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I am having a problem when mapping my short reads 150bp (paired-end reads) to the genome fasta.
I would like to have all unique reads (no mismatching, minimum reads 150 bp) out that are mapped to the genome.
Here I face the problem: I assigned 20 threads (20 cores) but my job ended up with error. Why it is happening and what is the solution?. Each file 23 GB big (R1 and R2)
I would like to have all unique reads (no mismatching, minimum reads 150 bp) out that are mapped to the genome.
Here I face the problem: I assigned 20 threads (20 cores) but my job ended up with error. Why it is happening and what is the solution?. Each file 23 GB big (R1 and R2)
Code:
job starting at 09:42:42
java -ea -Xmx60001m -Xms60001m -cp /sw/bioinfo/bbmap/38.61b/rackham/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 pairedonly=t ambiguous=toss killbadpairs=t pairlen=1000 trimq=20 mintrimlength=120 minaveragequality=20 rescuemismatches=1 outm=2008-27-201.aligned.sam outu=2008-27-201.unaligned.sam showprogress=10000 scafstats=2008_27.scafstats in=/crex/proj/snic2020-6-16/datasets/human_depleted/Ki-2008-27-201_unmapped_R1.fq.gz in2=/crex/proj/snic2020-6-16/datasets/human_depleted/Ki-2008-27-201_unmapped_R2.fq.gz threads=auto
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, pairedonly=t, ambiguous=toss, killbadpairs=t, pairlen=1000, trimq=20, mintrimlength=120, minaveragequality=20, rescuemismatches=1, outm=2008-27-201.aligned.sam, outu=2008-27-201.unaligned.sam, showprogress=10000, scafstats=2008_27.scafstats, in=/crex/proj/snic2020-6-16/datasets/human_depleted/Ki-2008-27-201_unmapped_R1.fq.gz, in2=/crex/proj/snic2020-6-16/datasets/human_depleted/Ki-2008-27-201_unmapped_R2.fq.gz, threads=auto]
Version 38.61
Scaffold statistics will be written to 2008_27.scafstats
Set threads to 20
Ambiguously mapped reads will be considered unmapped.
Set genome to 1
Loaded Reference: 2.025 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 3.261 seconds.
Analyzed Index: 2.517 seconds.
Started output stream: 0.371 seconds.
Started output stream: 0.023 seconds.
Creating scaffold statistics table: 0.065 seconds.
Cleared Memory: 0.516 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 20 mapping threads.
Exception in thread "Thread-6" java.lang.AssertionError: A00605:23:HHNVHDSXX:1:1101:13711:1783 1:N:0:TAATGCGC+AGGCGAAG 0 -1 + -1 -1 00000000000000000000000 1 0 0 ATGTTGAATATGCTTTGTTTTATGTTATAATCAGGTGCTATTTAATTGTTTGACTGTTGGTGATTGCAGGTTTTGGAGAAAAGGAGGAGCTCATCCAGATCAACAAAGCTTGGACTTCTACAACAGCGTTTGGACAAAGGTAAGAACGAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF . . . .
at align2.AbstractMapThread.rescue(AbstractMapThread.java:1200)
at align2.BBMapThread.processReadPair(BBMapThread.java:1097)
at align2.AbstractMapThread.run(AbstractMapThread.java:536)
Detecting finished threads: 0Exception in thread "Thread-18" java.lang.AssertionError: A00605:23:HHNVHDSXX:1:1101:16107:1705 2:N:0:TAATGCGC+AGGCGAAG 601 -1 + -1 -1 00000000001000000000000 1 0 0 CCGACCCTCCAAGAGTGTCTGGTATGTGTGGCTGAATTCTGGGTCGCTTTTGTAGAGAAGTGGCCAATCAGAAGTCTCGTGCCCGCAAGAGTTGAGCACGGTGGTTAGCGCCATGATCGGTGGTCGACTGAGGCAATCTGCAACATTATTG FFFFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FF,FFF . . . . 1,1,28300816,28300966,0,00,14,14532,14556,14557,145561,1,28300816,28300966,0,00,14,14532,14556,14557,14556
at align2.AbstractMapThread.rescue(AbstractMapThread.java:1200)
at align2.BBMapThread.processReadPair(BBMapThread.java:1090)
at align2.AbstractMapThread.run(AbstractMapThread.java:536)
Exception in thread "Thread-24" java.lang.AssertionError: A00605:23:HHNVHDSXX:1:1101:8558:1626 1:N:0:TAATGCGC+AGGCGAAG 1002 -1 + -1 -1 00000000000000000000000 1 0 0 GAAAACGGCTCCCACTTATTCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCTGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTAGATAGTAGATAGGGACAGTGGGAA FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFF . . . . 1,0,14943298,14943448,0,00,10,11843,11823,15526,118231,0,14943298,14943448,0,00,10,11843,11823,15526,11823 1,0,15184887,15185037,0,00,11,11685,11645,11646,116451,0,15184887,15185037,0,00,11,11685,11645,11646,11645
