SEQ and QUAL are of different length

[Chen Dong]

Hi,

I was running align_and_estimate_abundance.pl on trinity docker and run into the error message below. Is is a issue of my file or the script itself? Help please.

[E::sam_parse1] SEQ and QUAL are of different length

[W::sam_read1] Parse error at line 479034

[main_samview] truncated file.

Error, cmd: set -o pipefail && bowtie -q --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 200 /home/arcadeo/Public/guayule_transcriptome/AfterQC/good/Tetraploid/trinity_out_dir_May/Trinity.fasta.bowtie -1 /home/highp12_S8_L001_R1_001.good.fastq -2 /home/highp12_S8_L001_R2_001.good.fastq | samtools view -F 4 -S -b | samtools sort -n -o bowtie.bam  died with ret: 256 at /usr/local/bin/trinityrnaseq/util/align_and_estimate_abundance.pl line 790.

Thank you!

Chen

[Brian Haas]

Hi

usually something like this would mean that there's a problem with the file.  Try running fastqc on the fastqs and see if it reports any error.

If you need to skip the bowtie step, you could try running Trinity with --no_bowtie

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas