When I run mapexome.py, it shows error. How can I fix it? Appreciate ahead.
EXECUTING READ MAPPING WITH MAPEXOME...
mapExome for sample F-00-02-44707, files found: F-00-02-44707.fastq F-00-02-44707.R1.fastq F-00-02-44707.R2.fastq
F-00-02-44707.fastq is an empty unpaired fastq. File has been removed.
Traceback (most recent call last):
File "/home/MToolBox-master/MToolBox/mapExome.py", line 66, in
if not os.path.exists(folder): os.mkdir(folder)
OSError: [Errno 71] Protocol error: 'OUT_F-00-02-44707'
Compression of fastq files from bam/sam input files...
mkdir: cannot create directory ‘processed_fastq’: Protocol error
Done.
SAM files post-processing...
SORTING OUT.sam FILES WITH PICARDTOOLS...
[Fri Jun 02 13:05:54 CDT 2017] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/Sequence/test_MTB/OUT_F-00-02-44707/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Fri Jun 02 13:05:54 CDT 2017] Executing as jing@jing-VirtualBox on Linux 4.8.0-53-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11; Picard version: 1.98(1547)
[Fri Jun 02 13:05:54 CDT 2017] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=62390272
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" net.sf.picard.PicardException: Cannot read non-existent file: /Sequence/test_MTB/OUT_F-00-02-44707/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
When I run mapexome.py, it shows error. How can I fix it? Appreciate ahead.
EXECUTING READ MAPPING WITH MAPEXOME...
mapExome for sample F-00-02-44707, files found: F-00-02-44707.fastq F-00-02-44707.R1.fastq F-00-02-44707.R2.fastq F-00-02-44707.fastq is an empty unpaired fastq. File has been removed. Traceback (most recent call last): File "/home/MToolBox-master/MToolBox/mapExome.py", line 66, in
if not os.path.exists(folder): os.mkdir(folder)
OSError: [Errno 71] Protocol error: 'OUT_F-00-02-44707'
Compression of fastq files from bam/sam input files... mkdir: cannot create directory ‘processed_fastq’: Protocol error Done.
SAM files post-processing...
SORTING OUT.sam FILES WITH PICARDTOOLS...
[Fri Jun 02 13:05:54 CDT 2017] net.sf.picard.sam.SortSam INPUT=OUT.sam OUTPUT=OUT.sam.bam SORT_ORDER=coordinate TMP_DIR=[/Sequence/test_MTB/OUT_F-00-02-44707/tmp] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Fri Jun 02 13:05:54 CDT 2017] Executing as jing@jing-VirtualBox on Linux 4.8.0-53-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11; Picard version: 1.98(1547) [Fri Jun 02 13:05:54 CDT 2017] net.sf.picard.sam.SortSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=62390272 To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp Exception in thread "main" net.sf.picard.PicardException: Cannot read non-existent file: /Sequence/test_MTB/OUT_F-00-02-44707/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