updating samtools to new version

[ifiddes]

Which is on github!

I am not directly committing this because I was getting the weird error with the HMM I was getting the other day (despite submodules being updated) with the test data but not actual sample data - see below:

log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Parsed arguments and set up logging
log.txt: This analysis target has read fastq file: tests/output/processedReadFastqFiles/fake_readtype/reads.fq, reference fasta file: tests/output/processedReferenceFastaFiles/reference.fa, sam file: tests/output/analysis_fake_readtype/experiment_reads.fq_reference.fa_BwaParamsRealignEm/mapping.sam and will output to the directory: tests/output/analysis_fake_readtype/experiment_reads.fq_reference.fa_BwaParamsRealignEm/analysis_AlignmentUncertainty
log.txt: Got the wrong number of transitions in the input state machine file /hive/users/ifiddes/nanopore/nanopore/mappers/last_em_575_M13_2D_hmm.txt, got 27 instead of 11
log.txt:
log.txt: Traceback (most recent call last):
log.txt: File "/hive/users/ifiddes/nanopore/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/hive/users/ifiddes/nanopore/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/hive/users/ifiddes/nanopore/nanopore/analyses/alignmentUncertainty.py", line 42, in run
log.txt: (cigarString, tempRefFile, tempReadFile, tempPosteriorProbsFile, hmmFile, tempCigarFile))
log.txt: File "/hive/users/ifiddes/nanopore/submodules/sonLib/bioio.py", line 184, in system
log.txt: raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
log.txt: RuntimeError: Command: echo cigar: MOUSE_1_read_1 0 3070 + HUMAN 23005 26227 + 1 M 2 I 1 M 5 D 5 M 6 D 2 M 2 D 2 M 2 D 1 M 3 D 1 M 1 D 4 M 1 D 1 M 2 D 5 M 1 D 2 M 6 I 1 M 1 D 6 M 3 I 1 M 2 I 1 M 3 I 3 M 2 I 2 M 2 I 3 M 3 I 4 M 2 D 2 M 2 D 1 M 3 I 3 M 3 I 2 M 3 D 1 M 2 I 2 M 2 D 6 M 3 D 2 M 5 I 1 M 2 D 1 M 2 I 3 M 2 I 7 M 2 I 8 M 4 D 3 M 3 D 2 M 2 D 2 M 3 D 3 M 3 I 3 M 3 D 3 M 2 I 2 M 3 I 