Errors with RSEM/bowtie2

Question

[ofarinas621]

Hi,

I keep getting an error message after running the align_estimate_abundance step for RNA-seq, specifically using RSEM and bowtie2. I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST.

The error message is this:

CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000 --end-to-end -k 200  -q -X 800 -x /fs/ess/PAS1182/Olivia/NYCHA/cd_hit_est/CD_HIT_EST_NYCHA_1.fasta.bowtie2 -1 /tmp/slurmtmp.37615063/trinity_output37615063/unfixrm_1048_bed_260_317_S183_L006_R1_001.cor.fq.P.qtrim.gz -2 /tmp/slurmtmp.37615063/trinity_output37615063/unfixrm_1048_bed_260_317_S183_L006_R2_001.cor.fq.P.qtrim.gz -p 80 | samtools view -@ 80 -F 4 -S -b | samtools sort -@ 80 -n -o bowtie2.bam 
Error, fewer reads in file specified with -2 than in file specified with -1
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Error, cmd: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000 --end-to-end -k 200  -q -X 800 -x /fs/ess/PAS1182/Olivia/NYCHA/cd_hit_est/CD_HIT_EST_NYCHA_1.fasta.bowtie2 -1 /tmp/slurmtmp.37615063/trinity_output37615063/unfixrm_1048_bed_260_317_S183_L006_R1_001.cor.fq.P.qtrim.gz -2 /tmp/slurmtmp.37615063/trinity_output37615063/unfixrm_1048_bed_260_317_S183_L006_R2_001.cor.fq.P.qtrim.gz -p 80 | samtools view -@ 80 -F 4 -S -b | samtools sort -@ 80 -n -o bowtie2.bam  died with ret: 256 at /users/PAS1182/ofarinas621/local/src/trinityrnaseq-v2.15.2/util/align_and_estimate_abundance.pl line 729.

Some other posts have said that it could be mismatched reads, but I don't know how to fix this, given that I already did the trimming steps.

Any help would be greatly appreciated.

Thanks,

Olivia

[GenoMax]

I have previously run Trinity with the Trimmomatic step as well as CD-HIT-EST.

I assume you did the above to generate the transcriptome, which are then using with bowtie2 after creating an index from it?