted in one of your earlier emails. Would you mind sending me your large dataset with 30008 lines, so that I can take a look at what might be going wrong?
Thanks, Guru Galaxy team.
On Aug 5, 2010, at 1:32 PM, Minh Bui wrote:
Hi Jacob, Guru
I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. When I sort the table (c2) , it returns a table without sorting it. When I filter the table (c2=='Unmapped'), it returns an empty table. Screenshot: http://img514.imageshack.us/img514/6047/screenshotks.png
My data after convertion looks like this:
GIQPZ7U01A1A82-W3_11_11 Partial 99 95 chr3 17443613 17443685 - GIQPZ7U01BM124-W3_11_11 Partial 99 89 chr3 17443521 17443685 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 99 67 chr3 17443511 17443685 - GIQPZ7U01CB92X-W3_10_21 Partial 99 88 chr3 17443608 17443685 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Partial 96 95 chr3 17443615 17443685 - GIQPZ7U01CHEFR-W3_11_11 Partial 99 95 chr3 17443611 17443685 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 99 64 chr3 17443511 17443685 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 87 chr3 17443523 17443685 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 99 78 chr3 17443625 17443685 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 91 chr3 17443509 17443685 - GIQPZ7U01CGAG5-W3_10_21 Partial 99 88 chr3 17443521 17443685 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 98 79 chr3 17443608 17443685 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 98 78 chr3 17443608 17443685 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443685
.....
P.S: I am using Ubuntu.
On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu>wrote:
I just had this exact issue. For me, the problem was caused by my default shell (different than login shell) being set to dash instead of bash. Dash doesn't respect the $'\t' trick, and so fails. The sorter.py script performs a system call (os.system(...)) which uses /bin/sh. On Ubuntu (me) and perhaps other distro's, /bin/sh is a symbolic link to dash.
To see if this is your issue, do: $ ls -l /bin/sh
If it points to dash, then either do: $ sudo dpkg-reconfigure dash # for debian-based systems like ubuntu then choose "No-- Don't install dash" OR $ sudo ln -s /bin/sh bash
-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort
table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3
17443511
17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155
GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155
GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155
On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote: this - - -
GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
> Hi, > I always get this error when I use Sort feature > *"An error occurred running this job: sort: multi-character tab `$\t'"* > Even I already use Text Manipulation->Convert to convert my table to > Tabs > format. > > Here is the screenshot of what happen (I want to sort C2 on job #12) : > http://img408.imageshack.us/img408/7906/screenshotbu.png > > > Could someone please show me how to fix this? > Thank you. >
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Hi Minh, Thanks for sending over the dataset. Here are my responses to your questions:
When I filter the table (c2=='Unmapped'), it returns an empty table.
It's normal behavior for the filter tool to skip lines that are incomplete. This, as you pointed out, is the reason why filtering with condition c2=='Unmapped' returns an empty dataset. You can however achieve the same by using "Select" tool under "Filter and sort" section, with the condition NOT matching the pattern Unmapped.
When I sort the table (c2) , it returns a table without sorting it.
I'm still unable to reproduce this issue. It definitely seems like the sort command on your machine might be treating certain options differently. May be if you could send us the tool options chosen by you(or the generated command line), we could try debugging it further. Thanks, Guru Galaxy team. On Aug 6, 2010, at 9:41 AM, Minh Bui wrote:
Hi Guru, I attached the original 454 GS Mapper in the email. Thank you for helping me.
On Thu, Aug 5, 2010 at 2:01 PM, Guruprasad Ananda <gua110@bx.psu.edu> wrote: Hi Minh,
I'm unable to reproduce this behavior with the small dataset pasted in one of your earlier emails. Would you mind sending me your large dataset with 30008 lines, so that I can take a look at what might be going wrong?
Thanks, Guru Galaxy team.
On Aug 5, 2010, at 1:32 PM, Minh Bui wrote:
Hi Jacob, Guru
I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. When I sort the table (c2) , it returns a table without sorting it. When I filter the table (c2=='Unmapped'), it returns an empty table. Screenshot: http://img514.imageshack.us/img514/6047/screenshotks.png
My data after convertion looks like this: GIQPZ7U01A1A82-W3_11_11 Partial 99 95 chr3 17443613 17443685 - GIQPZ7U01BM124-W3_11_11 Partial 99 89 chr3 17443521 17443685 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 99 67 chr3 17443511 17443685 - GIQPZ7U01CB92X-W3_10_21 Partial 99 88 chr3 17443608 17443685 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Partial 96 95 chr3 17443615 17443685 - GIQPZ7U01CHEFR-W3_11_11 Partial 99 95 chr3 17443611 17443685 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 99 64 chr3 17443511 17443685 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 87 chr3 17443523 17443685 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 99 78 chr3 17443625 17443685 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 91 chr3 17443509 17443685 - GIQPZ7U01CGAG5-W3_10_21 Partial 99 88 chr3 17443521 17443685 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 98 79 chr3 17443608 17443685 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 98 78 chr3 17443608 17443685 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443685 .....
