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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Plase check if you provide correct parameters/options for the pipeline! #99

Open haoyanioz opened 6 years ago

haoyanioz commented 6 years ago

Dear RSEM developer, I performed STAR+RSEM pipeline, but got an error as below!

rsem-run-em /disk7/snowfinch/RSEM/reference/O_taczanowskii 3 /disk7/snowfinch/STAR/RSEM/XZ17016-rest /disk7/snowfinch/STAR/RSEM/XZ17016-rest.temp/XZ17016-rest /disk7/snowfinch/STAR/RSEM/XZ17016-rest.stat/XZ17016-rest -p 40 -b /disk7/snowfinch/STAR/XZ17016-rest/XZ17016-restAligned.toTranscriptome.out.bam 0 Refs.loadRefs finished! Thread 0 : N = 156701, NHit = 158731 DAT 6000000 reads left Thread 1 : N = 156480, NHit = 158731 Thread 2 : N = 156415, NHit = 158731 Thread 3 : N = 156569, NHit = 158731 Thread 4 : N = 156512, NHit = 158731 Thread 5 : N = 156711, NHit = 158731 Thread 6 : N = 156447, NHit = 158731 Thread 7 : N = 156578, NHit = 158731 DAT 5000000 reads left Thread 8 : N = 156458, NHit = 158731 Thread 9 : N = 156528, NHit = 158731 Thread 10 : N = 156502, NHit = 158731 Thread 11 : N = 156415, NHit = 158731 Thread 12 : N = 156541, NHit = 158731 Thread 13 : N = 156494, NHit = 158731 DAT 4000000 reads left Thread 14 : N = 156613, NHit = 158731 Thread 15 : N = 156653, NHit = 158731 Thread 16 : N = 156485, NHit = 158731 Thread 17 : N = 156493, NHit = 158731 Thread 18 : N = 156466, NHit = 158731 Thread 19 : N = 156468, NHit = 158731 DAT 3000000 reads left Thread 20 : N = 156458, NHit = 158731 Thread 21 : N = 156449, NHit = 158731 Thread 22 : N = 156557, NHit = 158731 Thread 23 : N = 156473, NHit = 158731 Thread 24 : N = 156529, NHit = 158731 Thread 25 : N = 156547, NHit = 158731 Thread 26 : N = 156468, NHit = 158731 DAT 2000000 reads left Thread 27 : N = 156562, NHit = 158731 Thread 28 : N = 156496, NHit = 158731 Thread 29 : N = 156601, NHit = 158731 Thread 30 : N = 156634, NHit = 158731 Thread 31 : N = 156546, NHit = 158731 Thread 32 : N = 156520, NHit = 158731 DAT 1000000 reads left Thread 33 : N = 156559, NHit = 158731 Thread 34 : N = 156687, NHit = 158731 Thread 35 : N = 156514, NHit = 158731 Thread 36 : N = 156466, NHit = 158731 Thread 37 : N = 156615, NHit = 158731 Thread 38 : N = 156609, NHit = 158731 Thread 39 : N = 156545, NHit = 158737 EM_init finished! 1000000 READS PROCESSED 2000000 READS PROCESSED 3000000 READS PROCESSED 4000000 READS PROCESSED 5000000 READS PROCESSED 6000000 READS PROCESSED estimateFromReads, N1 finished. The alignment of fragment A00262:56:H37FCDSXX:3:1432:17833:13745 to transcript 15598 starts at -131 from the forward direction, which should be a non-negative number! It is possible that the aligner you use gave different read lengths for a same read in SAM file. Found unknown sequence letter ?at function get_rbase_id! Found unknown sequence letter at function get_rbase_id! Found unknown sequence letter at function get_base_id! Found unknown sequence letter ; at function get_rbase_id! Found unknown sequence letter at function get_rbase_id! "rsem-run-em /disk7/snowfinch/RSEM/reference/O_taczanowskii 3 /disk7/snowfinch/STAR/RSEM/XZ17016-rest /disk7/snowfinch/STAR/RSEM/XZ17016-rest.temp/XZ17016-rest /disk7/snowfinch/STAR/RSEM/XZ17016-rest.stat/XZ17016-rest -p 40 -b /disk7/snowfinch/STAR/XZ17016-rest/XZ17016-restAligned.toTranscriptome.out.bam 0" failed! Plase check if you provide correct parameters/options for the pipeline!

Command: /home/share/STAR-2.6.0a/bin/Linux_x86_64/STAR --runThreadN 40 --genomeDir /disk7/snowfinch/STAR/reference/Baiyao --readFilesIn XZ17016-rest.R1.clean.fastq.gz XZ17016-rest.R2.clean.fastq.gz --readFilesCommand gunzip -c --sjdbGTFfile /disk7/snowfinch/new/Baiyao.gtf --outFileNamePrefix XZ17016-rest --quantMode TranscriptomeSAM GeneCounts

rsem-calculate-expression --paired-end --alignments -p 40 /disk7/snowfinch/STAR/XZ17016-rest/XZ17016-restAligned.toTranscriptome.out.bam /disk7/snowfinch/RSEM/reference/O_taczanowskii --append-names /disk7/snowfinch/STAR/RSEM/XZ17016-rest

Version: STAR_2.6.0a; RSEM v1.2.31

Very strange, and I have to say that when I used the same commands to run other samples according to the genomes of other species, there was not any problem. Do you know where I mistake and could you give me some suggestion?

Best wishes Y

zhengjiantao commented 3 years ago

I have the same error. Have you solved it?