Hello everypony!
I am using GSNAP to map my RNA-seq paired-end reads to a reference genome. It used to run normally (a few months ago), but I needed to remap some stuff using the exact same command line as before and now GSNAP decided not to work anymore.
It starts the alignment normally and then after a short while gives out Bus error:10.
This is how it looks like:
Does anybody know what could be wrong this time and how to fix it?
Thanks in advance!
Ana Marija
I am using GSNAP to map my RNA-seq paired-end reads to a reference genome. It used to run normally (a few months ago), but I needed to remap some stuff using the exact same command line as before and now GSNAP decided not to work anymore.
It starts the alignment normally and then after a short while gives out Bus error:10.
This is how it looks like:
Code:
gsnap -d oregonR_reference --quality-protocol illumina -N 1 -s /Volumes/Temp/Anna/reference/oregonR_reference/oregonR_reference.maps/dmel-all-transcript-r5.49-Parent1.iit -t 20 -A sam --split-output dmel_oregonR_t13_rep1 /Volumes/Temp/Anna/reads/trimmed_reads/oregon/dmel_oregonR_t13_rep1_1 /Volumes/Temp/Anna/reads/trimmed_reads/oregon/dmel_oregonR_t13_rep1_2 1 > log13r1.txt 2 > err13r1.txt GSNAP version 2014-02-28 called with args: gsnap -D /Volumes/Temp/Anna/reference/ -d oregonR_reference --quality-protocol illumina -N 1 -s /Volumes/Temp/Anna/reference/oregonR_reference/oregonR_reference.maps/dmel-all-transcript-r5.49-Parent1.iit -t 20 -A sam --split-output dmel_oregonR_t13_rep1 /Volumes/Temp/Anna/reads/trimmed_reads/oregon/dmel_oregonR_t13_rep1_1 /Volumes/Temp/Anna/reads/trimmed_reads/oregon/dmel_oregonR_t13_rep1_2 1 2 Checking compiler assumptions for popcnt: 000041A7 clz=17 clz=0 popcount=7 Checking compiler assumptions for SSE2: 000041A7 10D63AF1 xor=10D67B56 Checking compiler assumptions for SSE4.1: -89 -15 max=241 Novel splicing (-N) and known splicing (-s) both turned on => assume reads are RNA-Seq Note: >1 sequence detected, so index files are being memory mapped. GSNAP can run slowly at first while the computer starts to accumulate pages from the hard disk into its cache. To copy index files into RAM instead of memory mapping, use -B 3, -B 4, or -B 5, if you have enough RAM. For more speed, also try multiple threads (-t <int>), if you have multiple processors or cores. Pre-loading compressed genome (oligos).....,...,...,...,...,...,...,...,..done (63,276,204 bytes, 15449 pages, 0.17 sec) Pre-loading compressed genome (bits).....,...,...,...,...,...,...,...,..done (63,276,204 bytes, 15449 pages, 0.16 sec) Pre-loading suffix array...............................................................................................................................,............................................................................................................................................done (674,946,152 bytes) Looking for index files in directory /Volumes/Temp/Anna/reference//oregonR_reference Pointers file is oregonR_reference.ref12153bitpackptrs Offsets file is oregonR_reference.ref12153bitpackcomp Positions file is oregonR_reference.ref153positions Offsets compression type: bitpack Allocating memory for ref offset pointers, kmer 15, interval 3...done (134,217,736 bytes, 1.45 sec) Allocating memory for ref offsets, kmer 15, interval 3...done (226,957,088 bytes, 2.48 sec) Pre-loading ref positions, kmer 15, interval 3........................................................................................done (215,791,212 bytes, 52684 pages, 0.60 sec) Reading splicing file /Volumes/Temp/Anna/reference/oregonR_reference/oregonR_reference.maps/dmel-all-transcript-r5.49-Parent1.iit locally...found donor and acceptor tags, so treating as splicesites file splice distances present...37770 unique splicesites... Non-standard nucleotide N near splice site YHet_Parent1:291284. Discarding... 37769 splicesites are valid...splicetrie_obs has 37773 entries...splicetrie_max has 3858412 entries...done GMAP modes: pairsearch, indel_knownsplice, terminal, improvement Starting alignment Bus error: 10
Thanks in advance!
Ana Marija
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