bwa , 2 files fastq to 1 sam

Question

[PROFESOR]

i have this problem, please, help me, I'm trying it too from Mac OS Catalina

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? Genom is online now Report Post

Answer 1

[ATpoint]

If the second file is really in a new line then bwa runs only on the first file, send the output to stdout (so to screen) and the second file is being interpreted as a new command (obviously one that does not exist). If you want to have commands spanning multiple lines then you have to indicate that with \.

[PROFESOR]

this is the syntax i have entered

bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz

/ V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz

V350019555_L03_B5GHUMqcnrRAABA-556

.sam

is it ok?, in any case I will confirm the results that you show me when you have done it

[GenoMax]

No that is not OK. As ATpoint said above put the entire command on one line (it can wrap around automatically in your terminal ) or use the back slash at end of first line

bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz \

V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz >  V350019555_L03_B5GHUMqcnrRAABA-556.sam

[ATpoint]

My recommendation is to spend some time first on Unix basics, there are many guided tutorials on the web before continuing. You must know the basics before diving into analysis.

[PROFESOR]

I saw something in the bioinformatics subject, but not much. I follow the instructions of a bioinformatician, who gave me these commands. If something occurs to you, can you recommend it to me?

[GenoMax]

Nice UNIX primer: http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part1