Although the paired reads were checked with two different scripts for unpaired reads before running TransAbyss-Analyze, an error saying "the paired-end accessions do not match" is output before aborting. The message essentially says “Paired-end accessions FCC6B7TACXX:7:1101:10524:57301# and FCC6B7TACXX:7:1101:9245:1994# do not match”.
Command:
transabyss-analyze -a TrAb_Merged_1_1.fa -1 RG11_NR_P3_R1.fq.gz -2 RG11_NR_P3_R2.fq.gz --SS --ref Gh1 --cfg /work/satishg/transcriptome.cfg --annodir /work/satishg/Gh1.gtf --analyze fusion -o /work/satishg/TrAn_RG11_Gh1 -t 20
Error Message:
/work/satishg/TrAn_RG11_Gh1/reads_to_genome/cluster/transabyss.local.sh: line 3: ulimit: core file size: cannot modify limit: Operation not permitted
GSNAP version 2014-12-29 called with args: gsnap --gunzip -d Gh1 -D /work/satishg -t 18 --format sam -N 1 -m 10 /work/satishg/RG11_NR_P3_R1.fq.gz /work/satishg/RG11_NR_P3_R2.fq.gz
Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=-58 => compiler sign extends
Finished checking compiler assumptions
Novel splicing (-N) turned on => assume reads are RNA-Seq
Paired-end accessions FCC6B7TACXX:7:1101:10524:57301# and FCC6B7TACXX:7:1101:9245:1994# do not match
real 0m0.623s
user 0m0.009s
sys 0m0.056s
ERROR: Execution of script ended with a non-zero exit-status.
I tried running it with three different read pairs, but all terminate with the same error.
Command:
transabyss-analyze -a TrAb_Merged_1_1.fa -1 RG11_NR_P3_R1.fq.gz -2 RG11_NR_P3_R2.fq.gz --SS --ref Gh1 --cfg /work/satishg/transcriptome.cfg --annodir /work/satishg/Gh1.gtf --analyze fusion -o /work/satishg/TrAn_RG11_Gh1 -t 20
Error Message:
/work/satishg/TrAn_RG11_Gh1/reads_to_genome/cluster/transabyss.local.sh: line 3: ulimit: core file size: cannot modify limit: Operation not permitted
GSNAP version 2014-12-29 called with args: gsnap --gunzip -d Gh1 -D /work/satishg -t 18 --format sam -N 1 -m 10 /work/satishg/RG11_NR_P3_R1.fq.gz /work/satishg/RG11_NR_P3_R2.fq.gz
Checking compiler assumptions for popcnt: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=-58 => compiler sign extends
Finished checking compiler assumptions
Novel splicing (-N) turned on => assume reads are RNA-Seq
Paired-end accessions FCC6B7TACXX:7:1101:10524:57301# and FCC6B7TACXX:7:1101:9245:1994# do not match
real 0m0.623s
user 0m0.009s
sys 0m0.056s
ERROR: Execution of script ended with a non-zero exit-status.
I tried running it with three different read pairs, but all terminate with the same error.
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