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(a)dkfz.de <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/