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ArtRand / signalAlign

HMM-HDP models for MinION signal alignments
MIT License
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R7.3 from different kits and MinIONs #6

Closed JohnUrban closed 7 years ago

JohnUrban commented 7 years ago

Hi,

I have recently put a genome together and want to see if there is evidence for methylation. A previous paper reported some evidence using an antibody on polytene chromosomes. So I am excited by the possibility that it can be detected at the sequence level with nanopore data.

Can the methylation detection for signalAlign still work with R7.3 data? That is all I have for this organism. Well I have the following: SQK-MAP002, r7.3 (5mer) SQK-MAP004, r7.3 (5mer) SQK-MAP005, r7.3 (5mer) SQK-MAP006, r7.3_e6_70bps_6mer, MkI

If the newest code doesn't support it, is there a way to access an older version that does? Can I mix those datasets above? If not, the last one makes up ~67% of the data I have so I'd likely use that one if possible.

Many thanks,

John

JohnUrban commented 7 years ago

In the organism I am studying, there was recent low resolution evidence (immunofluorescence using an antibody for methyl-C) that there is methylation of the genome. However, these experiments were far from definitive.

I am interested in using R7.3 nanopore data to: (i) see if it provides further evidence for methylation in the genome (ii) identify regions in the genome that are methylated (iii) potentially find evidence/regions for other marks that signalAlign supports

Could you let me know if these goals are possible with signalAlign? If so, what steps do I need to take? Thank you for any advice you can give.

So far I have tried running the demo, but keep getting errors such as this:

     11619 Segmentation fault      | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5

Any ideas on how to proceed with the demo?

ArtRand commented 7 years ago

Hello John,

You can use the older data. As for your older data: MAP006: What metrichor version is this base-called with? This should be supported, or supportable, using the current models. Send me the metrichor version or you can change what you need at (https://github.com/ArtRand/signalAlign/blob/master/scripts/signalAlignLib.py#L261).

MAP005 and older: As long there is a model in the HDF5s these can be supported. I don't know the structure of the HDF, however so you might have to go in and change the code.

I'll update the repo with a script that makes an ad hoc model out of a fast5 file, with that you can train the HDP and do all the rest.

If you want, send me an example file of each type: arand@soe.ucsc.edu

Thanks, A

JohnUrban commented 7 years ago

I just sent you some example files for my MAP006 data.

In the mean time, I have not been able to get the demo with the demo data to run correctly.

The command I have used is:

DATA=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/
REF=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_sequences/E.coli_K12.fasta
THMM=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm
CHMM=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
TM=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp
CM=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp
R=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_regions/test_sites_bal_1.tgt
L=/gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_regions/test_labels_bal_1.tsv
OUT=demo/
ERR=demo_run.err

./runSignalAlign \
        -d $DATA \
        -r $REF \
        -T $THMM \
        -C $CHMM \
        -tH $TM \
        -cH $CM \
        -x cytosine2 \
        -smt=threeStateHdp \
        -q $R \
        -p $L \
        -f variantCaller \
        -o $OUT \
        2> $OUT/$ERR

Here is an example of the demo/demo_run.err file:

Command Line: ./runSignalAlign -d /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/ -r /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_sequences/E.coli_K12.fasta -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm -tH /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -cH /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -x cytosine2 -smt=threeStateHdp -q /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_regions/test_sites_bal_1.tgt -p /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_regions/test_labels_bal_1.tsv -f variantCaller -o demo/