at align2.AbstractMapThread.rescue(AbstractMapThread.java:1200)
at align2.BBMapThread.processReadPair(BBMapThread.java:1097)
at align2.AbstractMapThread.run(AbstractMapThread.java:536)
Exception in thread "Thread-14" java.lang.AssertionError: A00605:23:HHNVHDSXX:1:1101:2293:1016 2:N:0:TAATGCGC+AGGCGAAG 1404 -1 + -1 -1 00000000001000000000000 1 0 0 NATAGAGACAAGCTTTTATAGATAGAGAGGAAAGAGATAGGATCAACCACAATATTCATGGGATTGGCTTTATCACTTAGAAACTTCCATGAAAGGTGGCAAACCACTTCCCTTCTATGGAGATTCG !FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF . . . . 1,0,37647506,37647634,0,00,6,7881,8211,0,82111,0,37647506,37647634,0,00,6,7881,8211,0,8211
at align2.AbstractMapThread.rescue(AbstractMapThread.java:1200)
at align2.BBMapThread.processReadPair(BBMapThread.java:1090)
at align2.AbstractMapThread.run(AbstractMapThread.java:536)
Exception in thread "Thread-8" java.lang.AssertionError: A00605:23:HHNVHDSXX:1:1101:3766:2785 2:N:0:TAATGCGC+AGGCGAAG 3802 -1 + -1 -1 00000000001000000000000 1 0 0 GCAATGGATCGGTAGCATTACCCCAAATATGGATGGTATGGAGAGACCATGGTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF . . . . 1,0,21465899,21466010,0,00,1,1003,0,0,01,0,21465899,21466010,0,00,1,1003,0,0,0 1,0,27814628,27814681,0,00,4,4856,4856,4857,48561,0,27814628,27814681,0,00,4,4856,4856,4857,4856
at align2.AbstractMapThread.rescue(AbstractMapThread.java:1200)
-------------------
---------------------
-----------------------------
, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19
**************************************************************************
Warning! 20 mapping threads did not terminate normally.
Check the error log; the output may be corrupt or incomplete.
Please submit the full stderr output as a bug report, not just this message.
**************************************************************************
------------------ Results ------------------
Genome: 1
Key Length: 13
Max Indel: 16000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 212 (28878 bases)
Mapping: 0.669 seconds.
Reads/sec: 316.77
kBases/sec: 43.15
Pairing data: pct pairs num pairs pct bases num bases
mated pairs: 2.8302% 3 1.9600% 566
bad pairs: 0.0000% 0 0.0000% 0
insert size avg: 97.67
Read 1 data: pct reads num reads pct bases num bases
mapped: 2.8302% 3 1.9552% 283
unambiguous: 2.8302% 3 1.9552% 283
ambiguous: 0.0000% 0 0.0000% 0
low-Q discards: 0.9434% 1 1.0432% 151
perfect best site: 0.0000% 0 0.0000% 0
semiperfect site: 0.0000% 0 0.0000% 0
rescued: 0.0000% 0
Match Rate: NA NA 86.9258% 246
Error Rate: 100.0000% 3 9.1873% 26
Sub Rate: 100.0000% 3 9.1873% 26
Del Rate: 0.0000% 0 0.0000% 0
Ins Rate: 0.0000% 0 0.0000% 0
N Rate: 33.3333% 1 3.8869% 11
Read 2 data: pct reads num reads pct bases num bases
mapped: 2.8302% 3 1.9647% 283
unambiguous: 2.8302% 3 1.9647% 283
ambiguous: 0.0000% 0 0.0000% 0
low-Q discards: 1.8868% 2 1.8189% 262
perfect best site: 0.0000% 0 0.0000% 0
semiperfect site: 0.0000% 0 0.0000% 0
rescued: 0.0000% 0
Match Rate: NA NA 89.0459% 252
Error Rate: 100.0000% 3 9.5406% 27
Sub Rate: 100.0000% 3 9.5406% 27
Del Rate: 0.0000% 0 0.0000% 0
Ins Rate: 0.0000% 0 0.0000% 0
N Rate: 33.3333% 1 1.4134% 4
Exception in thread "main" java.lang.AssertionError:
The number of reads out does not add up to the number of reads in.
This may indicate that a mapping thread crashed.
If you submit a bug report, include the entire console output, not just this error message.
3+0+0+82+1+0 = 86 != 106
at align2.AbstractMapper.printOutputStats(AbstractMapper.java:1961)
at align2.AbstractMapper.printOutput(AbstractMapper.java:1059)
at align2.BBMap.testSpeed(BBMap.java:522)
at align2.BBMap.main(BBMap.java:35)
job finishing at 09:42:59
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