Problem with large degradomes

[juancresc]

When using large degradomes, even with high-end computers I got a bowtie/samtools error

Error while flushing and closing output
Command: /home/juan/Desktop/juan/bio/sw/bowtie-1.2.2-linux-x86_64/bowtie-align-s --wrapper basic-0 -f -v 1 --best -k 1 --norc -S /home/juan/Desktop/juan/bio/mrcv/data/res/04_02_19/DEG-cdna.fasta /home/juan/Desktop/juan/bio/mrcv/data/degradome/SRR3690386.trimmed.fasta 

I could trace the error to this command:

bowtie -f -v 1 --best -k 1 --norc -S /home/juan/Desktop/juan/bio/mrcv/data/res/04_02_19/DEG-cdna.fasta /home/juan/Desktop/juan/bio/mrcv/data/degradome/SRR3690386.trimmed.fasta | sed -e 's/SO:unsorted/SO:coordinate/' | samtools view -S -b -u - 2> /dev/null | samtools sort -T /home/juan/Desktop/juan/bio/mrcv/data/res/04_02_19/DEG-cdna.fasta_sorted_sorttemp -O bam - > /home/juan/Desktop/juan/bio/mrcv/data/res/04_02_19/DEG-cdna.fasta_sorted.bam 2> /dev/null          

And divide the commands in single calls using intermediate files (avoid piping). The result code is:

$sort_call = "samtools sort -T $tmp_sort -O bam file_3 > $full_bam_name";
    } else {
	$sort_call = "samtools sort - $bam_name";
    }
    if($opt_q) {
	    system "bowtie -f -v 1 --best -k 1 --norc -S $opt_n $opt_e 2> /dev/null \| sed -e 's/SO:unsorted/SO:coordinate/' 2> /dev/null \| samtools view -S -b -u - 2> /dev/null \| $sort_call 2> /dev/null";
    } else {
        system "bowtie -f -v 1 --best -k 1 --norc -S $opt_n $opt_e > file_1";
        system "sed -e 's/SO:unsorted/SO:coordinate/' file_1 > file_2";
        system "samtools view -S -b -u file_2 > file_3";
        system "$sort_call";
	    #system "bowtie -f -v 1 --best -k 1 --norc -S $opt_n $opt_e \| sed -e 's/SO:unsorted/SO:coordinate/' \| samtools view -S -b -u - 2> /dev/null \| $sort_call 2> /dev/null";
    }

I was able to execute CleaveLand with large degradome this way.

Maybe it helps someone in the same situation

[jonbra]

I got the same error message, but when I increased the memory it was solved.