signalAlign - indexing reference
[bwa_index] Pack FASTA... 0.03 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.95 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.53 sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa index -p demo/tempFiles_alignment//temp_bwaIndex /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_sequences/E.coli_K12.fasta
[main] Real time: 1.618 sec; CPU: 1.577 sec
signalAlign - indexing reference, done
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (1654 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.007 CPU sec, 0.028 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch492_file245_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch492_file245_strand.fast5.fa
[main] Real time: 0.054 sec; CPU: 0.015 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch492_file245_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (2738 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.010 CPU sec, 0.040 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch146_file135_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch146_file135_strand.fast5.fa
[main] Real time: 0.059 sec; CPU: 0.019 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch146_file135_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (3912 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.029 CPU sec, 0.083 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5.fa
[main] Real time: 0.104 sec; CPU: 0.038 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5 68 3893 + gi_ecoli 2305627 2302056 - 1 M 9 I 1 M 8 I 1 M 1 I 1 M 15 I 1 M 9 I 1 M 11 I 1 M 6 D 1 M 5 D 1 M 1 D 1 M 10 I 1 M 6 I 1 M 3 I 1 M 10 D 1 M 2 D 1 M 10 I 2 M 6 I 1 M 6 I 2 M 1 I 3 M 1 I 1 M 5 I 3 M 2 I 1 M 15 D 1 M 7 D 1 M 5 D 1 M 2 I 1 M 4 D 1 M 2 I 1 M 19 I 1 M 30 I 1 M 11 I 4 M 3 I 1 M 11 I 1 M 9 D 1 M 24 D 5 M 6 I 4 M 25 D 1 M 3 D 1 M 3 I 1 M 2 I 1 M 1 I 3 M 2 I 3 M 13 I 5 M 11 D 1 M 11 I 1 M 1 I 3 M 9 I 3 M 3 I 1 M 4 I 1 M 1 I 2 M 13 D 1 M 2 D 1 M 8 I 1 M 12 D 1 M 3 I 1 M 8 I 1 M 19 I 1 M 6 I 1 M 2 I 1 M 1 I 1 M 4 I 1 M 10 I 1 M 2 I 1 M 4 I 1 M 18 I 1 M 2 I 2 M 5 I 1 M 11 I 4 M 4 D 1 M 6 I 3 M 19 D 1 M 10 I 1 M 8 D 2 M 7 D 1 M 6 D 1 M 2 I 1 M 2 I 1 M 14 I 3 M 5 D 1 M 4 D 1 M 13 I 1 M 6 I 2 M 4 I 3 M 8 I 2 M 5 I 2 M 8 I 1 M 7 D 1 M 10 I 1 M 1 I 1 M 14 I 1 M 10 I 1 M 10 D 1 M 9 I 1 M 6 I 2 M 8 D 1 M 7 I 1 M 4 I 1 M 6 I 1 M 5 I 4 M 2 I 1 M 6 I 3 M 26 I 2 M 3 D 1 M 2 D 1 M 11 I 1 M 1 I 1 M 4 I 1 M 8 D 2 M 4 D 1 M 6 I 2 M 6 D 1 M 10 I 2 M 24 I 1 M 23 I 3 M 1 I 1 M 10 D 2 M 21 I 1 M 9 D 1 M 3 I 1 M 3 I 1 M 10 I 1 M 19 I 1 M 18 I 2 M 29 D 2 M 14 D 2 M 8 I 4 M 6 I 1 M 4 D 1 M 4 I 1 M 17 I 3 M 2 I 1 M 9 I 1 M 1 I 1 M 45 I 1 M 5 I 2 M 6 I 1 M 6 D 1 M 14 I 1 M 6 D 2 M 11 D 1 M 13 I 1 M 1 I 1 M 21 I 2 M 11 I 3 M 9 D 1 M 9 I 2 M 1 I 1 M 4 D 1 M 1 D 2 M 21 I 2 M 15 D 2 M 7 I 1 M 1 I 1 M 18 I 1 M 7 I 1 M 13 I 2 M 10 D 1 M 6 I 3 M 18 D 1 M 7 D 1 M 41 I 1 M 3 I 1 M 1 I 1 M 4 I 1 M 2 I 1 M 3 D 1 M 4 D 1 M 3 D 1 M 6 I 1 M 4 D 1 M 25 I 1 M 52 D 1 M 9 D 1 M 27 I 2 M 24 I 3 M 5 D 1 M 7 I 1 M 14 I 2 M 18 I 3 M 45 D 2 M 12 I 2 M 9 D 1 M 9 I 2 M 53 I 4 M 19 I 2 M 2 I 1 M 4 I 1 M 28 I 2 M 3 I 1 M 11 I 2 M 4 I 1 M 6 I 1 M 17 D 1 M 8 I 1 M 27 I 1 M 37 D 2 M 11 I 2 M 5 I 1 M 11 I 1 M 18 I 1 M 13 D 1 M 14 I 1 M 34 I 6 M 9 I 1 M 1 I 1 M 6 I 2 M 18 D 1 M 15 I 1 M 36 D 2 M 6 I 3 M 37 I 2 M 19 D 2 M 19 D 1 M 6 I 2 M 4 I 1 M 5 I 1 M 8 I 1 M 4 I 1 M 19 I 2 M 10 I 1 M 5 I 1 M 3 I 1 M 11 I 1 M 1 I 1 M 2 I 1 M 4 I 1 M 10 I 5 M 2 I 1 M 5 I 1 M 6 D 2 M 41 I 1 M 2 I 1 M 10 D 2 M 6 I 2 M 7 I 1 M 1 I 3 M 6 I 2 M 2 I 1 M 21 I 1 M 27 I 1 M 2 D 1 M 16 D 2 M 15 I 2 M 4 I 1 M 19 I 2 M 4 I 1 M 9 D 2 M 8 D 2 M 11 D 1 M 14 I 1 M 22 D 1 M 5 I 1 M 3 I 1 M 5 I 1 M 3 I 3 M 5 I 2 M 24 I 2 M 6 I 1 M 16 I 2 M 17 I 1 M 81 I 1 M 3 I 2 M 32 I 1 M 9 I 1 M 4 I 2 M 1 I 1 M 7 I 2 M 71 D 1 M 7 D 1 M 6 D 1 M 4 I 1 M 7 I 1 M 5 I 1 M 9 I 1 M 5 I 2 M 6 D 1 M 2 D 1 M 5 D 1 M 21 I 3 M 19 I 1 M 12 D 1 M 7 I 1 M 29 I 2 M 13 D 1 M 3 I 1 M 6 D 1 M 4 I 1 M 10 D 2 M 10 I 1 M 18 I 1 M 9 D 1 M 5 I 3 M 11 I 1 M 40 I 2 M 5 I 3 M 12 D 1 M 5 I 2 M 1 I 1 M 4 D 1 M 14 D 1 M 7 I 4 M 5 I 2 M 10 I 2 M 9 I 1 M 18 I 4 M 10 D 1 M 23 I 1 M 3 I 1 M 9 I 1 M 34 I 2 M 4 I 2 M 1 I 1 M 4 I 1 M 6 I 1 M 11 I 1 M 5 D 1 M 20 I 3 M 11 I 1 M 8 I 2 M 1 I 2 M 5 D 1 M 7 D 1 M 3 I 1 M 29 D 1 M 5 D 1 M 12 D 1 M 10 D 1 M 16 I 1 M 1 I 2 M 1 I 1 M 6 I 1 M 2 D 1 M 3 D 2 M 2 D 2 M 12 I 2 M 1 I 1 M 14 I 1 M 1 I 1 M 2 D 1 M 11 | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5
[signalAlign] - using NanoporeHDPs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (3210 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.019 CPU sec, 0.041 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch308_file422_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch308_file422_strand.fast5.fa
[main] Real time: 0.055 sec; CPU: 0.028 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch308_file422_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (508 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.003 CPU sec, 0.015 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5.fa
[main] Real time: 0.028 sec; CPU: 0.011 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5 3 488 + gi_ecoli 1234292 1233788 - 1 M 6 D 2 M 8 D 1 M 16 D 2 M 6 I 1 M 6 I 1 M 5 D 1 M 4 I 1 M 2 D 1 M 1 D 1 M 7 D 4 M 6 D 2 M 5 D 1 M 7 D 2 M 8 D 1 M 4 D 1 M 23 I 2 M 8 D 1 M 4 D 1 M 4 I 1 M 3 I 2 M 6 I 1 M 3 D 1 M 10 I 3 M 8 D 4 M 5 I 1 M 5 D 1 M 8 I 1 M 14 I 2 M 1 I 3 M 12 I 2 M 4 D 1 M 10 D 1 M 12 I 2 M 19 I 2 M 4 D 1 M 2 D 1 M 5 D 4 M 19 D 1 M 4 D 1 M 9 I 1 M 11 D 1 M 19 D 1 M 10 D 1 M 19 D 1 M 8 I 2 M 23 D 6 M 6 D 1 M 6 D 2 M 13 I 2 M 1 I 1 M 4 D 1 M 1 D 1 M 5 I 1 M 2 I 2 M 19 D 2 M 6 I 1 M 4 | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5
[signalAlign] - using NanoporeHDPs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (5656 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.020 CPU sec, 0.092 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch412_file504_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch412_file504_strand.fast5.fa
[main] Real time: 0.129 sec; CPU: 0.030 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch412_file504_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (4056 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.025 CPU sec, 0.097 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch76_file426_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch76_file426_strand.fast5.fa
[main] Real time: 0.131 sec; CPU: 0.034 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch76_file426_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (17118 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.181 CPU sec, 0.547 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5.fa
[main] Real time: 0.570 sec; CPU: 0.190 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5 11 17095 + gi_ecoli 771637 788302 + 1 M 22 I 1 M 13 D 2 M 5 I 2 M 15 D 1 M 44 D 1 M 13 I 2 M 13 I 1 M 3 I 1 M 36 D 1 M 15 D 2 M 4 I 1 M 3 I 1 M 6 D 2 M 7 D 2 M 8 I 4 M 37 D 2 M 17 D 1 M 14 I 1 M 28 D 1 M 29 I 1 M 18 I 1 M 28 D 2 M 18 D 1 M 21 D 2 M 16 I 1 M 15 D 1 M 33 I 2 M 8 I 1 M 4 D 1 M 15 D 2 M 14 I 1 M 2 D 1 M 43 I 1 M 6 D 1 M 30 D 1 M 10 I 2 M 32 I 2 M 11 D 1 M 11 I 1 M 8 D 1 M 5 I 1 M 6 I 1 M 10 I 1 M 11 D 2 M 19 I 2 M 31 I 2 M 4 I 1 M 43 I 2 M 16 D 1 M 14 I 1 M 54 I 1 M 12 I 5 M 7 D 1 M 19 D 1 M 12 D 1 M 3 I 1 M 4 D 1 M 51 D 1 M 8 I 2 M 4 D 1 M 28 D 3 M 9 D 1 M 13 D 1 M 3 D 1 M 6 I 1 M 22 I 2 M 21 I 2 M 11 I 1 M 23 I 3 M 26 I 1 M 14 I 1 M 13 D 1 M 6 D 1 M 27 D 3 M 4 D 1 M 1 D 1 M 24 D 1 M 10 I 1 M 2 I 2 M 12 I 1 M 8 I 1 M 6 D 1 M 8 I 1 M 17 I 2 M 10 D 1 M 18 I 2 M 4 I 1 M 3 I 1 M 19 I 1 M 11 I 2 M 33 D 1 M 5 I 2 M 11 D 3 M 8 D 1 M 2 D 1 M 1 D 1 M 13 D 1 M 43 I 1 M 13 I 1 M 20 D 1 M 6 D 3 M 36 I 2 M 10 I 2 M 8 D 3 M 2 D 1 M 4 D 1 M 8 I 1 M 19 D 1 M 9 I 4 M 11 D 1 M 33 D 1 M 18 I 3 M 30 D 1 M 16 I 1 M 14 D 1 M 18 I 1 M 34 I 3 M 7 I 1 M 14 D 2 M 17 D 1 M 5 I 2 M 33 I 4 M 22 D 1 M 6 I 2 M 7 I 2 M 53 I 2 M 7 I 1 M 2 D 2 M 21 I 2 M 17 D 1 M 11 D 1 M 19 I 2 M 40 D 1 M 19 D 1 M 5 D 2 M 11 D 1 M 18 I 2 M 2 I 1 M 5 D 1 M 8 I 2 M 21 D 1 M 7 D 1 M 16 