Error in executing STAR Aligner

Question

[otieno43]

Hello guys.

I am want to map RNA seq reads to the genome using STAR with the option to generate result that I can fit into RSEM for downstream analysis. However, I get an EXIT CODE 102 error which I am unable to resolve. Can someone help me solve this. Below is the script and the error:

Script

STAR --genomeDir /gpfs/ysm/project/aksoy/ea432/Gff_midgut/STAR/star_index \
--runThreadN 64 \
--readFilesIn /gpfs/ysm/pi/attardo/from_louise/Gff_SP_midgut/TN-SN_1_107_086_S16_L002_R1_001.fastq.gz/TN-SN_1_107_086_S16_L002_R2_001.fastq.gz \
--readFilesCommand zcat \
--outFilterScoreMinOverLread 0.4 \
--outFilterMatchNminOverLread 0.4 \
--outFilterMismatchNmax 40 \
--outFilterMismatchNoverLmax 0.05 \
--outFilterType BySJout \
--outSJfilterOverhangMin −1 25 25 25 \
--outSJfilterCountUniqueMin −1 10 10 10 \
--outSAMtype BAM SortedByCoordinate Unsorted \
--quantMode TranscriptomeSAM \
--outFileNamePrefix /gpfs/ysm/project/aksoy/ea432/Gff_midgut/STAR/mappingResults_RSEM/Gff_MgSN_1

Error

terminate called after throwing an instance of 'std::out_of_range'
  what():  vector::_M_range_check: __n (which is 1) >= this->size() (which is 1)
/var/spool/slurmd/job22928454/slurm_script: line 33: 28402 Aborted                 STAR --genomeDir /gpfs/ysm/projec
t/aksoy/ea432/Gff_midgut/STAR/star_index --runThreadN 64 --readFilesIn /gpfs/ysm/pi/attardo/from_louise/Gff_SP_midgut/TN-SN_1_107_086_S16_L002_R1_001.fastq.gz/TN-SN_1_107_086_S16_L002_R2_001.fastq.gz --readFilesCommand zcat --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMismatchNmax 40 --outFilterMismatchNoverLmax 0.05 --outFilterType BySJout --outSJfilterOverhangMin −1 25 25 25 --outSJfilterCountUniqueMin −1 10 10 10 --outSAMtype BAM SortedByCoordinate Unsorted --quantMode TranscriptomeSAM --outFileNamePrefix /gpfs/ysm/project/aksoy/ea432/Gff_midgut/STAR/mappingResults_RSEM/Gff_MgSN_1

Answer 1

[Jeremy Leipzig]

looks like you may have some idiosyncrasies with your GTF file? https://github.com/alexdobin/STAR/issues/84

[otieno43]

Sorry Jeremy, I have not quite understood what this means. I used GFF to generate index and it was finished successfully.

[Jeremy Leipzig]

what species is this?

[otieno43]

Glossina fuscipes (tsetse fly)

[Jeremy Leipzig]

ok here's how I would debug this:

• run STAR without annotations
• compare your annotations to the ones included for model organisms here, paying attention to potential problems such as repeated identifiers
• truncate your annotation file to 10% or so, see if it crashes. If not, then add more portions until it does