P.S: I am using Ubuntu.
On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu> wrote: I just had this exact issue. For me, the problem was caused by my default shell (different than login shell) being set to dash instead of bash. Dash doesn't respect the $'\t' trick, and so fails. The sorter.py script performs a system call (os.system(...)) which uses /bin/sh. On Ubuntu (me) and perhaps other distro's, /bin/sh is a symbolic link to dash.
To see if this is your issue, do: $ ls -l /bin/sh
If it points to dash, then either do: $ sudo dpkg-reconfigure dash # for debian-based systems like ubuntu then choose "No-- Don't install dash" OR $ sudo ln -s /bin/sh bash
-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort this table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3 17443511 17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
> Hi, > I always get this error when I use Sort feature > *"An error occurred running this job: sort: multi-character tab `$\t'"* > Even I already use Text Manipulation->Convert to convert my table to > Tabs > format. > > Here is the screenshot of what happen (I want to sort C2 on job #12) : > http://img408.imageshack.us/img408/7906/screenshotbu.png > > > Could someone please show me how to fix this? > Thank you. >
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You might try running the python command directly, outside of galaxy, to try to track down the source of the error. I also can't repro your issue, though out datasets differ. Look in the log file at galaxy_dist/paster.log for something along the lines of: galaxy.jobs.runners.local DEBUG 2010-08-05 11:24:04,018 executing: python /home/wbiesing/galaxy_dist/tools/filters/sorter.py --input=/home/wbiesing/galaxy_dist/database/files/000/dataset_25.dat --out_file1=/home/wbiesing/galaxy_dist/database/files/000/dataset_46.dat --column=1 --style=alpha --order=ASC 2 num ASC Which is the output for my sort command. Does sorting work on smaller datasets for you? -- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587 On Thu, Aug 5, 2010 at 10:32 AM, Minh Bui <buiduyminh@gmail.com> wrote:
Hi Jacob, Guru
I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. When I sort the table (c2) , it returns a table without sorting it. When I filter the table (c2=='Unmapped'), it returns an empty table. Screenshot: http://img514.imageshack.us/img514/6047/screenshotks.png
My data after convertion looks like this:
GIQPZ7U01A1A82-W3_11_11 Partial 99 95 chr3 17443613 17443685 - GIQPZ7U01BM124-W3_11_11 Partial 99 89 chr3 17443521 17443685 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 99 67 chr3 17443511 17443685 - GIQPZ7U01CB92X-W3_10_21 Partial 99 88 chr3 17443608 17443685 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Partial 96 95 chr3 17443615 17443685 - GIQPZ7U01CHEFR-W3_11_11 Partial 99 95 chr3 17443611 17443685 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 99 64 chr3 17443511 17443685 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 87 chr3 17443523 17443685 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 99 78 chr3 17443625 17443685 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 91 chr3 17443509 17443685 - GIQPZ7U01CGAG5-W3_10_21 Partial 99 88 chr3 17443521 17443685 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 98 79 chr3 17443608 17443685 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 98 78 chr3 17443608 17443685 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443685
.....
P.S: I am using Ubuntu.
On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu>wrote:
I just had this exact issue. For me, the problem was caused by my default shell (different than login shell) being set to dash instead of bash. Dash doesn't respect the $'\t' trick, and so fails. The sorter.py script performs a system call (os.system(...)) which uses /bin/sh. On Ubuntu (me) and perhaps other distro's, /bin/sh is a symbolic link to dash.