I 1 M 5 D 1 M 15 I 1 M 12 I 1 M 57 D 3 M 2 D 1 M 7 I 1 M 4 I 1 M 5 D 2 M 3 D 2 M 9 D 2 M 3 D 2 M 6 D 1 M 5 D 1 M 6 D 1 M 1 D 1 M 7 I 1 M 7 I 1 M 44 D 2 M 13 D 1 M 3 D 2 M 11 I 1 M 7 I 1 M 11 D 2 M 2 D 1 M 11 I 3 M 3 D 1 M 23 D 2 M 10 D 2 M 28 D 2 M 20 D 2 M 3 D 1 M 1 D 1 M 5 I 1 M 4 I 1 M 15 D 2 M 17 I 2 M 9 D 1 M 12 I 1 M 18 I 2 M 13 I 2 M 34 D 2 M 42 D 1 M 30 D 1 M 3 D 1 M 10 D 1 M 5 D 2 M 36 D 2 M 5 D 1 M 19 D 2 M 10 D 1 M 18 I 2 M 7 D 2 M 3 D 2 M 25 I 1 M 15 D 2 M 10 I 1 M 9 I 1 M 8 I 1 M 20 D 1 M 6 D 1 M 1 D 1 M 13 D 1 M 36 D 2 M 4 D 1 M 21 D 3 M 9 I 2 M 9 I 2 M 7 I 1 M 1 I 1 M 8 D 1 M 5 I 1 M 52 I 1 M 6 D 1 M 2 D 1 M 7 D 1 M 56 I 3 M 29 D 3 M 7 I 3 M 1 I 1 M 10 I 4 M 23 I 2 M 5 D 1 M 18 I 1 M 2 I 1 M 4 I 2 M 3 D 1 M 8 I 1 M 14 I 1 M 5 I 1 M 3 I 1 M 3 D 1 M 1 D 1 M 5 I 1 M 15 D 1 M 7 I 1 M 2 D 2 M 13 I 1 M 5 I 1 M 9 D 1 M 12 I 2 M 8 D 1 M 9 D 1 M 36 D 2 M 20 I 5 M 4 I 1 M 5 D 1 M 15 I 1 M 11 D 1 M 10 D 2 M 23 D 1 M 27 I 1 M 18 I 2 M 13 D 1 M 4 D 2 M 57 I 1 M 15 D 1 M 7 I 1 M 7 D 1 M 14 I 1 M 14 D 1 M 18 D 1 M 29 D 1 M 14 D 1 M 13 D 2 M 37 I 1 M 3 I 1 M 1 I 1 M 4 D 1 M 16 I 4 M 25 D 1 M 18 I 1 M 16 D 1 M 25 D 1 M 14 I 1 M 3 D 1 M 6 D 1 M 15 I 1 M 15 D 1 M 1 D 1 M 18 D 2 M 5 D 1 M 10 I 1 M 3 I 1 M 51 I 1 M 27 D 3 M 2 D 1 M 10 I 1 M 14 I 2 M 13 I 1 M 31 D 2 M 2 D 1 M 8 I 2 M 7 I 2 M 5 I 1 M 43 D 1 M 8 I 1 M 23 D 1 M 5 D 3 M 1 D 1 M 10 D 1 M 11 D 2 M 17 D 1 M 5 D 1 M 14 D 1 M 23 D 1 M 26 D 1 M 18 I 2 M 19 D 1 M 16 D 1 M 25 D 1 M 17 I 1 M 3 D 1 M 60 I 1 M 14 I 4 M 4 I 2 M 18 I 1 M 3 I 2 M 16 I 1 M 14 I 1 M 4 D 2 M 14 D 1 M 3 I 3 M 7 D 2 M 15 D 1 M 23 I 1 M 20 I 1 M 5 I 3 M 7 D 2 M 26 I 1 M 13 D 1 M 12 D 1 M 10 I 5 M 14 D 1 M 2 D 1 M 16 D 1 M 9 D 3 M 4 I 1 M 28 I 3 M 2 I 1 M 11 I 1 M 17 I 2 M 22 D 1 M 9 I 4 M 1 I 1 M 3 I 2 M 2 D 1 M 15 I 4 M 10 I 1 M 5 I 3 M 12 D 1 M 22 D 2 M 3 D 1 M 10 I 2 M 11 I 1 M 5 D 1 M 6 D 1 M 7 I 1 M 3 I 1 M 1 I 2 M 10 I 2 M 3 I 2 M 11 D 2 M 22 I 1 M 4 D 1 M 11 D 1 M 4 D 1 M 7 I 2 M 25 D 1 M 13 I 2 M 25 I 1 M 7 I 1 M 5 D 3 M 14 D 3 M 10 D 1 M 9 I 2 M 23 I 1 M 3 I 1 M 3 D 2 M 6 I 2 M 9 D 1 M 6 D 1 M 13 D 1 M 9 I 1 M 7 D 2 M 5 D 2 M 8 D 5 M 1 D 1 M 3 I 1 M 3 D 1 M 12 I 1 M 6 D 1 M 2 D 1 M 5 I 1 M 4 D 3 M 1 D 3 M 4 D 1 M 2 D 2 M 1 D 1 M 4 D 1 M 12 D 1 M 17 D 2 M 7 I 1 M 8 D 1 M 9 D 1 M 10 D 1 M 7 D 3 M 2 D 2 M 1 D 1 M 2 D 2 M 2 D 1 M 4 D 1 M 1 D 1 M 16 D 1 M 10 D 2 M 7 I 1 M 15 D 1 M 11 D 1 M 2 D 1 M 3 D 1 M 49 D 1 M 2 D 1 M 40 I 1 M 6 I 2 M 29 I 1 M 2 I 1 M 1 I 1 M 19 D 2 M 13 I 1 M 23 D 1 M 5 D 3 M 27 D 1 M 2 D 2 M 13 I 1 M 17 D 1 M 9 D 1 M 10 D 2 M 31 D 2 M 11 I 1 M 19 I 4 M 5 I 1 M 8 I 2 M 8 D 1 M 7 I 4 M 2 I 1 M 6 D 2 M 7 D 1 M 4 I 2 M 7 D 2 M 31 D 1 M 7 I 1 M 52 D 1 M 25 D 2 M 48 I 2 M 7 D 1 M 34 I 1 M 33 I 1 M 8 I 1 M 17 D 2 M 6 I 3 M 12 I 1 M 7 I 1 M 14 D 1 M 1 D 1 M 3 I 1 M 2 I 3 M 9 D 1 M 10 I 4 M 27 I 2 M 82 D 1 M 14 D 2 M 5 I 2 M 13 D 1 M 14 D 1 M 3 D 2 M 3 D 1 M 16 D 1 M 42 I 1 M 8 D 3 M 6 D 1 M 18 I 3 M 13 I 1 M 14 D 1 M 30 I 2 M 29 I 4 M 13 I 2 M 32 D 1 M 30 I 1 M 7 I 1 M 11 I 1 M 8 D 1 M 4 D 2 M 31 I 2 M 6 D 1 M 4 D 1 M 17 I 1 M 8 I 1 M 1 I 1 M 15 I 4 M 4 I 1 M 21 I 1 M 3 I 1 M 3 D 1 M 9 I 2 M 20 D 1 M 10 D 1 M 7 I 1 M 15 I 1 M 29 I 2 M 6 D 1 M 14 D 1 M 3 D 1 M 53 I 1 M 6 I 1 M 19 I 1 M 3 I 1 M 13 I 3 M 7 I 1 M 20 I 1 M 4 I 4 M 6 D 1 M 56 D 1 M 56 D 1 M 12 I 1 M 43 I 4 M 1 I 1 M 1 I 2 M 25 D 1 M 8 D 1 M 22 D 1 M 31 I 1 M 3 I 1 M 6 I 1 M 8 I 1 M 41 I 2 M 3 I 1 M 5 I 1 M 17 I 1 M 20 I 1 M 9 I 1 M 1 I 1 M 6 D 1 M 13 I 1 M 4 I 4 M 22 D 1 M 4 D 1 M 4 I 5 M 3 I 1 M 13 I 3 M 19 I 1 M 2 I 3 M 12 I 2 M 8 D 1 M 1 D 1 M 2 D 1 M 11 I 3 M 4 I 1 M 15 I 3 M 9 I 2 M 2 I 2 M 3 D 1 M 13 D 1 M 13 D 1 M 10 I 1 M 15 I 3 M 5 I 1 M 9 D 1 M 11 I 1 M 13 I 2 M 12 I 1 M 14 I 2 M 8 I 1 M 3 D 1 M 20 D 1 M 13 I 4 M 5 I 1 M 5 I 2 M 3 I 3 M 4 I 3 M 2 I 1 M 10 I 5 M 1 I 2 M 6 I 1 M 6 I 1 M 4 D 1 M 32 I 1 M 3 I 1 M 10 I 1 M 5 I 3 M 11 I 3 M 15 I 1 M 9 I 4 M 17 I 1 M 6 D 1 M 10 I 3 M 6 D 1 M 4 I 1 M 2 I 1 M 23 I 2 M 5 D 1 M 10 I 2 M 4 I 3 M 7 I 7 M 5 I 5 M 11 I 1 M 8 I 1 M 6 I 2 M 9 I 3 M 1 I 1 M 8 I 5 M 25 I 3 M 6 I 1 M 5 I 1 M 4 I 3 M 4 I 3 M 1 I 1 M 10 I 1 M 25 D 1 M 18 I 1 M 10 I 2 M 3 I 2 M 7 D 2 M 12 I 3 M 23 I 1 M 5 I 1 M 6 I 1 M 14 D 1 M 6 I 1 M 3 I 5 M 3 I 1 M 6 I 2 M 1 I 1 M 8 I 3 M 4 D 1 M 11 D 1 M 5 I 2 M 8 I 1 M 2 I 1 M 14 I 1 M 7 I 1 M 9 I 1 M 15 I 1 M 4 I 2 M 10 I 5 M 4 I 1 M 1 I 4 M 9 I 1 M 9 D 2 M 2 D 1 M 6 I 2 M 8 D 1 M 23 I 1 M 7 I 1 M 4 D 1 M 9 I 3 M 30 D 1 M 7 I 6 M 20 D 1 M 2 D 1 M 7 D 1 M 4 D 1 M 3 D 1 M 3 D 1 M 11 I 1 M 8 D 1 M 5 D 1 M 5 D 1 M 9 I 3 M 4 I 1 M 10 D 1 M 2 D 3 M 7 D 1 M 1 D 1 M 11 I 2 M 25 I 7 M 7 D 1 M 3 D 1 M 1 D 1 M 16 I 1 M 12 I 1 M 6 I 1 M 6 I 5 M 4 I 1 M 5 D 1 M 16 I 1 M 10 I 1 M 8 I 3 M 6 I 2 M 7 I 5 M 3 I 1 M 5 D 1 M 12 I 1 M 6 I 3 M 4 I 1 M 2 D 1 M 3 D 1 M 16 D 3 M 2 D 1 M 4 I 1 M 17 D 1 M 2 I 1 M 27 I 1 M 7 D 1 M 19 D 1 M 5 I 3 M 2 I 2 M 23 I 1 M 5 I 1 M 4 D 1 M 1 D 1 M 14 I 2 M 2 I 1 M 1 I 1 M 11 I 3 M 8 D 1 M 10 I 3 M 5 I 2 M 16 I 2 M 7 I 2 M 1 I 3 M 3 I 3 M 4 I 1 M 8 D 1 M 5 I 1 M 11 I 1 M 8 I 2 M 1 I 2 M 3 I 4 M 12 D 1 M 21 D 1 M 10 I 8 M 2 I 3 M 8 D 1 M 12 D 1 M 4 D 2 M 1 D 1 M 11 D 1 M 9 I 2 M 1 I 1 M 2 I 2 M 16 D 1 M 13 I 1 M 1 I 1 M 6 I 2 M 13 D 1 M 7 D 1 M 2 I 1 M 4 I 1 M 2 D 1 M 10 I 3 M 5 D 1 M 4 I 1 M 3 I 1 M 4 D 1 M 2 I 1 M 3 D 1 M 36 I 1 M 11 I 5 M 4 I 1 M 9 I 2 M 7 I 6 M 3 I 1 M 6 I 1 M 12 I 1 M 4 I 1 M 27 I 1 M 17 I 1 M 1 I 1 M 6 I 1 M 21 D 1 M 6 D 1 M 25 D 2 M 12 D 1 M 10 D 1 M 19 I 1 M 28 I 3 M 11 I 2 M 5 D 1 M 21 I 2 M 15 I 2 M 13 I 1 M 17 I 2 M 14 I 1 M 8 D 1 M 19 D 1 M 12 D 1 M 5 D 2 M 14 D 1 M 11 D 1 M 6 D 1 M 8 I 1 M 9 D 1 M 4 D 4 M 6 D 5 M 9 D 1 M 2 D 3 M 38 I 1 M 1 I 1 M 1 I 1 M 5 D 1 M 4 D 1 M 4 D 1 M 10 D 1 M 14 D 1 M 4 D 1 M 11 D 1 M 5 I 1 M 12 I 3 M 6 I 2 M 13 D 4 M 8 D 3 M 4 I 2 M 19 D 2 M 15 I 2 M 42 I 2 M 8 I 1 M 12 I 1 M 15 D 2 M 17 D 1 M 7 I 1 M 1 I 2 M 18 D 1 M 12 D 1 M 31 I 1 M 6 I 3 M 22 I 1 M 22 I 1 M 2 I 5 M 8 I 2 M 4 I 1 M 18 D 1 M 19 I 1 M 6 I 1 M 11 D 1 M 20 I 1 M 40 D 2 M 8 D 3 M 6 I 3 M 23 I 2 M 5 I 1 M 25 I 1 M 17 I 2 M 19 D 1 M 3 I 1 M 4 I 1 M 1 I 1 M 13 D 1 M 7 D 2 M 11 D 1 M 15 D 1 M 16 D 4 M 8 I 1 M 6 I 2 M 8 D 1 M 14 I 3 M 19 D 1 M 24 I 2 M 2 I 2 M 4 I 1 M 32 D 4 M 21 I 2 M 19 I 1 M 2 I 1 M 3 I 3 M 21 D 1 M 11 D 1 M 4 D 1 M 5 D 1 M 4 D 1 M 8 I 1 M 5 I 1 M 3 D 1 M 25 D 1 M 8 I 1 M 4 D 1 M 20 I 2 M 23 D 1 M 3 D 1 M 13 I 1 M 21 D 1 M 35 I 5 M 19 D 1 M 4 I 1 M 22 D 2 M 7 D 1 M 2 D 3 M 21 D 1 M 7 I 1 M 12 I 2 M 13 I 2 M 5 D 1 M 34 I 1 M 7 I 1 M 1 I 1 M 32 I 2 M 1 I 1 M 7 D 1 M 11 I 1 M 16 D 1 M 11 D 1 M 3 D 1 M 6 I 2 M 22 D 2 M 10 I 2 M 14 I 2 M 2 I 1 M 11 D 2 M 37 D 1 M 9 I 1 M 8 D 2 M 47 D 1 M 5 D 1 M 1 D 1 M 1 D 1 M 14 D 1 M 3 D 1 M 11 I 1 M 22 D 2 M 11 I 1 M 2 I 1 M 5 I 1 M 18 D 1 M 6 I 2 M 6 I 2 M 3 I 1 M 19 D 1 M 2 I 1 M 18 I 1 M 14 D 1 M 26 D 3 M 8 D 2 M 19 I 2 M 18 I 1 M 21 D 1 M 12 D 1 M 10 I 2 M 24 D 1 M 24 D 1 M 13 D 1 M 6 I 1 M 1 I 1 M 21 I 1 M 8 I 2 M 10 I 1 M 19 D 1 M 18 I 2 M 6 I 2 M 19 I 3 M 3 I 2 M 55 I 1 M 12 I 2 M 36 D 1 M 5 I 1 M 11 D 2 M 4 I 1 M 23 I 1 M 31 D 1 M 9 I 2 M 3 I 1 M 19 D 2 M 8 D 1 M 34 D 1 M 11 I 2 M 4 I 1 M 25 I 1 M 1 I 2 M 9 D 1 M 13 I 1 M 6 I 1 M 30 I 1 M 5 I 5 M 42 D 1 M 1 D 1 M 3 D 1 M 2 D 4 M 5 I 1 M 4 I 1 M 1 I 2 M 17 I 1 M 2 I 2 M 4 I 2 M 7 I 1 M 16 I 1 M 53 D 3 M 28 D 1 M 3 D 1 M 2 I 1 M 7 I 1 M 3 I 1 M 4 D 1 M 6 I 3 M 37 D 2 M 18 I 2 M 39 I 1 M 4 I 2 M 19 D 1 M 17 D 1 M 18 D 1 M 5 I 1 M 16 I 1 M 6 D 1 M 2 D 1 M 8 I 1 M 13 I 3 M 17 I 1 M 17 D 1 M 7 D 1 M 24 I 3 M 5 D 1 M 19 I 2 M 5 I 2 M 14 D 3 M 45 D 1 M 8 I 2 M 8 I 1 M 7 I 1 M 12 D 6 M 7 I 1 M 8 D 1 M 17 I 2 M 23 D 1 M 26 I 3 M 24 D 1 M 3 D 1 M 10 I 1 M 14 D 2 M 62 D 2 M 19 D 1 M 5 D 1 M 8 I 2 M 6 D 1 M 6 I 1 M 4 I 1 M 2 D 1 M 25 D 1 M 2 I 1 M 6 I 2 M 24 D 3 M 14 D 1 M 3 I 1 M 15 D 1 M 2 D 1 M 10 D 4 M 10 D 1 M 7 I 1 M 1 I 1 M 12 I 2 M 8 I 2 M 5 I 1 M 28 D 1 M 41 I 1 M 15 D 1 M 2 D 1 M 2 D 1 M 18 I 2 M 4 I 3 M 21 D 1 M 11 D 2 M 4 D 1 M 31 I 1 M 4 I 2 M 15 I 1 M 8 I 2 M 11 I 1 M 3 I 1 M 23 D 2 M 10 I 2 M 2 I 2 M 1 I 1 M 14 D 1 M 14 D 1 M 6 D 1 M 8 I 1 M 6 D 1 M 26 I 1 M 22 I 1 M 10 I 1 M 2 I 1 M 4 D 1 M 7 D 1 M 14 D 1 M 3 D 1 M 4 I 1 M 15 I 1 M 35 I 1 M 30 I 1 M 3 I 1 M 9 D 3 M 6 I 2 M 5 D 1 M 7 I 1 M 20 I 1 M 8 I 5 M 2 I 1 M 22 I 