Serious issues with picard-tools after upgrade to Galaxy version 19.01

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Serious issues with picard-tools after upgrade to Galaxy version 19.01

Previti
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

[hidden email] <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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Re: Serious issues with picard-tools after upgrade to Galaxy version 19.01

Previti
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
>
> [hidden email] <http://www.dkfz.de/>
> www.dkfz.de <http://www.dkfz.de/>
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
> Absender und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
> untersagt.
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/

--
*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

[hidden email] <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/