The process is getting killed when mapExome is running. Help would be much appreciated.
EXECUTING READ MAPPING WITH MAPEXOME...
mapExome for sample GW7_S23_001, files found: GW7_S23_001.R1.fastq.gz GW7_S23_001.R2.fastq.gz
Extracting FASTQ from SAM...
Reading Results...
MToolBox/MToolBox.sh: line 230: 29850 Killed mapExome.py -g ${gsnapexe} -D ${gsnapdb} -M ${mtdb} -H ${humandb} -a $i.R1.fastq -b $i.R2.fastq -o ${outputname}/OUT${i} ${mapExome_OPTS}
SAM files post-processing...
SORTING OUT.sam FILES WITH PICARDTOOLS...
[Mon Mar 15 14:41:12 CET 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/home/mtDNA/OUT_GW7_S23_001/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Mon Mar 15 14:41:12 CET 2021] Executing on Linux 4.15.0-136-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_282-8u282-b08-0ubuntu1~16.04-b08; Picard version: 1.98(1547)
[Mon Mar 15 14:41:12 CET 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1009254400
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" net.sf.picard.PicardException: Cannot read non-existent file: /home/mtDNA/OUT_GW7_S23_001/OUT.sam
at net.sf.picard.io.IoUtil.assertFileIsReadable(IoUtil.java:59)
at net.sf.picard.sam.SortSam.doWork(SortSam.java:61)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.sam.SortSam.main(SortSam.java:57)
Success.
[E::hts_open_format] fail to open file 'OUT.sam.bam'
samtools index: failed to open "OUT.sam.bam": No such file or directory
Skip Indel Realigner...
cat: OUT.sam.bam: No such file or directory
The process is getting killed when mapExome is running. Help would be much appreciated.
EXECUTING READ MAPPING WITH MAPEXOME...
mapExome for sample GW7_S23_001, files found: GW7_S23_001.R1.fastq.gz GW7_S23_001.R2.fastq.gz Extracting FASTQ from SAM... Reading Results... MToolBox/MToolBox.sh: line 230: 29850 Killed mapExome.py -g ${gsnapexe} -D ${gsnapdb} -M ${mtdb} -H ${humandb} -a $i.R1.fastq -b $i.R2.fastq -o ${outputname}/OUT${i} ${mapExome_OPTS}
SAM files post-processing...
SORTING OUT.sam FILES WITH PICARDTOOLS...
[Mon Mar 15 14:41:12 CET 2021] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/home/mtDNA/OUT_GW7_S23_001/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Mar 15 14:41:12 CET 2021] Executing on Linux 4.15.0-136-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_282-8u282-b08-0ubuntu1~16.04-b08; Picard version: 1.98(1547) [Mon Mar 15 14:41:12 CET 2021] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1009254400 To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp Exception in thread "main" net.sf.picard.PicardException: Cannot read non-existent file: /home/mtDNA/OUT_GW7_S23_001/OUT.sam at net.sf.picard.io.IoUtil.assertFileIsReadable(IoUtil.java:59) at net.sf.picard.sam.SortSam.doWork(SortSam.java:61) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.SortSam.main(SortSam.java:57) Success.
[E::hts_open_format] fail to open file 'OUT.sam.bam' samtools index: failed to open "OUT.sam.bam": No such file or directory Skip Indel Realigner... cat: OUT.sam.bam: No such file or directory