5 M 27 D 2 M 6 D 2 M 6 I 1 M 5 I 2 M 1 I 2 M 3 I 3 M 1 I 1 M 2 I 1 M 11 I 3 M 6 I 4 M 8 I 1 M 3 I 3 M 13 I 1 M 6 D 1 M 2 D 1 M 4 I 2 M 16 I 7 M 13 I 4 M 6 I 2 M 1 I 3 M 3 I 1 M 4 I 1 M 5 D 1 M 12 D 1 M 5 D 1 M 6 D 3 M 16 I 2 M 2 I 1 M 25 I 2 M 9 D 1 M 12 D 1 M 16 I 1 M 17 I 4 M 17 D 3 M 4 I 1 M 18 I 1 M 11 I 1 M 14 I 1 M 2 D 1 M 5 D 3 M 39 D 1 M 7 D 1 M 2 D 1 M 19 I 1 M 4 I 1 M 2 I 1 M 8 I 1 M 25 D 1 M 18 D 1 M 20 D 1 M 26 D 1 M 11 D 2 M 7 D 1 M 15 I 1 M 15 D 1 M 3 I 1 M 9 I 1 M 3 I 1 M 10 D 1 M 6 D 1 M 3 D 1 M 20 I 1 M 13 D 1 M 2 D 1 M 5 D 2 M 21 I 1 M 34 I 2 M 10 D 2 M 8 I 2 M 11 I 1 M 26 I 4 M 6 D 1 M 12 I 1 M 5 I 1 M 18 D 1 M 6 D 3 M 11 D 1 M 7 D 1 M 18 I 2 M 6 D 1 M 15 D 1 M 22 D 1 M 14 I 2 M 13 I 1 M 39 D 1 M 3 D 1 M 16 D 4 M 24 D 1 M 3 I 1 M 3 D 1 M 3 I 3 M 5 I 1 M 8 I 2 M 10 D 3 M 1 D 1 M 13 I 1 M 28 D 1 M 14 D 1 M 3 I 1 M 3 I 5 M 3 I 1 M 9 I 4 M 3 I 1 M 8 I 2 M 3 I 1 M 2 I 1 M 9 I 2 M 4 I 2 M 3 I 2 M 13 I 5 M 4 D 1 M 66 I 2 M 28 D 1 M 3 D 1 M 15 D 1 M 49 I 1 M 10 I 4 M 8 I 1 M 2 I 3 M 4 D 1 M 2 I 1 M 40 I 4 M 5 D 2 M 4 D 3 M 9 I 1 M 1 I 2 M 4 I 2 M 4 I 1 M 8 D 2 M 13 D 1 M 4 I 1 M 19 I 2 M 38 I 1 M 4 D 1 M 4 D 1 M 8 D 2 M 13 D 1 M 3 D 1 M 52 I 2 M 11 D 1 M 6 I 2 M 1 I 1 M 18 I 1 M 3 I 3 M 29 I 1 M 20 D 2 M 2 I 1 M 21 I 1 M 3 I 1 M 10 I 1 M 5 I 1 M 4 I 2 M 28 I 4 M 17 D 1 M 40 I 2 M 1 I 1 M 51 I 1 M 29 D 1 M 17 D 1 M 51 D 2 M 9 I 3 M 3 D 1 M 8 I 1 M 2 D 1 M 77 I 1 M 42 I 2 M 1 I 1 M 12 D 2 M 3 I 1 M 24 D 1 M 23 I 2 M 1 I 1 M 7 D 1 M 31 I 1 M 13 I 3 M 1 I 1 M 34 D 2 M 4 D 1 M 25 D 2 M 11 D 1 M 29 D 2 M 42 D 1 M 1 D 2 M 4 I 1 M 9 D 1 M 1 D 1 M 22 I 2 M 3 I 1 M 9 I 1 M 7 D 1 M 3 I 1 M 8 D 1 M 14 I 1 M 14 I 6 M 3 I 2 M 4 I 1 M 2 I 1 M 4 D 1 M 15 D 1 M 16 I 1 M 21 I 1 M 5 D 1 M 7 I 1 M 1 I 1 M 3 D 2 M 10 | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5
[signalAlign] - using NanoporeHDPs
signalAlign - starting template alignment
sh: line 1: 11618 Done                    echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5 68 3893 + gi_ecoli 2305627 2302056 - 1 M 9 I 1 M 8 I 1 M 1 I 1 M 15 I 1 M 9 I 1 M 11 I 1 M 6 D 1 M 5 D 1 M 1 D 1 M 10 I 1 M 6 I 1 M 3 I 1 M 10 D 1 M 2 D 1 M 10 I 2 M 6 I 1 M 6 I 2 M 1 I 3 M 1 I 1 M 5 I 3 M 2 I 1 M 15 D 1 M 7 D 1 M 5 D 1 M 2 I 1 M 4 D 1 M 2 I 1 M 19 I 1 M 30 I 1 M 11 I 4 M 3 I 1 M 11 I 1 M 9 D 1 M 24 D 5 M 6 I 4 M 25 D 1 M 3 D 1 M 3 I 1 M 2 I 1 M 1 I 3 M 2 I 3 M 13 I 5 M 11 D 1 M 11 I 1 M 1 I 3 M 9 I 3 M 3 I 1 M 4 I 1 M 1 I 2 M 13 D 1 M 2 D 1 M 8 I 1 M 12 D 1 M 3 I 1 M 8 I 1 M 19 I 1 M 6 I 1 M 2 I 1 M 1 I 1 M 4 I 1 M 10 I 1 M 2 I 1 M 4 I 1 M 18 I 1 M 2 I 2 M 5 I 1 M 11 I 4 M 4 D 1 M 6 I 3 M 19 D 1 M 10 I 1 M 8 D 2 M 7 D 1 M 6 D 1 M 2 I 1 M 2 I 1 M 14 I 3 M 5 D 1 M 4 D 1 M 13 I 1 M 6 I 2 M 4 I 3 M 8 I 2 M 5 I 2 M 8 I 1 M 7 D 1 M 10 I 1 M 1 I 1 M 14 I 1 M 10 I 1 M 10 D 1 M 9 I 1 M 6 I 2 M 8 D 1 M 7 I 1 M 4 I 1 M 6 I 1 M 5 I 4 M 2 I 1 M 6 I 3 M 26 I 2 M 3 D 1 M 2 D 1 M 11 I 1 M 1 I 1 M 4 I 1 M 8 D 2 M 4 D 1 M 6 I 2 M 6 D 1 M 10 I 2 M 24 I 1 M 23 I 3 M 1 I 1 M 10 D 2 M 21 I 1 M 9 D 1 M 3 I 1 M 3 I 1 M 10 I 1 M 19 I 1 M 18 I 2 M 29 D 2 M 14 D 2 M 8 I 4 M 6 I 1 M 4 D 1 M 4 I 1 M 17 I 3 M 2 I 1 M 9 I 1 M 1 I 1 M 45 I 1 M 5 I 2 M 6 I 1 M 6 D 1 M 14 I 1 M 6 D 2 M 11 D 1 M 13 I 1 M 1 I 1 M 21 I 2 M 11 I 3 M 9 D 1 M 9 I 2 M 1 I 1 M 4 D 1 M 1 D 2 M 21 I 2 M 15 D 2 M 7 I 1 M 1 I 1 M 18 I 1 M 7 I 1 M 13 I 2 M 10 D 1 M 6 I 3 M 18 D 1 M 7 D 1 M 41 I 1 M 3 I 1 M 1 I 1 M 4 I 1 M 2 I 1 M 3 D 1 M 4 D 1 M 3 D 1 M 6 I 1 M 4 D 1 M 25 I 1 M 52 D 1 M 9 D 1 M 27 I 2 M 24 I 3 M 5 D 1 M 7 I 1 M 14 I 2 M 18 I 3 M 45 D 2 M 12 I 2 M 9 D 1 M 9 I 2 M 53 I 4 M 19 I 2 M 2 I 1 M 4 I 1 M 28 I 2 M 3 I 1 M 11 I 2 M 4 I 1 M 6 I 1 M 17 D 1 M 8 I 1 M 27 I 1 M 37 D 2 M 11 I 2 M 5 I 1 M 11 I 1 M 18 I 1 M 13 D 1 M 14 I 1 M 34 I 6 M 9 I 1 M 1 I 1 M 6 I 2 M 18 D 1 M 15 I 1 M 36 D 2 M 6 I 3 M 37 I 2 M 19 D 2 M 19 D 1 M 6 I 2 M 4 I 1 M 5 I 1 M 8 I 1 M 4 I 1 M 19 I 2 M 10 I 1 M 5 I 1 M 3 I 1 M 11 I 1 M 1 I 1 M 2 I 1 M 4 I 1 M 10 I 5 M 2 I 1 M 5 I 1 M 6 D 2 M 41 I 1 M 2 I 1 M 10 D 2 M 6 I 2 M 7 I 1 M 1 I 3 M 6 I 2 M 2 I 1 M 21 I 1 M 27 I 1 M 2 D 1 M 16 D 2 M 15 I 2 M 4 I 1 M 19 I 2 M 4 I 1 M 9 D 2 M 8 D 2 M 11 D 1 M 14 I 1 M 22 D 1 M 5 I 1 M 3 I 1 M 5 I 1 M 3 I 3 M 5 I 2 M 24 I 2 M 6 I 1 M 16 I 2 M 17 I 1 M 81 I 1 M 3 I 2 M 32 I 1 M 9 I 1 M 4 I 2 M 1 I 1 M 7 I 2 M 71 D 1 M 7 D 1 M 6 D 1 M 4 I 1 M 7 I 1 M 5 I 1 M 9 I 1 M 5 I 2 M 6 D 1 M 2 D 1 M 5 D 1 M 21 I 3 M 19 I 1 M 12 D 1 M 7 I 1 M 29 I 2 M 13 D 1 M 3 I 1 M 6 D 1 M 4 I 1 M 10 D 2 M 10 I 1 M 18 I 1 M 9 D 1 M 5 I 3 M 11 I 1 M 40 I 2 M 5 I 3 M 12 D 1 M 5 I 2 M 1 I 1 M 4 D 1 M 14 D 1 M 7 I 4 M 5 I 2 M 10 I 2 M 9 I 1 M 18 I 4 M 10 D 1 M 23 I 1 M 3 I 1 M 9 I 1 M 34 I 2 M 4 I 2 M 1 I 1 M 4 I 1 M 6 I 1 M 11 I 1 M 5 D 1 M 20 I 3 M 11 I 1 M 8 I 2 M 1 I 2 M 5 D 1 M 7 D 1 M 3 I 1 M 29 D 1 M 5 D 1 M 12 D 1 M 10 D 1 M 16 I 1 M 1 I 2 M 1 I 1 M 6 I 1 M 2 D 1 M 3 D 2 M 2 D 2 M 12 I 2 M 1 I 1 M 14 I 1 M 1 I 1 M 2 D 1 M 11
     11619 Segmentation fault      | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (168 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.001 CPU sec, 0.021 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch341_file269_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch341_file269_strand.fast5.fa
[main] Real time: 0.044 sec; CPU: 0.011 sec
unknown alignment flag, exiting
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch341_file269_strand.fast5 didn't map got flag: False
signalAlign - starting template alignment
sh: line 1: 11633 Done                    echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5 3 488 + gi_ecoli 1234292 1233788 - 1 M 6 D 2 M 8 D 1 M 16 D 2 M 6 I 1 M 6 I 1 M 5 D 1 M 4 I 1 M 2 D 1 M 1 D 1 M 7 D 4 M 6 D 2 M 5 D 1 M 7 D 2 M 8 D 1 M 4 D 1 M 23 I 2 M 8 D 1 M 4 D 1 M 4 I 1 M 3 I 2 M 6 I 1 M 3 D 1 M 10 I 3 M 8 D 4 M 5 I 1 M 5 D 1 M 8 I 1 M 14 I 2 M 1 I 3 M 12 I 2 M 4 D 1 M 10 D 1 M 12 I 2 M 19 I 2 M 4 D 1 M 2 D 1 M 5 D 4 M 19 D 1 M 4 D 1 M 9 I 1 M 11 D 1 M 19 D 1 M 10 D 1 M 19 D 1 M 8 I 2 M 23 D 6 M 6 D 1 M 6 D 2 M 13 I 2 M 1 I 1 M 4 D 1 M 1 D 1 M 5 I 1 M 2 I 2 M 19 D 2 M 6 I 1 M 4
     11634 Segmentation fault      | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (5524 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.034 CPU sec, 0.089 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5.fa
[main] Real time: 0.107 sec; CPU: 0.043 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5 25 5505 + gi_ecoli 886654 891931 + 1 M 5 I 3 M 41 D 1 M 2 D 2 M 13 D 1 M 31 I 4 M 5 D 2 M 23 I 1 M 12 D 1 M 5 I 1 M 12 D 2 M 22 D 1 M 6 I 1 M 4 D 1 M 4 D 1 M 16 I 1 M 11 I 1 M 8 I 3 M 14 D 1 M 35 I 2 M 52 D 1 M 18 I 1 M 9 I 1 M 90 I 2 M 8 I 1 M 6 I 3 M 13 I 1 M 9 I 2 M 12 I 1 M 9 I 1 M 2 I 4 M 1 I 1 M 2 I 2 M 2 I 1 M 4 I 3 M 32 D 1 M 8 I 5 M 1 I 1 M 8 I 1 M 25 D 2 M 14 D 1 M 5 D 1 M 25 I 3 M 28 I 2 M 4 I 1 M 20 D 1 M 12 I 4 M 13 D 1 M 17 D 2 M 12 D 1 M 4 D 1 M 5 I 2 M 29 D 1 M 2 D 3 M 14 I 1 M 2 I 2 M 3 I 1 M 23 I 3 M 7 I 1 M 13 I 1 M 3 D 1 M 84 I 2 M 5 I 1 M 9 I 1 M 7 D 1 M 12 I 1 M 4 D 1 M 15 I 1 M 17 I 1 M 4 I 1 M 39 I 7 M 2 I 2 M 5 I 1 M 6 D 1 M 11 D 1 M 3 I 1 M 16 I 1 M 1 I 1 M 29 D 1 M 11 I 2 M 19 I 1 M 31 D 3 M 11 I 4 M 33 I 2 M 40 D 1 M 6 I 1 M 9 D 2 M 19 D 1 M 42 D 2 M 2 D 1 M 56 D 1 M 18 D 3 M 13 I 2 M 14 D 1 M 15 I 2 M 3 I 1 M 27 I 2 M 2 I 2 M 1 I 1 M 20 D 3 M 7 I 4 M 12 D 2 M 7 I 2 M 28 I 3 M 8 I 1 M 13 I 2 M 12 I 4 M 17 D 4 M 17 I 1 M 17 D 1 M 11 I 1 M 23 I 1 M 21 D 1 M 2 D 2 M 2 D 1 M 15 I 6 M 24 I 2 M 25 I 2 M 4 I 1 M 33 I 1 M 8 I 1 M 41 I 1 M 40 I 1 M 31 D 1 M 11 I 2 M 11 I 1 M 8 I 4 M 2 I 3 M 12 I 1 M 4 D 1 M 21 D 1 M 7 I 1 M 4 I 1 M 5 I 1 M 9 I 3 M 16 I 1 M 7 D 2 M 16 D 1 M 10 I 1 M 1 I 1 M 1 I 1 M 40 I 2 M 10 D 1 M 54 I 2 M 57 I 5 M 25 I 5 M 26 I 1 M 3 I 1 M 2 I 1 M 52 I 4 M 2 D 2 M 17 I 1 M 50 D 1 M 10 I 1 M 1 I 3 M 14 D 1 M 3 D 1 M 11 I 1 M 2 I 1 M 8 I 2 M 25 D 1 M 11 I 3 M 18 D 1 M 24 I 1 M 12 D 1 M 5 D 1 M 22 I 2 M 19 D 1 M 35 I 2 M 9 D 2 M 8 I 2 M 45 D 1 M 31 D 1 M 12 I 3 M 21 D 1 M 2 I 3 M 19 I 3 M 54 D 3 M 11 D 2 M 12 I 2 M 3 D 2 M 4 I 2 M 7 I 4 M 3 I 1 M 2 I 1 M 29 D 1 M 72 D 1 M 33 D 2 M 13 D 1 M 9 D 1 M 3 I 1 M 18 I 3 M 2 I 1 M 55 I 2 M 13 I 1 M 6 D 1 M 12 I 1 M 20 I 1 M 34 I 1 M 11 D 1 M 5 D 1 M 3 D 