To see if this is your issue, do: $ ls -l /bin/sh
If it points to dash, then either do: $ sudo dpkg-reconfigure dash # for debian-based systems like ubuntu then choose "No-- Don't install dash" OR $ sudo ln -s /bin/sh bash
-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort
table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3
17443511
17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155
GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155
GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155
On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote: this - - -
GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
And the table after I converted it to tabular format looks like this:
On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote:
> Hi, > I always get this error when I use Sort feature > *"An error occurred running this job: sort: multi-character tab `$\t'"* > Even I already use Text Manipulation->Convert to convert my table to > Tabs > format. > > Here is the screenshot of what happen (I want to sort C2 on job #12) : > http://img408.imageshack.us/img408/7906/screenshotbu.png > > > Could someone please show me how to fix this? > Thank you. >
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Hi Jacob, I am not on my computer right now but ill give you the report as soon as I am back home. Thank you. On Thu, Aug 5, 2010 at 2:27 PM, Jacob Biesinger <jake.biesinger@uci.edu>wrote:
You might try running the python command directly, outside of galaxy, to try to track down the source of the error. I also can't repro your issue, though out datasets differ.
Look in the log file at galaxy_dist/paster.log for something along the lines of:
galaxy.jobs.runners.local DEBUG 2010-08-05 11:24:04,018 executing: python /home/wbiesing/galaxy_dist/tools/filters/sorter.py --input=/home/wbiesing/galaxy_dist/database/files/000/dataset_25.dat --out_file1=/home/wbiesing/galaxy_dist/database/files/000/dataset_46.dat --column=1 --style=alpha --order=ASC 2 num ASC
Which is the output for my sort command. Does sorting work on smaller datasets for you? -- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
On Thu, Aug 5, 2010 at 10:32 AM, Minh Bui <buiduyminh@gmail.com> wrote:
Hi Jacob, Guru
I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. When I sort the table (c2) , it returns a table without sorting it. When I filter the table (c2=='Unmapped'), it returns an empty table. Screenshot: http://img514.imageshack.us/img514/6047/screenshotks.png
My data after convertion looks like this:
GIQPZ7U01A1A82-W3_11_11 Partial 99 95 chr3 17443613 17443685 - GIQPZ7U01BM124-W3_11_11 Partial 99 89 chr3 17443521 17443685 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 99 67 chr3 17443511 17443685 - GIQPZ7U01CB92X-W3_10_21 Partial 99 88 chr3 17443608 17443685 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117 367155 - GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Partial 96 95 chr3 17443615 17443685 - GIQPZ7U01CHEFR-W3_11_11 Partial 99 95 chr3 17443611 17443685 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 99 64 chr3 17443511 17443685 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 87 chr3 17443523 17443685 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 99 78 chr3 17443625 17443685 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 91 chr3 17443509 17443685 - GIQPZ7U01CGAG5-W3_10_21 Partial 99 88 chr3 17443521 17443685 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 98 79 chr3 17443608 17443685 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 98 78 chr3 17443608 17443685 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443685
.....
P.S: I am using Ubuntu.
On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu>wrote:
I just had this exact issue. For me, the problem was caused by my default shell (different than login shell) being set to dash instead of bash. Dash doesn't respect the $'\t' trick, and so fails. The sorter.py script performs a system call (os.system(...)) which uses /bin/sh. On Ubuntu (me) and perhaps other distro's, /bin/sh is a symbolic link to dash.
To see if this is your issue, do: $ ls -l /bin/sh
If it points to dash, then either do: $ sudo dpkg-reconfigure dash # for debian-based systems like ubuntu then choose "No-- Don't install dash" OR $ sudo ln -s /bin/sh bash
-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
Hi Minh, Sorry for not getting back to you sooner. It looks like the sort command on your machine works differently from that on Galaxy, in that it doesn't recognize -t $'\t'as a valid option. Can you please make the following change and let me know if the tool ends in error state or not. galaxy_home_folder/tools/filters/sorter.py: line 42: replace cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) with cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols), outputfile, inputfile) Thanks, Guru. On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
Hi Hans, This is interesting. I copied that table from Galaxy (I couldnt sort
table). If the big file have errors, it should give me some kind of errors when I Convert it.
I don't know why but I still get the error. I'll run more tests to see what happen. I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine and I don't get any error. But when I try to filter C2=='Chimeric' or 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have chromosome, start-end position...), Galaxy can't filter them.
On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi
Does your small example really not work for you? It works fine for me (after copy paste and sort on C2), see attachment.
I suspect, there is an error in your big file?
