Hi I am trying to estimate transcript abundance from a transcriptome generated from paired-end RNA-seq data using Trinity. However, I am running into a consistent error while using the- The error is as follows:
CMD: set -o pipefail && bowtie -f --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /home/nbri/nasreen/Trinity_clr.fasta.bowtie -1 /home/nbri/nasreen/qf_leaf_1.fastq -2 /home/nbri/nasreen/qf_leaf_2.fastq | samtools view -F 4 -S -b -o RSEM_leaf.bowtie.bam - Error: reads file does not look like a FASTA file terminate called after throwing an instance of 'int' [samopen] SAM header is present: 228505 sequences. [sam_read1] reference 'ID:Bowtie VN:0.12.8 CL:"bowtie -f --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /home/nbri/nasreen/Trinity_clr.fasta.bowtie -1 /home/nbri/nasreen/qf_leaf_1.fastq -2 /home/nbri/nasreen/qf_leaf_2.fastq" 1 LN:204 @SQ SN:TRINITY_DN143039_c0_g1_i1 LN:229 @!' is recognized as '*'. [main_samview] truncated file. Error, cmd: set -o pipefail && bowtie -f --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /home/nbri/nasreen/Trinity_clr.fasta.bowtie -1 /home/nbri/nasreen/qf_leaf_1.fastq -2 /home/nbri/nasreen/qf_leaf_2.fastq | samtools vie w -F 4 -S -b -o RSEM_leaf.bowtie.bam - died with ret: 256 at /opt/HPC_Applications/trinityrnaseq-2.2.0/util/align_and_estimate_abundance.pl line 743.
the command which i have used-
/opt/HPC_Applications/trinityrnaseq-2.2.0/util/align_and_estimate_abundance.pl --seqType fastq --left qf_leaf_1.fastq --right qf_leaf_2.fastq --transcripts Trinity_clr_mod.fasta --output_prefix RSEM_leaf --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir align_111
please help
Nasreen