1 M 62 I 1 M 4 I 2 M 11 D 3 M 9 D 1 M 19 D 1 M 4 I 1 M 26 I 2 M 16 D 1 M 14 D 1 M 13 D 1 M 6 D 1 M 26 I 1 M 1 I 1 M 46 I 1 M 11 I 2 M 18 D 1 M 9 I 1 M 49 I 2 M 3 I 1 M 12 I 3 M 41 D 1 M 15 D 1 M 2 I 1 M 8 D 1 M 4 D 2 M 15 D 1 M 15 I 1 M 23 D 1 M 8 D 1 M 17 I 1 M 24 I 1 M 28 I 1 M 4 D 2 M 12 I 2 M 14 D 2 M 10 I 2 M 25 D 1 M 9 I 1 M 6 D 1 M 12 D 1 M 7 I 2 M 13 I 2 M 4 D 1 M 36 I 1 M 20 I 4 M 2 D 1 M 20 D 1 M 17 I 1 M 5 D 1 M 10 D 1 M 5 I 3 M 19 D 2 M 9 D 1 M 17 I 1 M 48 D 1 M 12 I 1 M 1 I 1 M 7 D 1 M 28 I 1 M 3 I 1 M 90 I 1 M 9 I 1 M 19 I 3 M 2 I 2 M 13 D 1 M 21 D 2 M 6 I 3 M 21 D 1 M 6 D 1 M 9 D 2 M 19 D 1 M 10 I 1 M 2 I 1 M 8 I 2 M 7 D 1 M 9 I 1 M 6 I 2 M 13 I 2 M 3 I 1 M 11 D 1 M 2 I 3 M 11 I 1 M 11 I 2 M 2 I 5 M 3 I 2 M 13 I 1 M 15 I 2 M 7 I 1 M 13 D 1 M 2 D 1 M 6 D 2 M 13 I 1 M 1 I 1 M 12 I 1 M 2 I 1 M 2 D 1 M 3 I 1 M 6 I 1 M 4 I 1 M 18 I 1 M 16 I 1 M 14 I 1 M 21 D 1 M 3 D 1 M 21 I 1 M 4 I 3 M 2 I 2 M 16 I 1 M 17 I 1 M 2 I 2 M 8 I 1 M 15 D 3 M 43 I 2 M 2 D 1 M 24 I 1 M 18 I 1 M 8 I 2 M 4 I 2 M 51 I 1 M 7 I 1 M 3 I 1 M 10 I 3 M 31 D 2 M 17 I 1 M 36 D 1 M 10 D 5 M 29 I 1 M 2 I 1 M 29 I 5 M 20 I 4 M 9 I 2 M 11 I 2 M 9 D 1 M 8 D 1 M 9 I 3 M 17 | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5
[signalAlign] - using NanoporeHDPs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (3851 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.027 CPU sec, 0.051 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch89_file296_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch89_file296_strand.fast5.fa
[main] Real time: 0.069 sec; CPU: 0.036 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch89_file296_strand.fast5 didn't map got flag: False
signalAlign - starting template alignment
sh: line 1: 11658 Done                    echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5 11 17095 + gi_ecoli 771637 788302 + 1 M 22 I 1 M 13 D 2 M 5 I 2 M 15 D 1 M 44 D 1 M 13 I 2 M 13 I 1 M 3 I 1 M 36 D 1 M 15 D 2 M 4 I 1 M 3 I 1 M 6 D 2 M 7 D 2 M 8 I 4 M 37 D 2 M 17 D 1 M 14 I 1 M 28 D 1 M 29 I 1 M 18 I 1 M 28 D 2 M 18 D 1 M 21 D 2 M 16 I 1 M 15 D 1 M 33 I 2 M 8 I 1 M 4 D 1 M 15 D 2 M 14 I 1 M 2 D 1 M 43 I 1 M 6 D 1 M 30 D 1 M 10 I 2 M 32 I 2 M 11 D 1 M 11 I 1 M 8 D 1 M 5 I 1 M 6 I 1 M 10 I 1 M 11 D 2 M 19 I 2 M 31 I 2 M 4 I 1 M 43 I 2 M 16 D 1 M 14 I 1 M 54 I 1 M 12 I 5 M 7 D 1 M 19 D 1 M 12 D 1 M 3 I 1 M 4 D 1 M 51 D 1 M 8 I 2 M 4 D 1 M 28 D 3 M 9 D 1 M 13 D 1 M 3 D 1 M 6 I 1 M 22 I 2 M 21 I 2 M 11 I 1 M 23 I 3 M 26 I 1 M 14 I 1 M 13 D 1 M 6 D 1 M 27 D 3 M 4 D 1 M 1 D 1 M 24 D 1 M 10 I 1 M 2 I 2 M 12 I 1 M 8 I 1 M 6 D 1 M 8 I 1 M 17 I 2 M 10 D 1 M 18 I 2 M 4 I 1 M 3 I 1 M 19 I 1 M 11 I 2 M 33 D 1 M 5 I 2 M 11 D 3 M 8 D 1 M 2 D 1 M 1 D 1 M 13 D 1 M 43 I 1 M 13 I 1 M 20 D 1 M 6 D 3 M 36 I 2 M 10 I 2 M 8 D 3 M 2 D 1 M 4 D 1 M 8 I 1 M 19 D 1 M 9 I 4 M 11 D 1 M 33 D 1 M 18 I 3 M 30 D 1 M 16 I 1 M 14 D 1 M 18 I 1 M 34 I 3 M 7 I 1 M 14 D 2 M 17 D 1 M 5 I 2 M 33 I 4 M 22 D 1 M 6 I 2 M 7 I 2 M 53 I 2 M 7 I 1 M 2 D 2 M 21 I 2 M 17 D 1 M 11 D 1 M 19 I 2 M 40 D 1 M 19 D 1 M 5 D 2 M 11 D 1 M 18 I 2 M 2 I 1 M 5 D 1 M 8 I 2 M 21 D 1 M 7 D 1 M 16 I 1 M 5 D 1 M 15 I 1 M 12 I 1 M 57 D 3 M 2 D 1 M 7 I 1 M 4 I 1 M 5 D 2 M 3 D 2 M 9 D 2 M 3 D 2 M 6 D 1 M 5 D 1 M 6 D 1 M 1 D 1 M 7 I 1 M 7 I 1 M 44 D 2 M 13 D 1 M 3 D 2 M 11 I 1 M 7 I 1 M 11 D 2 M 2 D 1 M 11 I 3 M 3 D 1 M 23 D 2 M 10 D 2 M 28 D 2 M 20 D 2 M 3 D 1 M 1 D 1 M 5 I 1 M 4 I 1 M 15 D 2 M 17 I 2 M 9 D 1 M 12 I 1 M 18 I 2 M 13 I 2 M 34 D 2 M 42 D 1 M 30 D 1 M 3 D 1 M 10 D 1 M 5 D 2 M 36 D 2 M 5 D 1 M 19 D 2 M 10 D 1 M 18 I 2 M 7 D 2 M 3 D 2 M 25 I 1 M 15 D 2 M 10 I 1 M 9 I 1 M 8 I 1 M 20 D 1 M 6 D 1 M 1 D 1 M 13 D 1 M 36 D 2 M 4 D 1 M 21 D 3 M 9 I 2 M 9 I 2 M 7 I 1 M 1 I 1 M 8 D 1 M 5 I 1 M 52 I 1 M 6 D 1 M 2 D 1 M 7 D 1 M 56 I 3 M 29 D 3 M 7 I 3 M 1 I 1 M 10 I 4 M 23 I 2 M 5 D 1 M 18 I 1 M 2 I 1 M 4 I 2 M 3 D 1 M 8 I 1 M 14 I 1 M 5 I 1 M 3 I 1 M 3 D 1 M 1 D 1 M 5 I 1 M 15 D 1 M 7 I 1 M 2 D 2 M 13 I 1 M 5 I 1 M 9 D 1 M 12 I 2 M 8 D 1 M 9 D 1 M 36 D 2 M 20 I 5 M 4 I 1 M 5 D 1 M 15 I 1 M 11 D 1 M 10 D 2 M 23 D 1 M 27 I 1 M 18 I 2 M 13 D 1 M 4 D 2 M 57 I 1 M 15 D 1 M 7 I 1 M 7 D 1 M 14 I 1 M 14 D 1 M 18 D 1 M 29 D 1 M 14 D 1 M 13 D 2 M 37 I 1 M 3 I 1 M 1 I 1 M 4 D 1 M 16 I 4 M 25 D 1 M 18 I 1 M 16 D 1 M 25 D 1 M 14 I 1 M 3 D 1 M 6 D 1 M 15 I 1 M 15 D 1 M 1 D 1 M 18 D 2 M 5 D 1 M 10 I 1 M 3 I 1 M 51 I 1 M 27 D 3 M 2 D 1 M 10 I 1 M 14 I 2 M 13 I 1 M 31 D 2 M 2 D 1 M 8 I 2 M 7 I 2 M 5 I 1 M 43 D 1 M 8 I 1 M 23 D 1 M 5 D 3 M 1 D 1 M 10 D 1 M 11 D 2 M 17 D 1 M 5 D 1 M 14 D 1 M 23 D 1 M 26 D 1 M 18 I 2 M 19 D 1 M 16 D 1 M 25 D 1 M 17 I 1 M 3 D 1 M 60 I 1 M 14 I 4 M 4 I 2 M 18 I 1 M 3 I 2 M 16 I 1 M 14 I 1 M 4 D 2 M 14 D 1 M 3 I 3 M 7 D 2 M 15 D 1 M 23 I 1 M 20 I 1 M 5 I 3 M 7 D 2 M 26 I 1 M 13 D 1 M 12 D 1 M 10 I 5 M 14 D 1 M 2 D 1 M 16 D 1 M 9 D 3 M 4 I 1 M 28 I 3 M 2 I 1 M 11 I 1 M 17 I 2 M 22 D 1 M 9 I 4 M 1 I 1 M 3 I 2 M 2 D 1 M 15 I 4 M 10 I 1 M 5 I 3 M 12 D 1 M 22 D 2 M 3 D 1 M 10 I 2 M 11 I 1 M 5 D 1 M 6 D 1 M 7 I 1 M 3 I 1 M 1 I 2 M 10 I 2 M 3 I 2 M 11 D 2 M 22 I 1 M 4 D 1 M 11 D 1 M 4 D 1 M 7 I 2 M 25 D 1 M 13 I 2 M 25 I 1 M 7 I 1 M 5 D 3 M 14 D 3 M 10 D 1 M 9 I 2 M 23 I 1 M 3 I 1 M 3 D 2 M 6 I 2 M 9 D 1 M 6 D 1 M 13 D 1 M 9 I 1 M 7 D 2 M 5 D 2 M 8 D 5 M 1 D 1 M 3 I 1 M 3 D 1 M 12 I 1 M 6 D 1 M 2 D 1 M 5 I 1 M 4 D 3 M 1 D 3 M 4 D 1 M 2 D 2 M 1 D 1 M 4 D 1 M 12 D 1 M 17 D 2 M 7 I 1 M 8 D 1 M 9 D 1 M 10 D 1 M 7 D 3 M 2 D 2 M 1 D 1 M 2 D 2 M 2 D 1 M 4 D 1 M 1 D 1 M 16 D 1 M 10 D 2 M 7 I 1 M 15 D 1 M 11 D 1 M 2 D 1 M 3 D 1 M 49 D 1 M 2 D 1 M 40 I 1 M 6 I 2 M 29 I 1 M 2 I 1 M 1 I 1 M 19 D 2 M 13 I 1 M 23 D 1 M 5 D 3 M 27 D 1 M 2 D 2 M 13 I 1 M 17 D 1 M 9 D 1 M 10 D 2 M 31 D 2 M 11 I 1 M 19 I 4 M 5 I 1 M 8 I 2 M 8 D 1 M 7 I 4 M 2 I 1 M 6 D 2 M 7 D 1 M 4 I 2 M 7 D 2 M 31 D 1 M 7 I 1 M 52 D 1 M 25 D 2 M 48 I 2 M 7 D 1 M 34 I 1 M 33 I 1 M 8 I 1 M 17 D 2 M 6 I 3 M 12 I 1 M 7 I 1 M 14 D 1 M 1 D 1 M 3 I 1 M 2 I 3 M 9 D 1 M 10 I 4 M 27 I 2 M 82 D 1 M 14 D 2 M 5 I 2 M 13 D 1 M 14 D 1 M 3 D 2 M 3 D 1 M 16 D 1 M 42 I 1 M 8 D 3 M 6 D 1 M 18 I 3 M 13 I 1 M 14 D 1 M 30 I 2 M 29 I 4 M 13 I 2 M 32 D 1 M 30 I 1 M 7 I 1 M 11 I 1 M 8 D 1 M 4 D 2 M 31 I 2 M 6 D 1 M 4 D 1 M 17 I 1 M 8 I 1 M 1 I 1 M 15 I 4 M 4 I 1 M 21 I 1 M 3 I 1 M 3 D 1 M 9 I 2 M 20 D 1 M 10 D 1 M 7 I 1 M 15 I 1 M 29 I 2 M 6 D 1 M 14 D 1 M 3 D 1 M 53 I 1 M 6 I 1 M 19 I 1 M 3 I 1 M 13 I 3 M 7 I 1 M 20 I 1 M 4 I 4 M 6 D 1 M 56 D 1 M 56 D 1 M 12 I 1 M 43 I 4 M 1 I 1 M 1 I 2 M 25 D 1 M 8 D 1 M 22 D 1 M 31 I 1 M 3 I 1 M 6 I 1 M 8 I 1 M 41 I 2 M 3 I 1 M 5 I 1 M 17 I 1 M 20 I 1 M 9 I 1 M 1 I 1 M 6 D 1 M 13 I 1 M 4 I 4 M 22 D 1 M 4 D 1 M 4 I 5 M 3 I 1 M 13 I 3 M 19 I 1 M 2 I 3 M 12 I 2 M 8 D 1 M 1 D 1 M 2 D 1 M 11 I 3 M 4 I 1 M 15 I 3 M 9 I 2 M 2 I 2 M 3 D 1 M 13 D 1 M 13 D 1 M 10 I 1 M 15 I 3 M 5 I 1 M 9 D 1 M 11 I 1 M 13 I 2 M 12 I 1 M 14 I 2 M 8 I 1 M 3 D 1 M 20 D 1 M 13 I 4 M 5 I 1 M 5 I 2 M 3 I 3 M 4 I 3 M 2 I 1 M 10 I 5 M 1 I 2 M 6 I 1 M 6 I 1 M 4 D 1 M 32 I 1 M 3 I 1 M 10 I 1 M 5 I 3 M 11 I 3 M 15 I 1 M 9 I 4 M 17 I 1 M 6 D 1 M 10 I 3 M 6 D 1 M 4 I 1 M 2 I 1 M 23 I 2 M 5 D 1 M 10 I 2 M 4 I 3 M 7 I 7 M 5 I 5 M 11 I 1 M 8 I 1 M 6 I 2 M 9 I 3 M 1 I 1 M 8 I 5 M 25 I 3 M 6 I 1 M 5 I 1 M 4 I 3 M 4 I 3 M 1 I 1 M 10 I 1 M 25 D 1 M 18 I 1 M 10 I 2 M 3 I 2 M 7 D 2 M 12 I 3 M 23 I 1 M 5 I 1 M 6 I 1 M 14 D 1 M 6 I 1 M 3 I 5 M 3 I 1 M 6 I 2 M 1 I 1 M 8 I 3 M 4 D 1 M 11 D 1 M 5 I 2 M 8 I 1 M 2 I 1 M 14 I 1 M 7 I 1 M 9 I 1 M 15 I 1 M 4 I 2 M 10 I 5 M 4 I 1 M 1 I 4 M 9 I 1 M 9 D 2 M 2 D 1 M 6 I 2 M 8 D 1 M 23 I 1 M 7 I 1 M 4 D 1 M 9 I 3 M 30 D 1 M 7 I 6 M 20 D 1 M 2 D 1 M 7 D 1 M 4 D 1 M 3 D 1 M 3 D 1 M 11 I 1 M 8 D 1 M 5 D 1 M 5 D 1 M 9 I 3 M 4 I 1 M 10 D 1 M 2 D 3 M 7 D 1 M 1 D 1 M 11 I 2 M 25 I 7 M 7 D 1 M 3 D 1 M 1 D 1 M 16 I 1 M 12 I 1 M 6 I 1 M 6 I 5 M 4 I 1 M 5 D 1 M 16 I 1 M 10 I 1 M 8 I 3 M 6 I 2 M 7 I 5 M 3 I 1 M 5 D 1 M 12 I 1 M 6 I 3 M 4 I 1 M 2 D 1 M 3 D 1 M 16 D 3 M 2 D 1 M 4 I 1 M 17 D 1 M 2 I 1 M 27 I 1 M 7 D 1 M 19 D 1 M 5 I 3 M 2 I 2 M 23 I 1 M 5 I 1 M 4 D 1 M 1 D 1 M 14 I 2 M 2 I 1 M 1 I 1 M 11 I 3 M 8 D 1 M 10 I 3 M 5 I 2 M 16 I 2 M 7 I 2 M 1 I 3 M 3 I 3 M 4 I 1 M 8 D 1 M 5 I 1 M 11 I 1 M 8 I 2 M 1 I 2 M 3 I 4 M 12 D 1 M 21 D 1 M 10 I 8 M 2 