gnavigator continues after GMAP failure

[sahammond]

In case of a GMAP failure, which has been observed when running with insufficient memory, gnavigator will use the incomplete alignment files and produce reports without any warnings. Instead, gnavigator should halt upon a GMAP failure.

[sahammond]

Fixed by 3f3a644

[KristinaGagalova]

Hi Austin, I have this log file here

GMAP version 2017-11-15 called with args: gmapl.avx2 -D /projects/spruceup_scratch/pglauca/WS77111/annotation/genome-annotation/Maker/Step0annoatation/PreRunEvaluation/Gnavigator/WS77111-v2_all.Sel1000bp/WS77111-v2_all.Sel1000bp/ -d WS77111-v2_all.Sel1000bp --microexon-spliceprob=0 --max-intronlength-ends=1000000 --max-intronlength-middle=1000000 --totallength=20000000 -t 6 -f 1 -x 10 -O --split-output=WS77111-v2_all.Sel1000bp -n 10 /projects/spruceup_scratch/pglauca/WS77111/annotation/genome-annotation/Maker/Step0annoatation/EvidentialGene/pg29/okayset/Complete/pg29.allComplete.fasta
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero extends
Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17 
Finished checking compiler assumptions
Pre-loading compressed genome (oligos)......done (7,952,004,912 bytes, 1941408 pages, 0.72 sec)
Pre-loading compressed genome (bits)......done (7,952,004,960 bytes, 1941408 pages, 0.65 sec)
Looking for index files in directory /projects/spruceup_scratch/pglauca/WS77111/annotation/genome-annotation/Maker/Step0annoatation/PreRunEvaluation/Gnavigator/WS77111-v2_all.Sel1000bp/WS77111-v2_all.Sel1000bp/
  Pages file is WS77111-v2_all.Sel1000bp.ref153offsets64pages
  Pointers file is WS77111-v2_all.Sel1000bp.ref153offsets64meta
  Offsets file is WS77111-v2_all.Sel1000bp.ref153offsets64strm
  Positions files are WS77111-v2_all.Sel1000bp.ref153positionsh and WS77111-v2_all.Sel1000bp.ref153positions
Offsets compression type: bitpack64
Allocating memory for ref offset pointers, kmer 15, interval 3...Attached new memory for /projects/spruceup_scratch/pglauca/WS77111/annotation/genome-annotation/Maker/Step0annoatation/PreRunEvaluation/Gnavigator/WS77111-v2_all.Sel1000bp/WS77111-v2_all.Sel1000bp//WS77111-v2_all.Sel1000bp.ref153offsets64meta...done (134,217,744 bytes, 0.14 sec)
Allocating memory for ref offsets, kmer 15, interval 3...Attached new memory for /projects/spruceup_scratch/pglauca/WS77111/annotation/genome-annotation/Maker/Step0annoatation/PreRunEvaluation/Gnavigator/WS77111-v2_all.Sel1000bp/WS77111-v2_all.Sel1000bp//WS77111-v2_all.Sel1000bp.ref153offsets64strm...done (820,701,872 bytes, 0.72 sec)
Attached new memory for /projects/spruceup_scratch/pglauca/WS77111/annotation/genome-annotation/Maker/Step0annoatation/PreRunEvaluation/Gnavigator/WS77111-v2_all.Sel1000bp/WS77111-v2_all.Sel1000bp//WS77111-v2_all.Sel1000bp.ref153offsets64pages...Pre-loading ref positions, kmer 15, interval 3......done (5,491,422,802 bytes, 1.42 sec)
...done (21,965,691,208 bytes, 1.73 sec)
Starting alignment
No paths found for E1.L.16720:rep1|evgclass=main,okay,match:E0.S.377105:rep3,pct:98/49/.;|aalen=113,52%,complete-utrpoor;
Signal received: SIGHUP
Calling Access_emergency_cleanup
Signal received: SIGSEGV
Calling Access_emergency_cleanup
Removed existing memory for shmid 91848707
Removed existing memory for shmid 91783169

You may want to run 'ipcs -m' to see if any shared memory segments are still in use
You can remove a shared memory segment manually by doing 'ipcrm -m <shmid>'

Problem sequence: E1.L.15605:rep1|evgclass=noclass,okay;|aalen=86,18%,complete-utrbad; (1431 bp)

=== Performing GMAP alignments ===

=== GNAVIGATOR RESULTS ===
56 (0.01%) complete sequences
13 (0.0%) duplicated sequences
20 (0.0%) fragmented sequences
18 (0.0%) partial sequences
30 (0.0%) poorly mapped sequences
825921 (99.98%) missing sequences
826058 (100.0%) sequences were evaluated

Looks like my GMAP was somehow interrupted but Gnavigator continued. This is the version I am using

/projects/spruceup_scratch/dev/AnalysisDownstream/Gnavigator/gnavigator/gnavigator.py

Is the bug fixed in here or it's another issue? Thanks Kristina

[sahammond]

I think the version that you pointed to is from before the commit that should fix that problem. You can try with my current development version and see if it still hangs.

/projects/btl/shammond/git/gnavigator/gnavigator.py

What seems to be GMAP's problem with that sequence? Is the ID too long?