4 M 2 I 1 M 1 I 1 M 2 D 3 M 2 D 4 M 3 I 1 M 1 I 1 M 2 D 1 M 1 D 3 M 1 D 1 M 5 D 4 M 2 D 2 M 2 D 1 M 2 I 1 M 2 D 1 M 1 I 1 M 3 D 7 M 2 I 4 M 7 I 2 M 2 I 1 M 6 D 5 M 3 I 2 M 2 D 1 M 2 D 3 M 2 I 1 M 1 I 1 M 5 I 3 M 1 I 1 M 1 I 1 M 2 I 1 M 2 D 4 M 1 I 2 M 2 D 1 M 2 I 7 M 3 I 2 M 3 I 1 M 8 I 2 M 1 D 3 M 1 I 2 M 2 I 1 M 2 I 2 M 2 I 2 M 1 I 2 M 3 D 2 M 1 I 1 M 2 D 1 M 1 D 1 M 2 D 4 M 1 D 1 M 1 I 1 M 3 D 3 M 1 I 2 M 2 I 1 M 7 I 6 M 2 I 2 M 1 I 1 M 2 I 1 M 3 I 6 M 2 I 1 M 2 D 2 M 5 I 1 M 6 D 5 M 2 I 1 M 7 D 6 M 1 I 3 M 3 D 4 M 10 D 4 M 2 D 1 M 5 D 1 M 2 D 3 M 6 I 3 M 1 I 2 M 2 I 2 M 1 I 2 M 3 D 1 M 4 D 1 M 1 I 4 M 4 D 6 M 6 I 2 M 3 I 2 M 1 I 4 M 2 I 3 M 1 I 1 M 3 D 2 M 2 I 6 M 1 I 1 M 2 I 1 M 1 I 10 M 1 D 1 M 2 D 1 M 1 I 1 M 3 I 3 M 2 I 4 M 1 I 3 M 3 D 4 M 2 D 1 M 1 D 4 M 1 I 2 M 1 D 1 M 4 D 3 M 4 D 1 M 3 I 3 M 2 D 2 M 3 I 2 M 1 I 2 M 1 D 1 M 2 I 3 M 2 I 2 M 3 I 2 M 2 I 1 M 1 I 1 M 2 I 1 M 1 D 1 M 2 I 6 M 3 D 2 M 4 I 1 M 3 D 1 M 1 I 3 M 1 D 1 M 2 D 5 M 2 I 1 M 2 I 1 M 5 D 3 M 4 D 5 M 3 I 1 M 2 D 4 M 2 D 2 M 1 D 2 M 3 D 3 M 4 D 1 M 2 D 6 M 1 D 1 M 1 D 3 M 3 D 2 M 2 I 1 M 3 D 3 M 2 I 2 M 3 I 1 M 1 D 3 M 2 I 2 M 3 I 2 M 3 I 2 M 1 D 1 M 1 I 2 M 7 I 2 M 2 I 2 M 2 D 1 M 1 D 1 M 10 D 10 M 2 I 1 M 3 D 3 M 3 I 2 M 2 D 1 M 2 I 13 M 6 I 5 M 1 I 4 M 2 D 1 M 1 D 2 M 4 D 3 M 2 I 1 M 3 D 3 M 2 I 2 M 1 D 1 M 4 I 1 M 4 I 5 M 2 D 2 M 3 I 1 M 1 I 2 M 8 I 1 M 2 D 1 M 3 D 1 M 1 D 1 M 2 D 3 M 2 D 1 M 13 D 4 M 2 I 1 M 1 D 6 M 1 I 1 M 1 D 1 M 1 D 1 M 2 I 1 M 3 D 1 M 2 I 7 M 5 D 6 M 4 D 2 M 1 I 1 M 3 D 1 M 1 D 1 M 1 D 3 M 6 I 8 M 2 D 6 M 3 I 3 M 1 D 2 M 4 I 4 M 4 I 5 M 2 D 2 M 6 D 1 M 1 D 2 M 1 I 2 M 4 D 2 M 2 D 5 M 1 D 3 M 2 I 3 M 1 D 2 M 5 D 2 M 2 D 2 M 1 I 3 M 1 D 1 M 4 D 1 M 2 I 4 M 2 D 2 M 3 I 2 M 1 I 1 M 3 D 6 M 2 I 1 M 2 D 1 M 2 D 1 M 2 D 3 M 2 I 3 M 2 D 2 M 4 D 1 M 1 D 3 M 2 D 1 M 1 D 1 M 1 I 1 M 1 D 1 M 3 D 3 M 2 I 1 M 3 D 2 M 1 I 5 M 1 D 1 M 2 I 3 M 2 I 3 M 2 I 2 M 2 D 2 M 8 I 2 M 2 D 5 M 2 I 2 M 1 D 8 M 6 D 1 M 4 D 3 M 4 I 1 M 3 D 1 M 3 D 4 M 3 I 4 M 2 I 5 M 