I 3 M 8 D 1 M 12 D 1 M 4 D 2 M 1 D 1 M 11 D 1 M 9 I 2 M 1 I 1 M 2 I 2 M 16 D 1 M 13 I 1 M 1 I 1 M 6 I 2 M 13 D 1 M 7 D 1 M 2 I 1 M 4 I 1 M 2 D 1 M 10 I 3 M 5 D 1 M 4 I 1 M 3 I 1 M 4 D 1 M 2 I 1 M 3 D 1 M 36 I 1 M 11 I 5 M 4 I 1 M 9 I 2 M 7 I 6 M 3 I 1 M 6 I 1 M 12 I 1 M 4 I 1 M 27 I 1 M 17 I 1 M 1 I 1 M 6 I 1 M 21 D 1 M 6 D 1 M 25 D 2 M 12 D 1 M 10 D 1 M 19 I 1 M 28 I 3 M 11 I 2 M 5 D 1 M 21 I 2 M 15 I 2 M 13 I 1 M 17 I 2 M 14 I 1 M 8 D 1 M 19 D 1 M 12 D 1 M 5 D 2 M 14 D 1 M 11 D 1 M 6 D 1 M 8 I 1 M 9 D 1 M 4 D 4 M 6 D 5 M 9 D 1 M 2 D 3 M 38 I 1 M 1 I 1 M 1 I 1 M 5 D 1 M 4 D 1 M 4 D 1 M 10 D 1 M 14 D 1 M 4 D 1 M 11 D 1 M 5 I 1 M 12 I 3 M 6 I 2 M 13 D 4 M 8 D 3 M 4 I 2 M 19 D 2 M 15 I 2 M 42 I 2 M 8 I 1 M 12 I 1 M 15 D 2 M 17 D 1 M 7 I 1 M 1 I 2 M 18 D 1 M 12 D 1 M 31 I 1 M 6 I 3 M 22 I 1 M 22 I 1 M 2 I 5 M 8 I 2 M 4 I 1 M 18 D 1 M 19 I 1 M 6 I 1 M 11 D 1 M 20 I 1 M 40 D 2 M 8 D 3 M 6 I 3 M 23 I 2 M 5 I 1 M 25 I 1 M 17 I 2 M 19 D 1 M 3 I 1 M 4 I 1 M 1 I 1 M 13 D 1 M 7 D 2 M 11 D 1 M 15 D 1 M 16 D 4 M 8 I 1 M 6 I 2 M 8 D 1 M 14 I 3 M 19 D 1 M 24 I 2 M 2 I 2 M 4 I 1 M 32 D 4 M 21 I 2 M 19 I 1 M 2 I 1 M 3 I 3 M 21 D 1 M 11 D 1 M 4 D 1 M 5 D 1 M 4 D 1 M 8 I 1 M 5 I 1 M 3 D 1 M 25 D 1 M 8 I 1 M 4 D 1 M 20 I 2 M 23 D 1 M 3 D 1 M 13 I 1 M 21 D 1 M 35 I 5 M 19 D 1 M 4 I 1 M 22 D 2 M 7 D 1 M 2 D 3 M 21 D 1 M 7 I 1 M 12 I 2 M 13 I 2 M 5 D 1 M 34 I 1 M 7 I 1 M 1 I 1 M 32 I 2 M 1 I 1 M 7 D 1 M 11 I 1 M 16 D 1 M 11 D 1 M 3 D 1 M 6 I 2 M 22 D 2 M 10 I 2 M 14 I 2 M 2 I 1 M 11 D 2 M 37 D 1 M 9 I 1 M 8 D 2 M 47 D 1 M 5 D 1 M 1 D 1 M 1 D 1 M 14 D 1 M 3 D 1 M 11 I 1 M 22 D 2 M 11 I 1 M 2 I 1 M 5 I 1 M 18 D 1 M 6 I 2 M 6 I 2 M 3 I 1 M 19 D 1 M 2 I 1 M 18 I 1 M 14 D 1 M 26 D 3 M 8 D 2 M 19 I 2 M 18 I 1 M 21 D 1 M 12 D 1 M 10 I 2 M 24 D 1 M 24 D 1 M 13 D 1 M 6 I 1 M 1 I 1 M 21 I 1 M 8 I 2 M 10 I 1 M 19 D 1 M 18 I 2 M 6 I 2 M 19 I 3 M 3 I 2 M 55 I 1 M 12 I 2 M 36 D 1 M 5 I 1 M 11 D 2 M 4 I 1 M 23 I 1 M 31 D 1 M 9 I 2 M 3 I 1 M 19 D 2 M 8 D 1 M 34 D 1 M 11 I 2 M 4 I 1 M 25 I 1 M 1 I 2 M 9 D 1 M 13 I 1 M 6 I 1 M 30 I 1 M 5 I 5 M 42 D 1 M 1 D 1 M 3 D 1 M 2 D 4 M 5 I 1 M 4 I 1 M 1 I 2 M 17 I 1 M 2 I 2 M 4 I 2 M 7 I 1 M 16 I 1 M 53 D 3 M 28 D 1 M 3 D 1 M 2 I 1 M 7 I 1 M 3 I 1 M 4 D 1 M 6 I 3 M 37 D 2 M 18 I 2 M 39 I 1 M 4 I 2 M 19 D 1 M 17 D 1 M 18 D 1 M 5 I 1 M 16 I 1 M 6 D 1 M 2 D 1 M 8 I 1 M 13 I 3 M 17 I 1 M 17 D 1 M 7 D 1 M 24 I 3 M 5 D 1 M 19 I 2 M 5 I 2 M 14 D 3 M 45 D 1 M 8 I 2 M 8 I 1 M 7 I 1 M 12 D 6 M 7 I 1 M 8 D 1 M 17 I 2 M 23 D 1 M 26 I 3 M 24 D 1 M 3 D 1 M 10 I 1 M 14 D 2 M 62 D 2 M 19 D 1 M 5 D 1 M 8 I 2 M 6 D 1 M 6 I 1 M 4 I 1 M 2 D 1 M 25 D 1 M 2 I 1 M 6 I 2 M 24 D 3 M 14 D 1 M 3 I 1 M 15 D 1 M 2 D 1 M 10 D 4 M 10 D 1 M 7 I 1 M 1 I 1 M 12 I 2 M 8 I 2 M 5 I 1 M 28 D 1 M 41 I 1 M 15 D 1 M 2 D 1 M 2 D 1 M 18 I 2 M 4 I 3 M 21 D 1 M 11 D 2 M 4 D 1 M 31 I 1 M 4 I 2 M 15 I 1 M 8 I 2 M 11 I 1 M 3 I 1 M 23 D 2 M 10 I 2 M 2 I 2 M 1 I 1 M 14 D 1 M 14 D 1 M 6 D 1 M 8 I 1 M 6 D 1 M 26 I 1 M 22 I 1 M 10 I 1 M 2 I 1 M 4 D 1 M 7 D 1 M 14 D 1 M 3 D 1 M 4 I 1 M 15 I 1 M 35 I 1 M 30 I 1 M 3 I 1 M 9 D 3 M 6 I 2 M 5 D 1 M 7 I 1 M 20 I 1 M 8 I 5 M 2 I 1 M 22 I 5 M 27 D 2 M 6 D 2 M 6 I 1 M 5 I 2 M 1 I 2 M 3 I 3 M 1 I 1 M 2 I 1 M 11 I 3 M 6 I 4 M 8 I 1 M 3 I 3 M 13 I 1 M 6 D 1 M 2 D 1 M 4 I 2 M 16 I 7 M 13 I 4 M 6 I 2 M 1 I 3 M 3 I 1 M 4 I 1 M 5 D 1 M 12 D 1 M 5 D 1 M 6 D 3 M 16 I 2 M 2 I 1 M 25 I 2 M 9 D 1 M 12 D 1 M 16 I 1 M 17 I 4 M 17 D 3 M 4 I 1 M 18 I 1 M 11 I 1 M 14 I 1 M 2 D 1 M 5 D 3 M 39 D 1 M 7 D 1 M 2 D 1 M 19 I 1 M 4 I 1 M 2 I 1 M 8 I 1 M 25 D 1 M 18 D 1 M 20 D 1 M 26 D 1 M 11 D 2 M 7 D 1 M 15 I 1 M 15 D 1 M 3 I 1 M 9 I 1 M 3 I 1 M 10 D 1 M 6 D 1 M 3 D 1 M 20 I 1 M 13 D 1 M 2 D 1 M 5 D 2 M 21 I 1 M 34 I 2 M 10 D 2 M 8 I 2 M 11 I 1 M 26 I 4 M 6 D 1 M 12 I 1 M 5 I 1 M 18 D 1 M 6 D 3 M 11 D 1 M 7 D 1 M 18 I 2 M 6 D 1 M 15 D 1 M 22 D 1 M 14 I 2 M 13 I 1 M 39 D 1 M 3 D 1 M 16 D 4 M 24 D 1 M 3 I 1 M 3 D 1 M 3 I 3 M 5 I 1 M 8 I 2 M 10 D 3 M 1 D 1 M 13 I 1 M 28 D 1 M 14 D 1 M 3 I 1 M 3 I 5 M 3 I 1 M 9 I 4 M 3 I 1 M 8 I 2 M 3 I 1 M 2 I 1 M 9 I 2 M 4 I 2 M 3 I 2 M 13 I 5 M 4 D 1 M 66 I 2 M 28 D 1 M 3 D 1 M 15 D 1 M 49 I 1 M 10 I 4 M 8 I 1 M 2 I 3 M 4 D 1 M 2 I 1 M 40 I 4 M 5 D 2 M 4 D 3 M 9 I 1 M 1 I 2 M 4 I 2 M 4 I 1 M 8 D 2 M 13 D 1 M 4 I 1 M 19 I 2 M 38 I 1 M 4 D 1 M 4 D 1 M 8 D 2 M 13 D 1 M 3 D 1 M 52 I 2 M 11 D 1 M 6 I 2 M 1 I 1 M 18 I 1 M 3 I 3 M 29 I 1 M 20 D 2 M 2 I 1 M 21 I 1 M 3 I 1 M 10 I 1 M 5 I 1 M 4 I 2 M 28 I 4 M 17 D 1 M 40 I 2 M 1 I 1 M 51 I 1 M 29 D 1 M 17 D 1 M 51 D 2 M 9 I 3 M 3 D 1 M 8 I 1 M 2 D 1 M 77 I 1 M 42 I 2 M 1 I 1 M 12 D 2 M 3 I 1 M 24 D 1 M 23 I 2 M 1 I 1 M 7 D 1 M 31 I 1 M 13 I 3 M 1 I 1 M 34 D 2 M 4 D 1 M 25 D 2 M 11 D 1 M 29 D 2 M 42 D 1 M 1 D 2 M 4 I 1 M 9 D 1 M 1 D 1 M 22 I 2 M 3 I 1 M 9 I 1 M 7 D 1 M 3 I 1 M 8 D 1 M 14 I 1 M 14 I 6 M 3 I 2 M 4 I 1 M 2 I 1 M 4 D 1 M 15 D 1 M 16 I 1 M 21 I 1 M 5 D 1 M 7 I 1 M 1 I 1 M 3 D 2 M 10
     11659 Segmentation fault      | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5
signalAlign - starting template alignment
sh: line 1: 11676 Done                    echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5 25 5505 + gi_ecoli 886654 891931 + 1 M 5 I 3 M 41 D 1 M 2 D 2 M 13 D 1 M 31 I 4 M 5 D 2 M 23 I 1 M 12 D 1 M 5 I 1 M 12 D 2 M 22 D 1 M 6 I 1 M 4 D 1 M 4 D 1 M 16 I 1 M 11 I 1 M 8 I 3 M 14 D 1 M 35 I 2 M 52 D 1 M 18 I 1 M 9 I 1 M 90 I 2 M 8 I 1 M 6 I 3 M 13 I 1 M 9 I 2 M 12 I 1 M 9 I 1 M 2 I 4 M 1 I 1 M 2 I 2 M 2 I 1 M 4 I 3 M 32 D 1 M 8 I 5 M 1 I 1 M 8 I 1 M 25 D 2 M 14 D 1 M 5 D 1 M 25 I 3 M 28 I 2 M 4 I 1 M 20 D 1 M 12 I 4 M 13 D 1 M 17 D 2 M 12 D 1 M 4 D 1 M 5 I 2 M 29 D 1 M 2 D 3 M 14 I 1 M 2 I 2 M 3 I 1 M 23 I 3 M 7 I 1 M 13 I 1 M 3 D 1 M 84 I 2 M 5 I 1 M 9 I 1 M 7 D 1 M 12 I 1 M 4 D 1 M 15 I 1 M 17 I 1 M 4 I 1 M 39 I 7 M 2 I 2 M 5 I 1 M 6 D 1 M 11 D 1 M 3 I 1 M 16 I 1 M 1 I 1 M 29 D 1 M 11 I 2 M 19 I 1 M 31 D 3 M 11 I 4 M 33 I 2 M 40 D 1 M 6 I 1 M 9 D 2 M 19 D 1 M 42 D 2 M 2 D 1 M 56 D 1 M 18 D 3 M 13 I 2 M 14 D 1 M 15 I 2 M 3 I 1 M 27 I 2 M 2 I 2 M 1 I 1 M 20 D 3 M 7 I 4 M 12 D 2 M 7 I 2 M 28 I 3 M 8 I 1 M 13 I 2 M 12 I 4 M 17 D 4 M 17 I 1 M 17 D 1 M 11 I 1 M 23 I 1 M 21 D 1 M 2 D 2 M 2 D 1 M 15 I 6 M 24 I 2 M 25 I 2 M 4 I 1 M 33 I 1 M 8 I 1 M 41 I 1 M 40 I 1 M 31 D 1 M 11 I 2 M 11 I 1 M 8 I 4 M 2 I 3 M 12 I 1 M 4 D 1 M 21 D 1 M 7 I 1 M 4 I 1 M 5 I 1 M 9 I 3 M 16 I 1 M 7 D 2 M 16 D 1 M 10 I 1 M 1 I 1 M 1 I 1 M 40 I 2 M 10 D 1 M 54 I 2 M 57 I 5 M 25 I 5 M 26 I 1 M 3 I 1 M 2 I 1 M 52 I 4 M 2 D 2 M 17 I 1 M 50 D 1 M 10 I 1 M 1 I 3 M 14 D 1 M 3 D 1 M 11 I 1 M 2 I 1 M 8 I 2 M 25 D 1 M 11 I 3 M 18 D 1 M 24 I 1 M 12 D 1 M 5 D 1 M 22 I 2 M 19 D 1 M 35 I 2 M 9 D 2 M 8 I 2 M 45 D 1 M 31 D 1 M 12 I 3 M 21 D 1 M 2 I 3 M 19 I 3 M 54 D 3 M 11 D 2 M 12 I 2 M 3 D 2 M 4 I 2 M 7 I 4 M 3 I 1 M 2 I 1 M 29 D 1 M 72 D 1 M 33 D 2 M 13 D 1 M 9 D 1 M 3 I 1 M 18 I 3 M 2 I 1 M 55 I 2 M 13 I 1 M 6 D 1 M 12 I 1 M 20 I 1 M 34 I 1 M 11 D 1 M 5 D 1 M 3 D 1 M 62 I 1 M 4 I 2 M 11 D 3 M 9 D 1 M 19 D 1 M 4 I 1 M 26 I 2 M 16 D 1 M 14 D 1 M 13 D 1 M 6 D 1 M 26 I 1 M 1 I 1 M 46 I 1 M 11 I 2 M 18 D 1 M 9 I 1 M 49 I 2 M 3 I 1 M 12 I 3 M 41 D 1 M 15 D 1 M 2 I 1 M 8 D 1 M 4 D 2 M 15 D 1 M 15 I 1 M 23 D 1 M 8 D 1 M 17 I 1 M 24 I 1 M 28 I 1 M 4 D 2 M 12 I 2 M 14 D 2 M 10 I 2 M 25 D 1 M 9 I 1 M 6 D 1 M 12 D 1 M 7 I 2 M 13 I 2 M 4 D 1 M 36 I 1 M 20 I 4 M 2 D 1 M 20 D 1 M 17 I 1 M 5 D 1 M 10 D 1 M 5 I 3 M 19 D 2 M 9 D 1 M 17 I 1 M 48 D 1 M 12 I 1 M 1 I 1 M 7 D 1 M 28 I 1 M 3 I 1 M 90 I 1 M 9 I 1 M 19 I 3 M 2 I 2 M 13 D 1 M 21 D 2 M 6 I 3 M 21 D 1 M 6 D 1 M 9 D 2 M 19 D 1 M 10 I 1 M 2 I 1 M 8 I 2 M 7 D 1 M 9 I 1 M 6 I 2 M 13 I 2 M 3 I 1 M 11 D 1 M 2 I 3 M 11 I 1 M 11 I 2 M 2 I 5 M 3 I 2 M 13 I 1 M 15 I 2 M 7 I 1 M 13 D 1 M 2 D 1 M 6 D 2 M 13 I 1 M 1 I 1 M 12 I 1 M 2 I 1 M 2 D 1 M 3 I 1 M 6 I 1 M 4 I 1 M 18 I 1 M 16 I 1 M 14 I 1 M 21 D 1 M 3 D 1 M 21 I 1 M 4 I 3 M 2 I 2 M 16 I 1 M 17 I 1 M 2 I 2 M 8 I 1 M 15 D 3 M 43 I 2 M 2 D 1 M 24 I 1 M 18 I 1 M 8 I 2 M 4 I 2 M 51 I 1 M 7 I 1 M 3 I 1 M 10 I 3 M 31 D 2 M 17 I 1 M 36 D 1 M 10 D 5 M 29 I 1 M 2 I 1 M 29 I 5 M 20 I 4 M 9 I 2 M 11 I 2 M 9 D 1 M 8 D 1 M 9 I 3 M 17
     11677 Segmentation fault      | ./signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5

