Hi, I am using the "Depth of coverage on BAM files" tool from the NGS: GATK Tools but encounter problem. While part of the BAM files proceed successfully, some BAM files end proceeding with a systematic error (see below). The entire BAM file dataset was generated with the same deepseq analysis pipeline (MiSeq Reporter, PCR amplicon Workflow) => alignemnent is done on Hs. hg19 and manifest is focused on specific regions. Does someone know how to solve this problem? Also, the chromosome X and Y appear to be exclude from the calculation. Is there any settings to select in order to include both sexual chromosomes? Is it expected? Kind Regards / Sandrine -- Sandrine Imbeaud INSERM, UMR U-674, IUH Université Paris Descartes Génomique Fonctionnelle des tumeurs solides 27 rue Juliette Dodu F75010 Paris, France TEL: +33 (0)1 53 72 51 98 FAX: +33 (0)1 53 72 51 92 MOBILE: +33 (0)6 12 69 80 29 http://www.inserm-u674.net/ Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/tmp [Mon Feb 10 07:08:03 CST 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/tmp-gatk-hPNp7B/gatk_input.fasta OUTPUT=/tmp/tmp-gatk-hPNp7B/dict1033574942916796988.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Feb 10 07:08:03 CST 2014] Executing as g2main@roundup49.tacc.utexas.edu on Linux 2.6.32-431.1.2.0.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057) [Mon Feb 10 07:08:04 CST 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2025324544 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found. ##### ERROR reads contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY] ##### ERROR reference contigs = [c1_27022371-27108741, c1_65310990-65312594, c1_103341958-103574198, c1_115256193-115258963, c11_533546-534529, c11_108093339-108239879, c12_25379959-25398502, c12_46123245-46302016, c12_49412540-49449288, c12_70910587-71031382, c12_121416337-121440487, c13_77618564-77901349, c16_337220-402825, c16_2097254-2138873, c17_7571510-7591038, c17_40474813-40500706, c19_10596592-10614570, c2_21224182-21267085, c2_178098515-178099162, c20_57484200-57484647, c3_41240709-41282027, c3_41265294-41266864, c3_47057688-47205620, c3_178928002-178948337, c4_74269729-74287296, c4_185308648-185395907, c5_1253083-1294978, c5_1294819-1295755, c5_55251637-55260189, c5_71402848-71505569, c6_36644019-36655290, c7_135242597-135333692, c7_140452856-140453348, c9_21967531-21994664, c9_135766517-135820181] ##### ERROR ------------------------------------------------------------------------------------------ mv: cannot stat `/galaxy-repl/main/files/007/581/dataset_7581988.dat.sample_summary': No such file or directory
Hello Sandrine, The sequence identifiers are a mismatch between the bam file and the custom reference genome. https://wiki.galaxyproject.org/Support#Reference_genomes I'll reply with more detail to your bug report about the same issue. Best, Jen Galaxy team On 2/10/14 6:09 AM, Sandrine Imbeaud wrote:
Hi,
I am using the "Depth of coverage on BAM files" tool from the NGS: GATK Tools but encounter problem. While part of the BAM files proceed successfully, some BAM files end proceeding with a systematic error (see below). The entire BAM file dataset was generated with the same deepseq analysis pipeline (MiSeq Reporter, PCR amplicon Workflow) => alignemnent is done on Hs. hg19 and manifest is focused on specific regions.
Does someone know how to solve this problem?
Also, the chromosome X and Y appear to be exclude from the calculation. Is there any settings to select in order to include both sexual chromosomes? Is it expected?
Kind Regards / Sandrine -- Sandrine Imbeaud INSERM, UMR U-674, IUH Université Paris Descartes
Génomique Fonctionnelle des tumeurs solides 27 rue Juliette Dodu F75010 Paris, France TEL: +33 (0)1 53 72 51 98 FAX: +33 (0)1 53 72 51 92 MOBILE: +33 (0)6 12 69 80 29 http://www.inserm-u674.net/
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/tmp [Mon Feb 10 07:08:03 CST 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/tmp-gatk-hPNp7B/gatk_input.fasta OUTPUT=/tmp/tmp-gatk-hPNp7B/dict1033574942916796988.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Feb 10 07:08:03 CST 2014] Executing as g2main@roundup49.tacc.utexas.edu on Linux 2.6.32-431.1.2.0.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_40-b43; Picard version: 1.58(1057) [Mon Feb 10 07:08:04 CST 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=2025324544 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Input files reads and reference have incompatible contigs: No overlapping contigs found. ##### ERROR reads contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY] ##### ERROR reference contigs = [c1_27022371-27108741, c1_65310990-65312594, c1_103341958-103574198, c1_115256193-115258963, c11_533546-534529, c11_108093339-108239879, c12_25379959-25398502, c12_46123245-46302016, c12_49412540-49449288, c12_70910587-71031382, c12_121416337-121440487, c13_77618564-77901349, c16_337220-402825, c16_2097254-2138873, c17_7571510-7591038, c17_40474813-40500706, c19_10596592-10614570, c2_21224182-21267085, c2_178098515-178099162, c20_57484200-57484647, c3_41240709-41282027, c3_41265294-41266864, c3_47057688-47205620, c3_178928002-178948337, c4_74269729-74287296, c4_185308648-185395907, c5_1253083-1294978, c5_1294819-1295755, c5_55251637-55260189, c5_71402848-71505569, c6_36644019-36655290, c7_135242597-135333692, c7_140452856-140453348, c9_21967531-21994664, c9_135766517-135820181] ##### ERROR ------------------------------------------------------------------------------------------ mv: cannot stat `/galaxy-repl/main/files/007/581/dataset_7581988.dat.sample_summary': No such file or directory
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org
participants (2)
-
Jennifer Jackson -
Sandrine Imbeaud