5 D 1 M 2 I 5 M 4 D 1 M 2 D 6 M 1 I 2 M 4 I 2 M 4 D 3 M 1 I 1 M 4 D 2 M 3 D 9 M 1 I 3 M 1 D 4 M 2 I 2 M 2 D 2 M 4 I 1 M 1 D 3 M 4 I 3 M 1 D 1 M 1 D 2 M 1 I 1 M 3 D 1 M 4 D 8 M 5 D 1 M 2 D 4 M 2 D 3 M 3 D 2 M 5 D 2 M 2 D 2 M 3 I 1 M 3 I 10 M 1 I 3 M 6 I 3 M 2 D 1 M 4 D 2 M 1 D 3 M 3 I 2 M 3 D 3 M 2 D 2 M 1 I 2 M 1 D 1 M 2 D 4 M 2 I 3 M 2 D 2 M 4 I 1 M 1 D 2 M 1 I 1 M 1 D 2 M 2 I 2 M 1 I 1 M 3 I 1 M 1 I 3 M 2 D 1 M 1 I 3 M 2 D 2 M 3 I 1 M 1 I 1 M 4 I 1 M 1 I 1 M 1 I 3 M 1 I 1 M 2 I 1 M 1 D 5 M 1 D 1 M 1 I 2 M 1 D 5 M 8 D 1 M 5 D 2 M 1 I 5 M 2 I 2 M 4 I 3 M 4 I 2 M 1 D 1 M 2 D 6 M 1 D 3 M 3 D 1 M 2 I 1 M 4 D 1 M 1 I 2 M 2 D 4 M 1 I 1 M 1 D 2 M 3 D 2 M 3 D 1 M 1 I 2 M 2 D 3 M 2 D 2 M 4 I 2 M 1 I 1 M 1 I 2 M 2 D 2 M 1 D 2 M 4 D 4 M 3 D 1 M 1 I 1 M 4 D 3 M 2 D 2 M 1 I 2 M 1 I 6 M 2 D 3 M 2 D 1 M 3 D 1 M 2 D 1 M 1 D 1 M 4 I 1 M 2 I 2 M 1 D 2 M 1 I 2 M 1 D 1 M 2 I 2 M 3 I 4 M 1 D 1 M 2 D 1 M 1 I 2 M 2 D 1 M 3 D 2 M 2 I 3 M 7 D 2 M 2 I 2 M 3 D 2 M 3 D 2 M 2 I 2 M 1 D 4 M 2 D 7 M 2 I 2 M 7 D 4 M 4 I 1 M 1 D 1 M 2 I 2 M 6 D 1 M 1 I 1 M 4 I 1 M 3 D 1 M 1 I 4 M 4 I 1 M 2 D 2 M 3 D 1 M 4 D 1 M 1 I 9 M 2 I 2 M 3 I 1 M 2 I 4 M 2 I 1 M 2 D 2 M 3 D 6 M 2 D 5 M 2 D 1 M 4 I 3 M 2 D 3 M 3 D 5 M 2 I 4 M 1 I 1 M 3 I 2 M 1 I 2 M 3 I 1 M 1 D 4 M 3 I 2 M 1 I 1 M 2 D 3 M 3 D 4 M 1 I 1 M 5 I 5 M 2 D 7 M 1 D 2 M 5 D 3 M 3 D 1 M 3 I 2 M 2 D 4 M 1 D 2 M 2 I 2 M 2 D 5 M 3 D 3 M 5 I 1 M 1 D 1 M 2 I 1 M 2 I 3 M 3 D 1 M 1 I 2 M 2 I 4 M 5 D 2 M 3 D 4 M 1 D 1 M 1 D 1 M 3 D 3 M 2 D 2 M 2 D 2 M 5 D 9 M 3 I 1 M 3 I 1 M 2 D 3 M 2 D 1 M 1 D 2 M 7 D 2 M 1 I 3 M 3 D 8 M 4 I 1 M 1 D 3 M 2 D 2 M 1 I 1 M 7 I 1 M 2 D 5 M 1 D 2 M 2 D 1 M 1 D 3 M 1 D 2 M 2 D 2 M 4 I 5 M 1 I 2 M 8 D 1 M 2 D 1 M 2 D 1 M 1 I 1 M 2 I 1 M 2 I 3 M 2 D 2 M 6 D 1 M 1 I 2 M 2 D 1 M 2 I 8 M 5 I 6 M 2 D 1 M 1 I 3 M 3 D 1 M 8 D 4 M 1 I 1 M 1 I 2 M 2 I 3 M 3 I 1 M 1 I 1 M 2 D 2 M 6 D 1 M 2 D 11 M 4 I 4 M 2 I 3 M 4 D 8 M 1 D 1 M 3 D 2 M 3 D 4 M 6 I 4 M 2 D 3 M 3 D 4 M 2 D 4 M 3 I 5 M 3 I 5 M 5 I 1 M 4 D 6 M 1 D 1 