Hi, I have been merging 2 paired-end fastq files using
cat file1.fq.gz file2.fq.gz > outputfile.fq.gz
I then mapped the output file and all went fine. However when I try to transform the created sam file in a bam file I get this error:
[W::sam_read1] Parse error at line 23309928
[main_samview] truncated file.
So I watched at the actual line and everything seems ok and does look in the correct format. However, I think I know what makes it bug but I don't know why. Indeed, in the 3rd field (the chr/ref field) I do have "GL000214.1" as you can see below:
ERR1019070.25381935 16 GL000214.1 -1 16 100M * 0 0 CACTATTATTCTCCAAATGATGCGTGCCTCCCTAGAGTCCAGGCTATCTGCATATCTAATTTTTCCCACAAATTACTGTTTTGAATTGCACTGAATTCAA @C@DB?DFHAHHFGGEDGIG@IGGDFGGGIIIIIIIE?GHGH>G?GDFGHGDFGG<FHGEEHGIIGEH@EAGGCEC>777?CFFCE>>CACCDC3>@5>3 XS:i:1
I checked and this "GL000214.1" is declared in the header of my SAMfile tho'...
I did the same process on another dataset, and I do have the same bug caused (probably) by the same issue; the 3rd field contain accession "GLXXXXXXX" that it does not recognise ?
Do you know how can I by pass this or if I did merged it the wrong way ?
Cheers and thank you !