#  signalAlign - finished alignments

cat: demo/tempFiles_alignment//*.tsv: No such file or directory

Do you have any advice on how to proceed?

ArtRand commented 7 years ago

Hello John,

Thanks for catching this problem. The old (7.3) models were in an out-of-date format. I updated the repo, so pull the latest commit and it should work. Also, the didn't map message simply means that the read doesn't map to a region that you're querying (i.e. there isn't a potentially methylated cytosine there) - so it's not an error. Good luck.

JohnUrban commented 7 years ago

Hi Art,

Thanks! I updated everything and tried the demo again. I think it worked. The command used was same as above. Check out the output in the .err file:

Command Line: ./runSignalAlign -d /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/ -r /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_sequences/E.coli_K12.fasta -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm -tH /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -cH /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -x cytosine2 -smt=threeStateHdp -q /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_regions/test_sites_bal_1.tgt -p /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_regions/test_labels_bal_1.tsv -f variantCaller -o demo/

signalAlign - indexing reference
[bwa_index] Pack FASTA... 0.04 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.28 seconds elapse.
[bwa_index] Update BWT... 0.02 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.66 sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa index -p demo/tempFiles_alignment//temp_bwaIndex /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/test_sequences/E.coli_K12.fasta
[main] Real time: 2.593 sec; CPU: 2.049 sec
signalAlign - indexing reference, done
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (1654 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.007 CPU sec, 0.007 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch492_file245_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch492_file245_strand.fast5.fa
[main] Real time: 0.013 sec; CPU: 0.016 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch492_file245_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (2738 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.010 CPU sec, 0.040 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch146_file135_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch146_file135_strand.fast5.fa
[main] Real time: 0.064 sec; CPU: 0.021 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch146_file135_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (3912 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.029 CPU sec, 0.070 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5.fa
[main] Real time: 0.087 sec; CPU: 0.039 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5 68 3893 + gi_ecoli 2305627 2302056 - 1 M 9 I 1 M 8 I 1 M 1 I 1 M 15 I 1 M 9 I 1 M 11 I 1 M 6 D 1 M 5 D 1 M 1 D 1 M 10 I 1 M 6 I 1 M 3 I 1 M 10 D 1 M 2 D 1 M 10 I 2 M 6 I 1 M 6 I 2 M 1 I 3 M 1 I 1 M 5 I 3 M 2 I 1 M 15 D 1 M 7 D 1 M 5 D 1 M 2 I 1 M 4 D 1 M 2 I 1 M 19 I 1 M 30 I 1 M 11 I 4 M 3 I 1 M 11 I 1 M 9 D 1 M 24 D 5 M 6 I 4 M 25 D 1 M 3 D 1 M 3 I 1 M 2 I 1 M 1 I 3 M 2 I 3 M 13 I 5 M 11 D 1 M 11 I 1 M 1 I 3 M 9 I 3 M 3 I 1 M 4 I 1 M 1 I 2 M 13 D 1 M 2 D 1 M 8 I 1 M 12 D 1 M 3 I 1 M 8 I 1 M 19 I 1 M 6 I 1 M 2 I 1 M 1 I 1 M 4 I 1 M 10 I 1 M 2 I 1 M 4 I 1 M 18 I 1 M 2 I 2 M 5 I 1 M 11 I 4 M 4 D 1 M 6 I 3 M 19 D 1 M 10 I 1 M 8 D 2 M 7 D 1 M 6 D 1 M 2 I 1 M 2 I 1 M 14 I 3 M 5 D 1 M 4 D 1 M 13 I 1 M 6 I 2 M 4 I 3 M 8 I 2 M 5 I 2 M 8 I 1 M 7 D 1 M 10 I 1 M 1 I 1 M 14 I 1 M 10 I 1 M 10 D 1 M 9 I 1 M 6 I 2 M 8 D 1 M 7 I 1 M 4 I 1 M 6 I 1 M 5 I 4 M 2 I 1 M 6 I 3 M 26 I 2 M 3 D 1 M 2 D 1 M 11 I 1 M 1 I 1 M 4 I 1 M 8 D 2 M 4 D 1 M 6 I 2 M 6 D 1 M 10 I 2 M 24 I 1 M 23 I 3 M 1 I 1 M 10 D 2 M 21 I 1 M 9 D 1 M 3 I 1 M 3 I 1 M 10 I 1 M 19 I 1 M 18 I 2 M 29 D 2 M 14 D 2 M 8 I 4 M 6 I 1 M 4 D 1 M 4 I 1 M 17 I 3 M 2 I 1 M 9 I 1 M 1 I 1 M 45 I 1 M 5 I 2 M 6 I 1 M 6 D 1 M 14 I 1 M 6 D 2 M 11 D 1 M 13 I 1 M 1 I 1 M 21 I 2 M 11 I 3 M 9 D 1 M 9 I 2 M 1 I 1 M 4 D 1 M 1 D 2 M 21 I 2 M 15 D 2 M 7 I 1 M 1 I 1 M 18 I 1 M 7 I 1 M 13 I 2 M 10 D 1 M 6 I 3 M 18 D 1 M 7 D 1 M 41 I 1 M 3 I 1 M 1 I 1 M 4 I 1 M 2 I 1 M 3 D 1 M 4 D 1 M 3 D 1 M 6 I 1 M 4 D 1 M 25 I 1 M 52 D 1 M 9 D 1 M 27 I 2 M 24 I 3 M 5 D 1 M 7 I 1 M 14 I 2 M 18 I 3 M 45 D 2 M 12 I 2 M 9 D 1 M 9 I 2 M 53 I 4 M 19 I 2 M 2 I 1 M 4 I 1 M 28 I 2 M 3 I 1 M 11 I 2 M 4 I 1 M 6 I 1 M 17 D 1 M 8 I 1 M 27 I 1 M 37 D 2 M 11 I 2 M 5 I 1 M 11 I 1 M 18 I 1 M 13 D 1 M 14 I 1 M 34 I 6 M 9 I 1 M 1 I 1 M 6 I 2 M 18 D 1 M 15 I 1 M 36 D 2 M 6 I 3 M 37 I 2 M 19 D 2 M 19 D 1 M 6 I 2 M 4 I 1 M 5 I 1 M 8 I 1 M 4 I 1 M 19 I 2 M 10 I 1 M 5 I 1 M 3 I 1 M 11 I 1 M 1 I 1 M 2 I 1 M 4 I 1 M 10 I 5 M 2 I 1 M 5 I 1 M 6 D 2 M 41 I 1 M 2 I 1 M 10 D 2 M 6 I 2 M 7 I 1 M 1 I 3 M 6 I 2 M 2 I 1 M 21 I 1 M 27 I 1 M 2 D 1 M 16 D 2 M 15 I 2 M 4 I 1 M 19 I 2 M 4 I 1 M 9 D 2 M 8 D 2 M 11 D 1 M 14 I 1 M 22 D 1 M 5 I 1 M 3 I 1 M 5 I 1 M 3 I 3 M 5 I 2 M 24 I 2 M 6 I 1 M 16 I 2 M 17 I 1 M 81 I 1 M 3 I 2 M 32 I 1 M 9 I 1 M 4 I 2 M 1 I 1 M 7 I 2 M 71 D 1 M 7 D 1 M 6 D 1 M 4 I 1 M 7 I 1 M 5 I 1 M 9 I 1 M 5 I 2 M 6 D 1 M 2 D 1 M 5 D 1 M 21 I 3 M 19 I 1 M 12 D 1 M 7 I 1 M 29 I 2 M 13 D 1 M 3 I 1 M 6 D 1 M 4 I 1 M 10 D 2 M 10 I 1 M 18 I 1 M 9 D 1 M 5 I 3 M 11 I 1 M 40 I 2 M 5 I 3 M 12 D 1 M 5 I 2 M 1 I 1 M 4 D 1 M 14 D 1 M 7 I 4 M 5 I 2 M 10 I 2 M 9 I 1 M 18 I 4 M 10 D 1 M 23 I 1 M 3 I 1 M 9 I 1 M 34 I 2 M 4 I 2 M 1 I 1 M 4 I 1 M 6 I 1 M 11 I 1 M 5 D 1 M 20 I 3 M 11 I 1 M 8 I 2 M 1 I 2 M 5 D 1 M 7 D 1 M 3 I 1 M 29 D 1 M 5 D 1 M 12 D 1 M 10 D 1 M 16 I 1 M 1 I 2 M 1 I 1 M 6 I 1 M 2 D 1 M 3 D 2 M 2 D 2 M 12 I 2 M 1 I 1 M 14 I 1 M 1 I 1 M 2 D 1 M 11 | /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/bin/signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5
[signalAlign] - using NanoporeHDPs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (3210 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.019 CPU sec, 0.044 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch308_file422_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch308_file422_strand.fast5.fa
[main] Real time: 0.061 sec; CPU: 0.030 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch308_file422_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (508 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.003 CPU sec, 0.015 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5.fa
[main] Real time: 0.029 sec; CPU: 0.013 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5 3 488 + gi_ecoli 1234292 1233788 - 1 M 6 D 2 M 8 D 1 M 16 D 2 M 6 I 1 M 6 I 1 M 5 D 1 M 4 I 1 M 2 D 1 M 1 D 1 M 7 D 4 M 6 D 2 M 5 D 1 M 7 D 2 M 8 D 1 M 4 D 1 M 23 I 2 M 8 D 1 M 4 D 1 M 4 I 1 M 3 I 2 M 6 I 1 M 3 D 1 M 10 I 3 M 8 D 4 M 5 I 1 M 5 D 1 M 8 I 1 M 14 I 2 M 1 I 3 M 12 I 2 M 4 D 1 M 10 D 1 M 12 I 2 M 19 I 2 M 4 D 1 M 2 D 1 M 5 D 4 M 19 D 1 M 4 D 1 M 9 I 1 M 11 D 1 M 19 D 1 M 10 D 1 M 19 D 1 M 8 I 2 M 23 D 6 M 6 D 1 M 6 D 2 M 13 I 2 M 1 I 1 M 4 D 1 M 1 D 1 M 5 I 1 M 2 I 2 M 19 D 2 M 6 I 1 M 4 | /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/bin/signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5
[signalAlign] - using NanoporeHDPs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (5656 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.022 CPU sec, 0.075 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch412_file504_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch412_file504_strand.fast5.fa
[main] Real time: 0.113 sec; CPU: 0.031 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch412_file504_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (4056 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.025 CPU sec, 0.092 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch76_file426_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch76_file426_strand.fast5.fa
[main] Real time: 0.114 sec; CPU: 0.034 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch76_file426_strand.fast5 didn't map got flag: False
signalAlign - starting template alignment
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (17118 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.178 CPU sec, 0.482 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5.fa
[main] Real time: 0.505 sec; CPU: 0.189 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5 11 17095 + gi_ecoli 771637 788302 + 1 M 22 I 1 M 13 D 2 M 5 I 2 M 15 D 1 M 44 D 1 M 13 I 2 M 13 I 1 M 3 I 1 M 36 D 1 M 15 D 2 M 4 I 1 M 3 I 1 M 6 D 2 M 7 D 2 M 8 I 4 M 37 D 2 M 17 D 1 M 14 I 1 M 28 D 1 M 29 I 1 M 18 I 1 M 28 D 2 M 18 D 1 M 21 D 2 M 16 I 1 M 15 D 1 M 33 I 2 M 8 I 1 M 4 D 1 M 15 D 2 M 14 I 1 M 2 D 1 M 43 I 1 M 6 D 1 M 30 D 1 M 10 I 2 M 32 I 2 M 11 D 1 M 11 I 1 M 8 D 1 M 5 I 1 M 6 I 1 M 10 I 1 M 11 D 2 M 19 I 2 M 31 I 2 M 4 I 1 M 43 I 2 M 16 D 1 M 14 I 1 M 54 I 1 M 12 I 5 M 7 D 1 M 19 D 1 M 12 D 1 M 3 I 1 M 4 D 1 M 51 D 1 M 8 I 2 M 4 D 1 M 28 D 3 M 9 D 1 M 13 D 1 M 3 D 1 M 6 I 1 M 22 I 2 M 21 I 2 M 11 I 1 M 23 I 3 M 26 I 1 M 14 I 1 M 13 D 1 M 6 D 1 M 27 D 3 M 4 D 1 M 1 D 1 M 24 D 1 M 10 I 1 M 2 I 2 M 12 I 1 M 8 I 1 M 6 D 1 M 8 I 1 M 17 I 2 M 10 D 1 M 18 I 2 M 4 I 1 M 3 I 1 M 19 I 1 M 11 I 2 M 33 D 1 M 5 I 2 M 11 D 3 M 8 D 1 M 2 D 1 M 1 D 1 M 13 D 1 M 43 I 1 M 13 I 1 M 20 D 1 M 6 D 3 M 36 I 2 M 10 I 2 M 8 D 3 M 2 D 1 M 4 D 1 M 8 I 1 M 19 D 1 M 9 I 4 M 11 D 1 M 33 D 1 M 18 I 3 M 30 D 1 M 16 I 1 M 14 D 1 M 18 I 1 M 34 I 3 M 7 I 1 M 14 D 2 M 17 D 1 M 5 I 2 M 33 I 4 M 22 D 1 M 6 I 2 M 7 I 2 M 53 I 2 M 7 I 1 M 2 D 2 M 21 I 2 M 17 D 1 M 11 D 1 M 19 I 2 M 40 D 1 M 19 D 1 M 5 D 2 M 11 D 1 M 18 I 2 M 2 I 1 M 5 D 1 M 8 I 2 M 21 D 1 M 7 D 1 M 16 I 1 M 5 D 1 M 15 I 1 M 12 I 1 M 57 D 3 M 2 D 1 M 7 I 1 M 4 I 1 M 5 D 2 M 3 D 2 M 9 D 2 M 3 D 2 M 6 D 1 M 5 D 1 M 6 D 1 M 1 D 1 M 7 I 1 M 7 I 1 M 44 D 2 M 13 D 1 M 3 D 2 M 11 I 1 M 7 I 1 M 11 D 2 M 2 D 1 M 11 I 3 M 3 D 1 M 23 D 2 M 10 D 2 M 28 D 2 M 20 D 2 M 3 D 1 M 1 D 1 M 5 I 1 M 4 I 1 M 15 D 2 M 17 I 2 M 9 D 1 M 12 I 1 M 18 I 2 M 13 I 2 M 34 D 2 M 42 D 1 M 30 D 1 M 3 D 1 M 10 D 1 M 5 D 2 M 36 D 2 M 5 D 1 M 19 D 2 M 10 D 1 M 18 I 2 M 7 D 2 M 3 D 2 M 25 I 1 M 15 D 2 M 10 I 1 M 9 I 1 M 8 I 1 M 20 D 1 M 6 D 1 M 1 D 1 M 13 D 1 M 36 D 2 M 4 D 1 M 21 D 3 M 9 I 2 M 9 I 2 M 7 I 1 M 1 I 1 M 8 D 1 M 5 I 1 M 52 I 1 M 6 D 1 M 2 D 1 M 7 D 1 M 56 I 3 M 29 D 3 M 7 I 3 M 1 I 1 M 10 I 4 M 23 I 2 M 5 D 1 M 18 I 1 M 2 I 1 M 4 I 2 M 3 D 1 M 8 I 1 M 14 I 1 M 5 I 1 M 3 I 1 M 3 D 1 M 1 D 1 M 5 I 1 M 15 D 1 M 7 I 1 M 2 D 2 M 13 I 1 M 5 I 1 M 9 D 1 M 12 I 2 M 8 D 1 M 9 D 1 M 36 D 2 M 20 I 5 M 4 I 1 M 5 D 1 M 15 I 1 M 11 D 1 M 10 D 2 M 23 D 1 M 27 I 1 M 18 I 2 M 13 D 1 M 4 D 2 M 57 I 1 M 15 D 1 M 7 I 1 M 7 D 1 M 14 I 1 M 14 D 1 M 18 D 1 M 29 D 1 M 14 D 1 M 13 D 2 M 37 I 1 M 3 I 1 M 1 I 1 M 4 D 1 M 16 I 4 M 25 D 1 M 18 I 1 M 16 D 1 M 25 D 1 M 14 I 1 M 3 D 1 M 6 D 1 M 15 I 1 M 15 D 1 M 1 D 1 M 18 D 2 M 5 D 1 M 10 I 1 M 3 I 1 M 51 I 1 M 27 D 3 M 2 D 1 M 10 I 1 M 14 I 2 M 13 I 1 M 31 D 2 M 2 D 1 M 8 I 2 M 7 I 2 M 5 I 1 M 43 D 1 M 8 I 1 M 23 D 1 M 5 D 3 M 1 D 1 M 10 D 1 M 11 D 2 M 17 D 1 M 5 D 1 M 14 D 1 M 23 D 1 M 26 D 1 M 18 I 2 M 19 D 1 M 16 D 1 M 25 D 1 M 17 I 1 M 3 D 1 M 60 I 1 M 14 I 4 M 4 I 2 M 18 I 1 M 3 I 2 M 16 I 1 M 14 I 1 M 4 D 2 M 14 D 1 M 3 I 3 M 7 D 2 M 15 D 1 M 23 I 1 M 20 I 1 M 5 I 3 M 7 D 2 M 26 I 1 M 13 D 1 M 12 D 1 M 10 I 5 M 14 D 1 M 2 D 1 M 16 D 1 M 9 D 3 M 4 I 1 M 28 I 3 M 2 I 1 M 11 I 1 M 17 I 2 M 22 D 1 M 9 I 4 M 1 I 1 M 3 I 2 M 2 D 1 M 15 I 4 M 10 I 1 M 5 I 3 M 12 D 1 M 22 D 2 M 3 D 1 M 10 I 2 M 11 I 1 M 5 D 1 M 6 D 1 M 7 I 1 M 3 I 1 M 1 I 2 M 10 I 2 M 3 I 2 M 11 D 2 M 22 I 1 M 4 D 1 M 11 D 1 M 4 D 1 M 7 I 2 M 25 D 1 M 13 I 2 M 25 I 1 M 7 I 1 M 5 D 3 M 14 D 3 M 10 D 1 M 9 I 2 M 23 I 1 M 3 I 1 M 3 D 2 M 6 I 2 M 9 D 1 M 6 D 1 M 13 D 1 M 9 I 1 M 7 D 2 M 5 D 2 M 8 D 5 M 1 D 1 M 3 I 1 M 3 D 1 M 12 I 1 M 6 D 1 M 2 D 1 M 5 I 1 M 4 D 3 M 1 D 3 M 4 D 1 M 2 D 2 M 1 D 1 M 4 D 1 M 12 D 1 M 17 D 2 M 7 I 1 M 8 D 1 M 9 D 1 M 10 D 1 M 7 D 3 M 2 D 2 M 1 D 1 M 2 D 2 M 2 D 1 M 4 D 1 M 1 D 1 M 16 D 1 M 10 D 2 M 7 I 1 M 15 D 1 M 11 D 1 M 2 D 1 M 3 D 1 M 49 D 1 M 2 D 1 M 40 I 1 M 6 I 2 M 29 I 1 M 2 I 1 M 1 I 1 M 19 D 2 M 13 I 1 M 23 D 1 M 5 D 3 M 27 D 1 M 2 D 2 M 13 I 1 M 17 D 1 M 9 D 1 M 10 D 2 M 31 D 2 M 11 I 1 M 19 I 4 M 5 I 1 M 8 I 2 M 8 D 1 M 7 I 4 M 2 I 1 M 6 D 2 M 7 D 1 M 4 I 2 M 7 D 2 M 31 D 1 M 7 I 1 M 52 D 1 M 25 D 2 M 48 I 2 M 7 D 1 M 34 I 1 M 33 I 1 M 8 I 1 M 17 D 2 M 6 I 3 M 12 I 1 M 7 I 1 M 14 D 1 M 1 D 1 M 3 I 1 M 2 I 3 M 9 D 1 M 10 I 4 M 27 I 2 M 82 D 1 M 14 D 2 M 5 I 2 M 13 D 1 M 14 D 1 M 3 D 2 M 3 D 1 M 16 D 1 M 42 I 1 M 8 D 3 M 6 D 1 M 18 I 3 M 13 I 1 M 14 D 1 M 30 I 2 M 29 I 4 M 13 I 2 M 32 D 1 M 30 I 1 M 7 I 1 M 11 I 1 M 8 D 1 M 4 D 2 M 31 I 2 M 6 D 1 M 4 D 1 M 17 I 1 M 8 I 1 M 1 I 1 M 15 I 4 M 4 I 1 M 21 I 1 M 3 I 1 M 3 D 1 M 9 I 2 M 20 D 1 M 10 D 1 M 7 I 1 M 15 I 1 M 29 I 2 M 6 D 1 M 14 D 1 M 3 D 1 M 53 I 1 M 6 I 1 M 19 I 1 M 3 I 1 M 13 I 3 M 7 I 1 M 20 I 1 M 4 I 4 M 6 D 1 M 56 D 1 M 56 D 1 M 12 I 1 M 43 I 4 M 1 I 1 M 1 I 2 M 25 D 1 M 8 D 1 M 22 D 1 M 31 I 1 M 3 I 1 M 6 I 1 M 8 I 1 M 41 I 2 M 3 I 1 M 5 I 1 M 17 I 1 M 20 I 1 M 9 I 1 M 1 I 1 M 6 D 1 M 13 I 1 M 4 I 4 M 22 D 1 M 4 D 1 M 4 I 5 M 3 I 1 M 13 I 3 M 19 I 1 M 2 I 3 M 12 I 2 M 8 D 1 M 1 D 1 M 2 D 1 M 11 I 3 M 4 I 1 M 15 I 3 M 9 I 2 M 2 I 2 M 3 D 1 M 13 D 1 M 13 D 1 M 10 I 1 M 15 I 3 M 5 I 1 M 9 D 1 M 11 I 1 M 13 I 2 M 12 I 1 M 14 I 2 M 8 