M 4 D 2 M 1 D 4 M 2 D 1 M 1 D 4 M 3 D 8 M 3 D 2 M 1 I 1 M 2 I 1 M 1 D 3 M 5 I 2 M 1 I 1 M 5 D 1 M 2 I 1 M 1 I 2 M 1 D 1 M 3 I 3 M 2 D 4 M 1 I 2 M 3 D 1 M 1 I 1 M 2 D 10 M 3 D 1 M 2 D 3 M 3 D 2 M 3 I 1 M 1 D 3 M 4 D 7 M 2 D 3 M 2 D 1 M 3 I 2 M 2 D 5 M 1 D 1 M 2 D 1 M 2 D 7 M 2 D 2 M 3 D 6 M 5 I 8 M 5 I 1 M 1 D 4 M 2 D 1 M 1 I 2 M 52 D 8 M 35 D 2 M 1 I 2 M 14 I 1 M 1 I 1 M 1 D 2 M 62 I 2 M 3 I 1 M 1 D 3 M 7 I 1 M 4 I 23 M 4 I 15 M 2 I 11 M 32 I 1 M 2 D 3 M 1 I 2 M 3 D 1 M 1 I 4 M 2 D 3 M 22 I 1 M 1 D 1 M 11 D 3 M 2 I 3 M 34 D 1 M 29 D 1 M 31 D 1 M 1 I 2 M 3 D 2 M 4 I 1 M 47 I 3 M 4 D 3 M 15 I 2 M 1 D 2 M 37 D 2 M 1 I 2 M 4 D 2 M 2 I 1 M 27 I 1 M 1 D 3 M 52 I 2 M 3 D 2 M 78 I 1 M 5 D 1 M 8 I 1 M 48 D 2 M 1 I 2 M 11 I 2 M 1 I 1 M 1 D 3 M 72 I 2 M 2 D 2 M 3 I 1 M 2 D 1 M 7 I 2 M 6 D 1 M 1 I 3 M 3 I 1 M 4 D 4 M 1 I 8 M 3 I 3 M 1 D 7 M 6 D 1 M 1 I 4 M 1 D 2 M 2 I 1 M 1 I 1 M 3 I 2 M 3 I 1 M 2 D 3 M 1 D 1 M 9 D 3 M 2 I 1 M 1 D 4 M 2 I 2 M 1 D 2 M 4 D 4 M 1 I 2 M 2 D 1 M 1 D 3 M 1 D 2 M 3 I 3 M 1 D 2 M 2 I 1 M 4 D 1 M 1 D 1 M 2 D 1 M 2 D 2 M 3 D 3 M 2 I 2 M 1 I 5 M 6 I 1 M 1 D 1 M 2 D 1 M 5 | cactus_realign /scratch/tmp/tmp_iohY9/localTempDir/ref.fa /scratch/tmp/tmp_iohY9/localTempDir/read.fa --rescoreByPosteriorProbIgnoringGaps --rescoreOriginalAlignment --diagonalExpansion=10 --splitMatrixBiggerThanThis=100 --outputPosteriorProbs=/scratch/tmp/tmp_iohY9/localTempDir/probs.tsv --loadHmm=/hive/users/ifiddes/nanopore/nanopore/mappers/last_em_575_M13_2D_hmm.txt > /scratch/tmp/tmp_iohY9/localTempDir/rescoredCigar.cig exited with non-zero status 1
log.txt: Exiting the slave because of a failed job on host kolossus
log.txt: Due to failure we are reducing the remaining retry count of job /cluster/home/ifiddes/ifiddes_hive/nanopore/testJobTree/jobs/t1/t2/t0/t3/t1/job to 0
log.txt: We have set the default memory of the failed job to 8589934592 bytes
Job: /cluster/home/ifiddes/ifiddes_hive/nanopore/testJobTree/jobs/t1/t2/t0/t3/t1/job is completely failed