GSNAP MEM usage

[clody23]

This one fails with 10Gb of mem.

MToolBox.sh -i F01318.sh

setting up MToolBox environment variables...
...done

setting up MToolBox variables in config file ...
...done


Check python version... (2.7 required)
OK.

Checking files to be used in MToolBox execution...

Checking mapExome parameters...
OK.

Checking assembleMTgenome parameters...
OK.

Checking mt-classifier parameters...
OK.
Input type is bam.
output files will be placed in /gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output

Converting bam to fastq... F013184_A_MT.bam
[Tue Feb 07 10:42:10 GMT 2017] net.sf.picard.sam.SamToFastq INPUT=F013184_A_MT.bam FASTQ=/gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/F013184_A_MT.R1.fastq SECOND_END_FASTQ=/gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/F013184_A_MT.R2.fastq UNPAIRED_FASTQ=/gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/F013184_A_MT.fastq TMP_DIR=[/gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/tmp] VALIDATION_STRINGENCY=SILENT    OUTPUT_PER_RG=false RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Tue Feb 07 10:42:10 GMT 2017] Executing as [email protected] on Linux 3.10.0-327.18.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_91-b14; Picard version: 1.108(1695) JdkDeflater
[Tue Feb 07 10:42:25 GMT 2017] net.sf.picard.sam.SamToFastq done. Elapsed time: 0.25 minutes.
Runtime.totalMemory()=2550136832
Done.

##### EXECUTING READ MAPPING WITH MAPEXOME...


mapExome for sample F013184_A_MT, files found: /gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/F013184_A_MT.fastq /gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/F013184_A_MT.R1.fastq /gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/F013184_A_MT.R2.fastq
F013184_A_MT.fastq is an empty unpaired fastq. File has been removed.
Mapping onto mtDNA...
/gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/MToolBox/bin/gmap/bin/gsnap -D /gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/MToolBox/gmapdb/ --gunzip -d chrM -A sam --nofails --pairmax-dna=500 --query-unk-mismatch=1 --read-group-id=sample --read-group-name=sample --read-group-library=sample --read-group-platform=sample -n 1 -Q -O -t 8 F013184_A_MT.R1.fastq F013184_A_MT.R2.fastq > /gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/OUT_F013184_A_MT/outmt.sam 2> /gpfs/nobackup/sds-pawg/ccalabre/eqtl_analysis/test_MToolBox/ernest_test/output/OUT_F013184_A_MT/logmt.txt
Extracting FASTQ from SAM...
Mapping onto complete human genome...single reads
Mapping onto complete human genome...pair reads
Terminated