Hans
On 07/28/2010 08:43 PM, Minh Bui wrote:
And the table after I converted it to tabular format looks like this:
GIQPZ7U01A1A82-W3_11_11 Full 90 100 chr3 17443613 17443686 - GIQPZ7U01BM124-W3_11_11 Partial 98 90 chr3 17443521 17443687 - GIQPZ7U01CG1P0-S3_11_11 Partial 98 65 chr2 162180459 162180499 - GIQPZ7U01B6DQ9-S3_11_11 Chimeric GIQPZ7U01ASQA4-NL3_10_21 Partial 98 67 chr3
17443511
17443686 - GIQPZ7U01CB92X-W3_10_21 Partial 98 89 chr3 17443608 17443686 - GIQPZ7U01AW16P-S3_10_23 Unmapped GIQPZ7U01B1FV1-S3_10_21 Partial 98 75 chr16 367117
367155 -
GIQPZ7U01B2PUV-S3_11_11 Chimeric GIQPZ7U01CC7BN-S3_10_23 Partial 97 84 chr19 18614552 18614649 - GIQPZ7U01BOQUL-NL3_10_21 Full 86 100 chr3 17443615 17443686 - GIQPZ7U01CHEFR-W3_11_11 Full 90 100 chr3 17443611 17443686 - GIQPZ7U01B2QVH-NL3_10_21 Partial 100 67 chr16 367117 367155 - GIQPZ7U01BH73U-S3_11_11 Unmapped GIQPZ7U01A2OJ8-NL3_10_23 Partial 98 65 chr3 17443511 17443686 - GIQPZ7U01B96JR-S3_10_21 Unmapped GIQPZ7U01BSF3A-W3_10_21 Partial 99 88 chr3 17443523 17443687 - GIQPZ7U01AY7DH-S3_10_21 Partial 99 90 chr4 38640070 38640237 + GIQPZ7U01B3I06-S3_10_23 Full 98 100 chr19 18614567 18614647 - GIQPZ7U01AMR6X-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01ALYU8-W3_10_21 Partial 98 80 chr3 17443625 17443687 - GIQPZ7U01BXRZ1-W3_10_21 Partial 95 92 chr3 17443509 17443686 - GIQPZ7U01CGAG5-W3_10_21 Partial 98 89 chr3 17443521 17443687 - GIQPZ7U01CBIX7-S3_10_23 Partial 96 85 chr19 18614551 18614649 - GIQPZ7U01A1RCP-S3_10_23 Partial 99 85 chr19 18614551 18614649 - GIQPZ7U01BYXFR-W3_10_21 Partial 97 80 chr3 17443608 17443686 - GIQPZ7U01B275Q-S3_10_21 Partial 97 67 chr16 367117 367155 - GIQPZ7U01AXBIJ-S3_11_11 Chimeric GIQPZ7U01BXW15-S3_10_23 Full 95 100 chr19 18614579 18614649 - GIQPZ7U01BV1GN-W3_10_21 Partial 97 80 chr3 17443608 17443687 - GIQPZ7U01BIYVC-S3_10_23 Partial 98 88 chr19 18614551 18614649 - GIQPZ7U01BS3VK-S3_10_23 Unmapped GIQPZ7U01BOGIN-NL3_10_21 Partial 99 61 chr3 17443519 17443686 - GIQPZ7U01B313G-S3_11_11 Partial 98 68 chr2 162180459 162180501 - GIQPZ7U01BCMVY-W3_10_23 Partial 99 57 chr16 367117 367155 - GIQPZ7U01BL41A-W3_10_23 Partial 95 49 chr15 50814744 50814785 + GIQPZ7U01B8EWK-NL3_10_21 Partial 98 64 chr3 17443511 17443686 - GIQPZ7U01BY5AD-NL3_10_21 Partial 97 64 chr3 17443511 17443686 - GIQPZ7U01CA6RX-S3_10_21 Unmapped GIQPZ7U01BQOHG-W3_10_21 Partial 98 89 chr3 17443521 17443686 -
On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com> wrote:
> And the table after I converted it to tabular format looks like
On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote: this this:
> > > > On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com> wrote: > >> Hi, >> I always get this error when I use Sort feature >> *"An error occurred running this job: sort: multi-character tab `$\t'"* >> Even I already use Text Manipulation->Convert to convert my table to >> Tabs >> format. >> >> Here is the screenshot of what happen (I want to sort C2 on job #12) : >> http://img408.imageshack.us/img408/7906/screenshotbu.png >> >> >> Could someone please show me how to fix this? >> Thank you. >> > >
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participants (5)
-
Guruprasad Ananda -
Hans-Rudolf Hotz -
Jacob Biesinger -
Kanwei Li -
Minh Bui