Closed snackens closed 4 months ago
Hi, Thank you for this good tools.
I tried to run with test example, but something wrong.
========
mapExome for sample SRR043366, files found: SRR043366.R1.fastq.gz SRR043366.R2.fastq.gz Mapping onto mtDNA... -D -D /usr/local/share/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 SRR043366.R1.fastq.gz SRR043366.R2.fastq.gz > /home/user/mtDNA/test/out//OUT_SRR043366/outmt.sam 2> /home/user/mtDNA/test/out//OUT_SRR043366/logmt.txt sh: 0: Illegal option -D Extracting FASTQ from SAM... Traceback (most recent call last): File "/home/user/MToolBox/mapExome.py", line 96, in f=open(mtoutsam) IOError: [Errno 2] No such file or directory: '/home/user/mtDNA/test/out//OUT_SRR043366/outmt.sam'
== I think -D -D /usr.... is wrong. Is this install problem?
Best regards,
Hi, Thank you for this good tools.
I tried to run with test example, but something wrong.
========
EXECUTING READ MAPPING WITH MAPEXOME...
mapExome for sample SRR043366, files found: SRR043366.R1.fastq.gz SRR043366.R2.fastq.gz Mapping onto mtDNA... -D -D /usr/local/share/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 SRR043366.R1.fastq.gz SRR043366.R2.fastq.gz > /home/user/mtDNA/test/out//OUT_SRR043366/outmt.sam 2> /home/user/mtDNA/test/out//OUT_SRR043366/logmt.txt sh: 0: Illegal option -D Extracting FASTQ from SAM... Traceback (most recent call last): File "/home/user/MToolBox/mapExome.py", line 96, in
f=open(mtoutsam)
IOError: [Errno 2] No such file or directory: '/home/user/mtDNA/test/out//OUT_SRR043366/outmt.sam'
== I think -D -D /usr.... is wrong. Is this install problem?
Best regards,