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gsneha26 / SegAlign

A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043
MIT License
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Error in LASTZ process! #39

Closed glennhickey closed 4 years ago

glennhickey commented 4 years ago

Command:

run_segalign /tmpoat8dml4.tmp tmp2a87d84z.tmp --format=cigar --notrivial --step=2 --ambiguous=iupac,100,100 --ydrop=3000

Input:

s3://glennhickey/share/tmp2a87d84z.tmp.gz
s3://glennhickey/share/tmpoat8dml4.tmp.gz

Output

Converting fasta files to 2bit format

Executing: "segalign /home/ubuntu/work/blast-fail/work/node-c9637ce3-5d13-43ff-a839-9ca5bfddbbe0-e26b862451c6400c819df9042d6a6135/tmp5bhda67a/9a6da48b-421e-44e6-ac6b-4
29281f9d00f/tmpoat8dml4.tmp /home/ubuntu/work/blast-fail/work/node-c9637ce3-5d13-43ff-a839-9ca5bfddbbe0-e26b862451c6400c819df9042d6a6135/tmp5bhda67a/9a6da48b-421e-44e6
-ac6b-429281f9d00f/tmp2a87d84z.tmp /home/ubuntu/work/blast-fail/output_22643/data_4076/  --format=cigar --notrivial --step=2 --ambiguous=iupac,100,100 --ydrop=3000"
Using 64 threads
Using 8 GPU(s)

Reading query file ...

Reading target file ...

Start alignment ...

Sending reference block 0 ...

Sending query block 0 with buffer 0 ...
Query block 0, interval 1/26 (0:10000000) with buffer 0
Query block 0, interval 2/26 (10000000:20000000) with buffer 0
Query block 0, interval 3/26 (20000000:30000000) with buffer 0
Query block 0, interval 4/26 (30000000:40000000) with buffer 0
[...]
Sending reference block 10 ...

Sending query block 0 with buffer 0 ...
Query block 0, interval 1/26 (0:10000000) with buffer 0
Query block 0, interval 2/26 (10000000:20000000) with buffer 0
Query block 0, interval 3/26 (20000000:30000000) with buffer 0
Query block 0, interval 4/26 (30000000:40000000) with buffer 0
Query block 0, interval 26/26 (250000000:259697043) with buffer 0
Query block 0, interval 5/26 (40000000:50000000) with buffer 0
Query block 0, interval 6/26 (50000000:60000000) with buffer 0
Query block 0, interval 7/26 (60000000:70000000) with buffer 0
Query block 0, interval 8/26 (70000000:80000000) with buffer 0
Query block 0, interval 9/26 (80000000:90000000) with buffer 0
Query block 0, interval 10/26 (90000000:100000000) with buffer 0
Query block 0, interval 11/26 (100000000:110000000) with buffer 0
Query block 0, interval 12/26 (110000000:120000000) with buffer 0
Query block 0, interval 13/26 (120000000:130000000) with buffer 0
Query block 0, interval 14/26 (130000000:140000000) with buffer 0
Query block 0, interval 15/26 (140000000:150000000) with buffer 0
Query block 0, interval 16/26 (150000000:160000000) with buffer 0
Query block 0, interval 17/26 (160000000:170000000) with buffer 0
Query block 0, interval 18/26 (170000000:180000000) with buffer 0
Query block 0, interval 20/26 (190000000:200000000) with buffer 0
Query block 0, interval 19/26 (180000000:190000000) with buffer 0
Query block 0, interval 21/26 (200000000:210000000) with buffer 0
Query block 0, interval 22/26 (210000000:220000000) with buffer 0
Query block 0, interval 23/26 (220000000:230000000) with buffer 0
Query block 0, interval 24/26 (230000000:240000000) with buffer 0
Query block 0, interval 25/26 (240000000:250000000) with buffer 0

real    4m26.554s
user    57m1.447s
sys     19m27.509s

Error in LASTZ process!

minus strand subrange is 1..1159682
FAILURE: query interval out of range (tmp9.block0.r4008435271.plus.segments: line 22, 1482007>1159682)
FAILURE: query interval out of range (tmp9.block0.r4613734159.minus.segments: line 19, 4294647925>1159682)
minus strand subrange is 1..1159682
FAILURE: query interval out of range (tmp9.block0.r4613734159.plus.segments: line 19, 1481984>1159682)
FAILURE: query interval out of range (tmp9.block0.r5128203719.minus.segments: line 31, 4294645060>1159682)
minus strand subrange is 1..1159682
FAILURE: query interval out of range (tmp9.block0.r5128203719.plus.segments: line 9, 1482007>1159682)
FAILURE: query interval out of range (tmp9.block0.r517840468.minus.segments: line 104, 4294614720>1159682)
minus strand subrange is 1..1159682
FAILURE: query interval out of range (tmp9.block0.r517840468.plus.segments: line 144, 1479179>1159682)
FAILURE: query interval out of range (tmp9.block0.r5628944441.minus.segments: line 35, 4294645065>1159682)
minus strand subrange is 1..1159682
FAILURE: query interval out of range (tmp9.block0.r5628944441.plus.segments: line 8, 1482007>1159682)

(exits with code 6)

For reference, the cactus command is 

cactus-blast ./js 10mammalsplus.txt Anc10.cigar --root Anc10 --pathOverrides tupChi1.fa.pp rheMac8.fa.pp hg38.fa.pp panTro6.fa.pp equCab3.fa.pp --pathOverrideNames Tree_shrew Rhesus Human Chimp Horse --realTimeLogging --logInfo --maxCores 64 --workDir ./work --cleanWorkDir never --configFile config.xml
gsneha26 commented 4 years ago

Thank you for pointing out this bug. It is fixed in the latest commit. Tested with the above dataset and it ran without any errors.