BWA 2 files fasq to 1 fil sam
I am creating a sam file, with 2 fastq files, using bwa
I apply the following command
bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz
V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz
> V350019555_L03_B5GHUMqcnrRAABA-556.sam
The alignment begins to be generated, but after 15 hours, the following appears, and it generates a 0-bit sam file
V350019555L3C006R0051051033 16 chr21 9651911 29 150M * TGTTTTCTCTTTTTACAGCAAGGACAGTTTATTAAACACACTGTTTTAAACCTTATTTTTTCTCTAAATAATATTTCATATAAGTCAATATGTAGACTTTATGTATTTTTAAAATGAAGACATAGCATTCCATTGAACTTAGACAAAAAT EFFFFFFEGFFFFGEFF9FEFFFFGGFCFFFFGFFFFFFDFFFFFFFFFFFFFGAFFFCGBFDF@G@FGFFGFGFFFFGFFFFGFGFCFFFFFFFDGFGFGFFGFFFFFAFFFFFFEFFFFFFFFFFGDFFFF@FG8FF?FFFFFFGFFF NM:i:1 MD:Z:23G126 AS:i:145 XS:i:131 XA:Z:chr4,+189704487,150M,4;
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz
[main] Real time: 26995.284 sec; CPU: 33394.341 sec
zsh: command not found: V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz
I have previously analyzed the files with fasqc, and they seem correct
What is happening, what should I do?
I am creating a sam file, with 2 fastq files, using bwa
I apply the following command
bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz
V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz
> V350019555_L03_B5GHUMqcnrRAABA-556.sam
The alignment begins to be generated, but after 15 hours, the following appears, and it generates a 0-bit sam file
V350019555L3C006R0051051033 16 chr21 9651911 29 150M * TGTTTTCTCTTTTTACAGCAAGGACAGTTTATTAAACACACTGTTTTAAACCTTATTTTTTCTCTAAATAATATTTCATATAAGTCAATATGTAGACTTTATGTATTTTTAAAATGAAGACATAGCATTCCATTGAACTTAGACAAAAAT EFFFFFFEGFFFFGEFF9FEFFFFGGFCFFFFGFFFFFFDFFFFFFFFFFFFFGAFFFCGBFDF@G@FGFFGFGFFFFGFFFFGFGFCFFFFFFFDGFGFGFFGFFFFFAFFFFFFEFFFFFFFFFFGDFFFF@FG8FF?FFFFFFGFFF NM:i:1 MD:Z:23G126 AS:i:145 XS:i:131 XA:Z:chr4,+189704487,150M,4;
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz
[main] Real time: 26995.284 sec; CPU: 33394.341 sec
zsh: command not found: V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz
I have previously analyzed the files with fasqc, and they seem correct
What is happening, what should I do?
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