I 1 M 3 D 1 M 20 D 1 M 13 I 4 M 5 I 1 M 5 I 2 M 3 I 3 M 4 I 3 M 2 I 1 M 10 I 5 M 1 I 2 M 6 I 1 M 6 I 1 M 4 D 1 M 32 I 1 M 3 I 1 M 10 I 1 M 5 I 3 M 11 I 3 M 15 I 1 M 9 I 4 M 17 I 1 M 6 D 1 M 10 I 3 M 6 D 1 M 4 I 1 M 2 I 1 M 23 I 2 M 5 D 1 M 10 I 2 M 4 I 3 M 7 I 7 M 5 I 5 M 11 I 1 M 8 I 1 M 6 I 2 M 9 I 3 M 1 I 1 M 8 I 5 M 25 I 3 M 6 I 1 M 5 I 1 M 4 I 3 M 4 I 3 M 1 I 1 M 10 I 1 M 25 D 1 M 18 I 1 M 10 I 2 M 3 I 2 M 7 D 2 M 12 I 3 M 23 I 1 M 5 I 1 M 6 I 1 M 14 D 1 M 6 I 1 M 3 I 5 M 3 I 1 M 6 I 2 M 1 I 1 M 8 I 3 M 4 D 1 M 11 D 1 M 5 I 2 M 8 I 1 M 2 I 1 M 14 I 1 M 7 I 1 M 9 I 1 M 15 I 1 M 4 I 2 M 10 I 5 M 4 I 1 M 1 I 4 M 9 I 1 M 9 D 2 M 2 D 1 M 6 I 2 M 8 D 1 M 23 I 1 M 7 I 1 M 4 D 1 M 9 I 3 M 30 D 1 M 7 I 6 M 20 D 1 M 2 D 1 M 7 D 1 M 4 D 1 M 3 D 1 M 3 D 1 M 11 I 1 M 8 D 1 M 5 D 1 M 5 D 1 M 9 I 3 M 4 I 1 M 10 D 1 M 2 D 3 M 7 D 1 M 1 D 1 M 11 I 2 M 25 I 7 M 7 D 1 M 3 D 1 M 1 D 1 M 16 I 1 M 12 I 1 M 6 I 1 M 6 I 5 M 4 I 1 M 5 D 1 M 16 I 1 M 10 I 1 M 8 I 3 M 6 I 2 M 7 I 5 M 3 I 1 M 5 D 1 M 12 I 1 M 6 I 3 M 4 I 1 M 2 D 1 M 3 D 1 M 16 D 3 M 2 D 1 M 4 I 1 M 17 D 1 M 2 I 1 M 27 I 1 M 7 D 1 M 19 D 1 M 5 I 3 M 2 I 2 M 23 I 1 M 5 I 1 M 4 D 1 M 1 D 1 M 14 I 2 M 2 I 1 M 1 I 1 M 11 I 3 M 8 D 1 M 10 I 3 M 5 I 2 M 16 I 2 M 7 I 2 M 1 I 3 M 3 I 3 M 4 I 1 M 8 D 1 M 5 I 1 M 11 I 1 M 8 I 2 M 1 I 2 M 3 I 4 M 12 D 1 M 21 D 1 M 10 I 8 M 2 I 3 M 8 D 1 M 12 D 1 M 4 D 2 M 1 D 1 M 11 D 1 M 9 I 2 M 1 I 1 M 2 I 2 M 16 D 1 M 13 I 1 M 1 I 1 M 6 I 2 M 13 D 1 M 7 D 1 M 2 I 1 M 4 I 1 M 2 D 1 M 10 I 3 M 5 D 1 M 4 I 1 M 3 I 1 M 4 D 1 M 2 I 1 M 3 D 1 M 36 I 1 M 11 I 5 M 4 I 1 M 9 I 2 M 7 I 6 M 3 I 1 M 6 I 1 M 12 I 1 M 4 I 1 M 27 I 1 M 17 I 1 M 1 I 1 M 6 I 1 M 21 D 1 M 6 D 1 M 25 D 2 M 12 D 1 M 10 D 1 M 19 I 1 M 28 I 3 M 11 I 2 M 5 D 1 M 21 I 2 M 15 I 2 M 13 I 1 M 17 I 2 M 14 I 1 M 8 D 1 M 19 D 1 M 12 D 1 M 5 D 2 M 14 D 1 M 11 D 1 M 6 D 1 M 8 I 1 M 9 D 1 M 4 D 4 M 6 D 5 M 9 D 1 M 2 D 3 M 38 I 1 M 1 I 1 M 1 I 1 M 5 D 1 M 4 D 1 M 4 D 1 M 10 D 1 M 14 D 1 M 4 D 1 M 11 D 1 M 5 I 1 M 12 I 3 M 6 I 2 M 13 D 4 M 8 D 3 M 4 I 2 M 19 D 2 M 15 I 2 M 42 I 2 M 8 I 1 M 12 I 1 M 15 D 2 M 17 D 1 M 7 I 1 M 1 I 2 M 18 D 1 M 12 D 1 M 31 I 1 M 6 I 3 M 22 I 1 M 22 I 1 M 2 I 5 M 8 I 2 M 4 I 1 M 18 D 1 M 19 I 1 M 6 I 1 M 11 D 1 M 20 I 1 M 40 D 2 M 8 D 3 M 6 I 3 M 23 I 2 M 5 I 1 M 25 I 1 M 17 I 2 M 19 D 1 M 3 I 1 M 4 I 1 M 1 I 1 M 13 D 1 M 7 D 2 M 11 D 1 M 15 D 1 M 16 D 4 M 8 I 1 M 6 I 2 M 8 D 1 M 14 I 3 M 19 D 1 M 24 I 2 M 2 I 2 M 4 I 1 M 32 D 4 M 21 I 2 M 19 I 1 M 2 I 1 M 3 I 3 M 21 D 1 M 11 D 1 M 4 D 1 M 5 D 1 M 4 D 1 M 8 I 1 M 5 I 1 M 3 D 1 M 25 D 1 M 8 I 1 M 4 D 1 M 20 I 2 M 23 D 1 M 3 D 1 M 13 I 1 M 21 D 1 M 35 I 5 M 19 D 1 M 4 I 1 M 22 D 2 M 7 D 1 M 2 D 3 M 21 D 1 M 7 I 1 M 12 I 2 M 13 I 2 M 5 D 1 M 34 I 1 M 7 I 1 M 1 I 1 M 32 I 2 M 1 I 1 M 7 D 1 M 11 I 1 M 16 D 1 M 11 D 1 M 3 D 1 M 6 I 2 M 22 D 2 M 10 I 2 M 14 I 2 M 2 I 1 M 11 D 2 M 37 D 1 M 9 I 1 M 8 D 2 M 47 D 1 M 5 D 1 M 1 D 1 M 1 D 1 M 14 D 1 M 3 D 1 M 11 I 1 M 22 D 2 M 11 I 1 M 2 I 1 M 5 I 1 M 18 D 1 M 6 I 2 M 6 I 2 M 3 I 1 M 19 D 1 M 2 I 1 M 18 I 1 M 14 D 1 M 26 D 3 M 8 D 2 M 19 I 2 M 18 I 1 M 21 D 1 M 12 D 1 M 10 I 2 M 24 D 1 M 24 D 1 M 13 D 1 M 6 I 1 M 1 I 1 M 21 I 1 M 8 I 2 M 10 I 1 M 19 D 1 M 18 I 2 M 6 I 2 M 19 I 3 M 3 I 2 M 55 I 1 M 12 I 2 M 36 D 1 M 5 I 1 M 11 D 2 M 4 I 1 M 23 I 1 M 31 D 1 M 9 I 2 M 3 I 1 M 19 D 2 M 8 D 1 M 34 D 1 M 11 I 2 M 4 I 1 M 25 I 1 M 1 I 2 M 9 D 1 M 13 I 1 M 6 I 1 M 30 I 1 M 5 I 5 M 42 D 1 M 1 D 1 M 3 D 1 M 2 D 4 M 5 I 1 M 4 I 1 M 1 I 2 M 17 I 1 M 2 I 2 M 4 I 2 M 7 I 1 M 16 I 1 M 53 D 3 M 28 D 1 M 3 D 1 M 2 I 1 M 7 I 1 M 3 I 1 M 4 D 1 M 6 I 3 M 37 D 2 M 18 I 2 M 39 I 1 M 4 I 2 M 19 D 1 M 17 D 1 M 18 D 1 M 5 I 1 M 16 I 1 M 6 D 1 M 2 D 1 M 8 I 1 M 13 I 3 M 17 I 1 M 17 D 1 M 7 D 1 M 24 I 3 M 5 D 1 M 19 I 2 M 5 I 2 M 14 D 3 M 45 D 1 M 8 I 2 M 8 I 1 M 7 I 1 M 12 D 6 M 7 I 1 M 8 D 1 M 17 I 2 M 23 D 1 M 26 I 3 M 24 D 1 M 3 D 1 M 10 I 1 M 14 D 2 M 62 D 2 M 19 D 1 M 5 D 1 M 8 I 2 M 6 D 1 M 6 I 1 M 4 I 1 M 2 D 1 M 25 D 1 M 2 I 1 M 6 I 2 M 24 D 3 M 14 D 1 M 3 I 1 M 15 D 1 M 2 D 1 M 10 D 4 M 10 D 1 M 7 I 1 M 1 I 1 M 12 I 2 M 8 I 2 M 5 I 1 M 28 D 1 M 41 I 1 M 15 D 1 M 2 D 1 M 2 D 1 M 18 I 2 M 4 I 3 M 21 D 1 M 11 D 2 M 4 D 1 M 31 I 1 M 4 I 2 M 15 I 1 M 8 I 2 M 11 I 1 M 3 I 1 M 23 D 2 M 10 I 2 M 2 I 2 M 1 I 1 M 14 D 1 M 14 D 1 M 6 D 1 M 8 I 1 M 6 D 1 M 26 I 1 M 22 I 1 M 10 I 1 M 2 I 1 M 4 D 1 M 7 D 1 M 14 D 1 M 3 D 1 M 4 I 1 M 15 I 1 M 35 I 1 M 30 I 1 M 3 I 1 M 9 D 3 M 6 I 2 M 5 D 1 M 7 I 1 M 20 I 1 M 8 I 5 M 2 I 1 M 22 I 5 M 27 D 2 M 6 D 2 M 6 I 1 M 5 I 2 M 1 I 2 M 3 I 3 M 1 I 1 M 2 I 1 M 11 I 3 M 6 I 4 M 8 I 1 M 3 I 3 M 13 I 1 M 6 D 1 M 2 D 1 M 4 I 2 M 16 I 7 M 13 I 4 M 6 I 2 M 1 I 3 M 3 I 1 M 4 I 1 M 5 D 1 M 12 D 1 M 5 D 1 M 6 D 3 M 16 I 2 M 2 I 1 M 25 I 2 M 9 D 1 M 12 D 1 M 16 I 1 M 17 I 4 M 17 D 3 M 4 I 1 M 18 I 1 M 11 I 1 M 14 I 1 M 2 D 1 M 5 D 3 M 39 D 1 M 7 D 1 M 2 D 1 M 19 I 1 M 4 I 1 M 2 I 1 M 8 I 1 M 25 D 1 M 18 D 1 M 20 D 1 M 26 D 1 M 11 D 2 M 7 D 1 M 15 I 1 M 15 D 1 M 3 I 1 M 9 I 1 M 3 I 1 M 10 D 1 M 6 D 1 M 3 D 1 M 20 I 1 M 13 D 1 M 2 D 1 M 5 D 2 M 21 I 1 M 34 I 2 M 10 D 2 M 8 I 2 M 11 I 1 M 26 I 4 M 6 D 1 M 12 I 1 M 5 I 1 M 18 D 1 M 6 D 3 M 11 D 1 M 7 D 1 M 18 I 2 M 6 D 1 M 15 D 1 M 22 D 1 M 14 I 2 M 13 I 1 M 39 D 1 M 3 D 1 M 16 D 4 M 24 D 1 M 3 I 1 M 3 D 1 M 3 I 3 M 5 I 1 M 8 I 2 M 10 D 3 M 1 D 1 M 13 I 1 M 28 D 1 M 14 D 1 M 3 I 1 M 3 I 5 M 3 I 1 M 9 I 4 M 3 I 1 M 8 I 2 M 3 I 1 M 2 I 1 M 9 I 2 M 4 I 2 M 3 I 2 M 13 I 5 M 4 D 1 M 66 I 2 M 28 D 1 M 3 D 1 M 15 D 1 M 49 I 1 M 10 I 4 M 8 I 1 M 2 I 3 M 4 D 1 M 2 I 1 M 40 I 4 M 5 D 2 M 4 D 3 M 9 I 1 M 1 I 2 M 4 I 2 M 4 I 1 M 8 D 2 M 13 D 1 M 4 I 1 M 19 I 2 M 38 I 1 M 4 D 1 M 4 D 1 M 8 D 2 M 13 D 1 M 3 D 1 M 52 I 2 M 11 D 1 M 6 I 2 M 1 I 1 M 18 I 1 M 3 I 3 M 29 I 1 M 20 D 2 M 2 I 1 M 21 I 1 M 3 I 1 M 10 I 1 M 5 I 1 M 4 I 2 M 28 I 4 M 17 D 1 M 40 I 2 M 1 I 1 M 51 I 1 M 29 D 1 M 17 D 1 M 51 D 2 M 9 I 3 M 3 D 1 M 8 I 1 M 2 D 1 M 77 I 1 M 42 I 2 M 1 I 1 M 12 D 2 M 3 I 1 M 24 D 1 M 23 I 2 M 1 I 1 M 7 D 1 M 31 I 1 M 13 I 3 M 1 I 1 M 34 D 2 M 4 D 1 M 25 D 2 M 11 D 1 M 29 D 2 M 42 D 1 M 1 D 2 M 4 I 1 M 9 D 1 M 1 D 1 M 22 I 2 M 3 I 1 M 9 I 1 M 7 D 1 M 3 I 1 M 8 D 1 M 14 I 1 M 14 I 6 M 3 I 2 M 4 I 1 M 2 I 1 M 4 D 1 M 15 D 1 M 16 I 1 M 21 I 1 M 5 D 1 M 7 I 1 M 1 I 1 M 3 D 2 M 10 | /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/bin/signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5
[signalAlign] - using NanoporeHDPs
signalAlign - starting template alignment
signalAlign - starting complement alignment
signalAlign - SUCCESS: finished alignment of query makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.fast5, exiting
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (168 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.002 CPU sec, 0.013 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch341_file269_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch341_file269_strand.fast5.fa
[main] Real time: 0.275 sec; CPU: 0.010 sec
unknown alignment flag, exiting
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch341_file269_strand.fast5 didn't map got flag: False
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (5524 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.033 CPU sec, 0.111 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5.fa
[main] Real time: 0.143 sec; CPU: 0.041 sec
signalAlign - NOTICE: template model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm complement model /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm
signalAlign - running command:  echo cigar: /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/tests/minion_test_reads/ecoli/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5 25 5505 + gi_ecoli 886654 891931 + 1 M 5 I 3 M 41 D 1 M 2 D 2 M 13 D 1 M 31 I 4 M 5 D 2 M 23 I 1 M 12 D 1 M 5 I 1 M 12 D 2 M 22 D 1 M 6 I 1 M 4 D 1 M 4 D 1 M 16 I 1 M 11 I 1 M 8 I 3 M 14 D 1 M 35 I 2 M 52 D 1 M 18 I 1 M 9 I 1 M 90 I 2 M 8 I 1 M 6 I 3 M 13 I 1 M 9 I 2 M 12 I 1 M 9 I 1 M 2 I 4 M 1 I 1 M 2 I 2 M 2 I 1 M 4 I 3 M 32 D 1 M 8 I 5 M 1 I 1 M 8 I 1 M 25 D 2 M 14 D 1 M 5 D 1 M 25 I 3 M 28 I 2 M 4 I 1 M 20 D 1 M 12 I 4 M 13 D 1 M 17 D 2 M 12 D 1 M 4 D 1 M 5 I 2 M 29 D 1 M 2 D 3 M 14 I 1 M 2 I 2 M 3 I 1 M 23 I 3 M 7 I 1 M 13 I 1 M 3 D 1 M 84 I 2 M 5 I 1 M 9 I 1 M 7 D 1 M 12 I 1 M 4 D 1 M 15 I 1 M 17 I 1 M 4 I 1 M 39 I 7 M 2 I 2 M 5 I 1 M 6 D 1 M 11 D 1 M 3 I 1 M 16 I 1 M 1 I 1 M 29 D 1 M 11 I 2 M 19 I 1 M 31 D 3 M 11 I 4 M 33 I 2 M 40 D 1 M 6 I 1 M 9 D 2 M 19 D 1 M 42 D 2 M 2 D 1 M 56 D 1 M 18 D 3 M 13 I 2 M 14 D 1 M 15 I 2 M 3 I 1 M 27 I 2 M 2 I 2 M 1 I 1 M 20 D 3 M 7 I 4 M 12 D 2 M 7 I 2 M 28 I 3 M 8 I 1 M 13 I 2 M 12 I 4 M 17 D 4 M 17 I 1 M 17 D 1 M 11 I 1 M 23 I 1 M 21 D 1 M 2 D 2 M 2 D 1 M 15 I 6 M 24 I 2 M 25 I 2 M 4 I 1 M 33 I 1 M 8 I 1 M 41 I 1 M 40 I 1 M 31 D 1 M 11 I 2 M 11 I 1 M 8 I 4 M 2 I 3 M 12 I 1 M 4 D 1 M 21 D 1 M 7 I 1 M 4 I 1 M 5 I 1 M 9 I 3 M 16 I 1 M 7 D 2 M 16 D 1 M 10 I 1 M 1 I 1 M 1 I 1 M 40 I 2 M 10 D 1 M 54 I 2 M 57 I 5 M 25 I 5 M 26 I 1 M 3 I 1 M 2 I 1 M 52 I 4 M 2 D 2 M 17 I 1 M 50 D 1 M 10 I 1 M 1 I 3 M 14 D 1 M 3 D 1 M 11 I 1 M 2 I 1 M 8 I 2 M 25 D 1 M 11 I 3 M 18 D 1 M 24 I 1 M 12 D 1 M 5 D 1 M 22 I 2 M 19 D 1 M 35 I 2 M 9 D 2 M 8 I 2 M 45 D 1 M 31 D 1 M 12 I 3 M 21 D 1 M 2 I 3 M 19 I 3 M 54 D 3 M 11 D 2 M 12 I 2 M 3 D 2 M 4 I 2 M 7 I 4 M 3 I 1 M 2 I 1 M 29 D 1 M 72 D 1 M 33 D 2 M 13 D 1 M 9 D 1 M 3 I 1 M 18 I 3 M 2 I 1 M 55 I 2 M 13 I 1 M 6 D 1 M 12 I 1 M 20 I 1 M 34 I 1 M 11 D 1 M 5 D 1 M 3 D 1 M 62 I 1 M 4 I 2 M 11 D 3 M 9 D 1 M 19 D 1 M 4 I 1 M 26 I 2 M 16 D 1 M 14 D 1 M 13 D 1 M 6 D 1 M 26 I 1 M 1 I 1 M 46 I 1 M 11 I 2 M 18 D 1 M 9 I 1 M 49 I 2 M 3 I 1 M 12 I 3 M 41 D 1 M 15 D 1 M 2 I 1 M 8 D 1 M 4 D 2 M 15 D 1 M 15 I 1 M 23 D 1 M 8 D 1 M 17 I 1 M 24 I 1 M 28 I 1 M 4 D 2 M 12 I 2 M 14 D 2 M 10 I 2 M 25 D 1 M 9 I 1 M 6 D 1 M 12 D 1 M 7 I 2 M 13 I 2 M 4 D 1 M 36 I 1 M 20 I 4 M 2 D 1 M 20 D 1 M 17 I 1 M 5 D 1 M 10 D 1 M 5 I 3 M 19 D 2 M 9 D 1 M 17 I 1 M 48 D 1 M 12 I 1 M 1 I 1 M 7 D 1 M 28 I 1 M 3 I 1 M 90 I 1 M 9 I 1 M 19 I 3 M 2 I 2 M 13 D 1 M 21 D 2 M 6 I 3 M 21 D 1 M 6 D 1 M 9 D 2 M 19 D 1 M 10 I 1 M 2 I 1 M 8 I 2 M 7 D 1 M 9 I 1 M 6 I 2 M 13 I 2 M 3 I 1 M 11 D 1 M 2 I 3 M 11 I 1 M 11 I 2 M 2 I 5 M 3 I 2 M 13 I 1 M 15 I 2 M 7 I 1 M 13 D 1 M 2 D 1 M 6 D 2 M 13 I 1 M 1 I 1 M 12 I 1 M 2 I 1 M 2 D 1 M 3 I 1 M 6 I 1 M 4 I 1 M 18 I 1 M 16 I 1 M 14 I 1 M 21 D 1 M 3 D 1 M 21 I 1 M 4 I 3 M 2 I 2 M 16 I 1 M 17 I 1 M 2 I 2 M 8 I 1 M 15 D 3 M 43 I 2 M 2 D 1 M 24 I 1 M 18 I 1 M 8 I 2 M 4 I 2 M 51 I 1 M 7 I 1 M 3 I 1 M 10 I 3 M 31 D 2 M 17 I 1 M 36 D 1 M 10 D 5 M 29 I 1 M 2 I 1 M 29 I 5 M 20 I 4 M 9 I 2 M 11 I 2 M 9 D 1 M 8 D 1 M 9 I 3 M 17 | /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/bin/signalMachine -o 0 -s 1 --sm3Hdp -f demo/tempFiles_alignment/forward_reference.txt -b demo/tempFiles_alignment/backward_reference.txt  -q demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5/temp_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5.npRead -T /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template_trained.hmm -C /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement_trained.hmm  -u demo/tempFiles_alignment/makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.sm3Hdp.tsv -v /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/template.multisetPrior2.nhdp -w /gpfs/data/sgerbi/jurban/software/signalAlign/signalAlign/HDP_models/ecoli_r7.3_models/complement.multisetPrior2.nhdp -L makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5
[signalAlign] - using NanoporeHDPs
signalAlign - starting complement alignment
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1 sequences (3851 bp)...
[M::mem_process_seqs] Processed 1 reads in 0.027 CPU sec, 0.093 real sec
[main] Version: 0.7.14-r1136
[main] CMD: bwa mem -x ont2d demo/tempFiles_alignment/temp_bwaIndex demo/tempFiles_alignment/tempFiles_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch89_file296_strand.fast5/temp_2Dseq_makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch89_file296_strand.fast5.fa
[main] Real time: 0.113 sec; CPU: 0.035 sec
signalAlign - makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch89_file296_strand.fast5 didn't map got flag: False
signalAlign - SUCCESS: finished alignment of query makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.fast5, exiting
signalAlign - starting template alignment
signalAlign - starting template alignment
signalAlign - starting complement alignment
signalAlign - SUCCESS: finished alignment of query makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.fast5, exiting
signalAlign - starting complement alignment
signalAlign - SUCCESS: finished alignment of query makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.fast5, exiting

#  signalAlign - finished alignments

The output directory was demo/. Inside it is: demo_run.err tempFiles_alignment and inside demo/tempFiles_alignment is:

backward_reference.txt
forward_reference.txt
makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch228_file112_strand.sm3Hdp.tsv
makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch454_file165_strand.sm3Hdp.tsv
makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch483_file327_strand.sm3Hdp.tsv
makeson_PC_MA_286_R7.3_gEcoli_10_26_15_2807_1_ch8_file441_strand.sm3Hdp.tsv
probs.tsv
temp_bwaIndex.amb
temp_bwaIndex.ann
temp_bwaIndex.bwt
temp_bwaIndex.pac
temp_bwaIndex.sa

Does everything look right?

ArtRand commented 7 years ago

Looks correct, closing this issue.