Update:
The bam file is usable as long as the correct sorting order is specified. The new datatype "qname_sorted.bam" is not automatically set if the sorting order is by "queryname" (Read identifier). As long as the bam is not mapped I get:
/Could not display BAM file, error was:file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False// / When I try to visualize it.
I hope I helped somebody with these infos.
Christopher
On 3/15/19 4:43 PM, Previti wrote:
Dear all,
I'm having serious issues with picard tools (latest Galaxy version 2.18.2.1 by devteam) after upgrading our galaxy to version 19.01 I've been running fastqtoSam on paired-end data:
_JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx200g -Xms256m'} && export _JAVA_OPTIONS && picard FastqToSam FASTQ="/opt/galaxy/galaxy/database/files/039/dataset_39081.dat" FASTQ2="/opt/galaxy/galaxy/database/files/039/dataset_39082.dat" QUALITY_FORMAT="Standard" OUTPUT="/opt/galaxy/galaxy/database/files/039/dataset_39441.dat" READ_GROUP_NAME="A" SAMPLE_NAME="sample-a" MIN_Q="0" MAX_Q="93" STRIP_UNPAIRED_MATE_NUMBER="false" ALLOW_AND_IGNORE_EMPTY_LINES="false" SORT_ORDER=coordinate VALIDATION_STRINGENCY="LENIENT" QUIET=true VERBOSITY=ERROR `if [ -n "$TMPDIR" ] ; then echo 'TMP_DIR=$TMPDIR' ; else if [ -n "$TEMP" ] ; then echo 'TMP_DIR=$TEMP' ; fi ; fi`
But the bam file I get is not readable and I also get following message:
Picked up _JAVA_OPTIONS: -Xmx200g -Xms256m 14:16:29.629 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/galaxy/galaxy/database/dependencies/_conda/envs/__picard@2.18.2/share/picard-2.18.2-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
does anybody know what's going on? The output "bam" file is the correct size (>20GB) but not readable...
Thanks and best regards, Christopher Previti
*Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician
German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661
christopher.previti@dkfz.de http://www.dkfz.de/ www.dkfz.de http://www.dkfz.de/
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