Open Heterosigma opened 1 year ago
I got the same problem, have u solved it?
Hi, I got this error once. But I found out that it had nothing to do with the indexed reference (I did try creating a new indexed reference). Instead, the problem lied in my rsem-calculate-expression arguments:
Trouble-causing script
rsem-calculate-expression \ --bowtie2 --bowtie2-path /usr/bin/bowtie2 --phred33-quals \ --paired-end \ --p 6 --output-genome-bam --sort-bam-by-coordinate \ sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq.gz \ sub1-Ca13mCh-LGC9389_L1_2_cleaned.fq.gz \ human \ sub1-Ca13mCh-LGC9389_L1_PE_quals \ 2>&1 | tee sub1-Ca13mCh-LGC9389_L1_log.txt
I just removed the --bowtie2-path flag and it worked.
New script
rsem-calculate-expression \ --bowtie2 --phred33-quals \ --paired-end \ --p 6 --output-genome-bam --sort-bam-by-coordinate \ sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq.gz \ sub1-Ca13mCh-LGC9389_L1_2_cleaned.fq.gz \ human \ sub1-Ca13mCh-LGC9389_L1_PE_quals \ 2>&1 | tee sub1-Ca13mCh-LGC9389_L1_log.txt
Hope this helps.
Hi, I tried rsem-calculate-expression using bowtie, and the mapping step appeared to be completed. Then I got the error message
"The SAM/BAM file declares less than one reference sequence!"
since the BAM file is created in the .temp directory , it appears strange to me. When I check the .stat directory, it is empty.
Also, the last several lines of the output say
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 -p 8 -a -m 200 -S task00831_Trinity3 -1 DNBSEQ_Haka1_012023_Read1.fq -2 DNBSEQ_Haka1_012023_Read2.fq 2> DNBSEQ_Haka1_012023.log | samtools view -b -o DNBSEQ_Haka1_012023.temp/DNBSEQ_Haka1_012023.bam -
rsem-parse-alignments task00831_Trinity3 DNBSEQ_Haka1_012023.temp/DNBSEQ_Haka1_012023 DNBSEQ_Haka1_012023.stat/DNBSEQ_Haka1_012023 DNBSEQ_Haka1_012023.temp/DNBSEQ_Haka1_012023.bam 3 -tag XM "rsem-parse-alignments task00831_Trinity3 DNBSEQ_Haka1_012023.temp/DNBSEQ_Haka1_012023 DNBSEQ_Haka1_012023.stat/DNBSEQ_Haka1_012023 DNBSEQ_Haka1_012023.temp/DNBSEQ_Haka1_012023.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!
Here, the task00831_Trinity3.fasta file was the original reference file, and the rsem-prepare-references was completed by
rsem-prepare-reference --bowtie --gff3 task00831_Trinity3.gff3 -p 20 --bowtie task00831_Trinity3 task00831_Trinity3
and the files with several different extensions were created.
Could somebody tell me what I did wrong??
When I try
rsem-parse-alignments task00831_Trinity3 DNBSEQ_Haka1_012023.temp/DNBSEQ_Haka1_012023.bam DNBSEQ_Haka1_012023.stat/DNBSEQ_Haka1_012023 DNBSEQ_Haka1_012023.temp/DNBSEQ_Haka1_012023.bam
I got the same message, "The SAM/BAM file declares less than one reference sequence!"