alntools bam2ec gets stuck

[mfrancesconi81]

Hi KB,

I solved the bowtie problem by installing it from sourceforge instead of
bioconda. But I still have trouble with alntools bam2ec.

I run the alntools bam2ec using emase.pooled.targets.info produced by
create-hybrid as transcript length file and the bam file produced by bowtie
using -a --best --strata -v -m 100 parameters as per your recommendation,
and -c 14 because I previously split the bam into 14 chuncks using alntools
split.

The program start running and immediately produces temporary files
(_bam2ec.0.bam, etc..) and output "Unexpected target found in BAM file:" and
the name of the first transcript found in each of the split bam files. Then
it keeps running for more than 6 hours without producing any other output
or updating any of the temporary files.

I tried to terminate using ctrl c without success. I had to close the
session on the cluster.

Below is the head of the bam file. A6 and A7 are the two haplotypes. Does
it look good to you? Any clue on what might be going wrong?

Thank you very much,

Mirko

D00733:255:CB6DCANXX:7:1110:1899:2181 16 FBtr0302317_A7 1819 255 50M * 0 0
TACCAAGCCGAGCACTCTGGAAGAGCTGAAGCATCAGCCGGTTATAGTGG
GGGGGGGGGGGFGGFCEGGGGGGGGGGGGGGGGGGGGGGGGCGGGCCCCC XA:i:0 MD:Z:50 NM:i:0
XM:i:3
D00733:255:CB6DCANXX:7:1110:1899:2181 16 FBtr0083452_A7 1819 255 50M * 0 0
TACCAAGCCGAGCACTCTGGAAGAGCTGAAGCATCAGCCGGTTATAGTGG
GGGGGGGGGGGFGGFCEGGGGGGGGGGGGGGGGGGGGGGGGCGGGCCCCC XA:i:0 MD:Z:50 NM:i:0
XM:i:3
D00733:255:CB6DCANXX:7:1110:1992:2183 16 FBtr0086537_A6 497 255 50M * 0 0
AGTCGGGTGCCGGCAACAACTGGGCCAAGGGTCATTACACAGAGGGTGCC
EGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCBBB XA:i:1 MD:Z:49T0 NM:i:1
XM:i:5
D00733:255:CB6DCANXX:7:1110:1992:2183 16 FBtr0086536_A7 392 255 50M * 0 0
AGTCGGGTGCCGGCAACAACTGGGCCAAGGGTCATTACACAGAGGGTGCC
EGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCBBB XA:i:1 MD:Z:49T0 NM:i:1
XM:i:5
D00733:255:CB6DCANXX:7:1110:1992:2183 16 FBtr0086537_A7 497 255 50M * 0 0
AGTCGGGTGCCGGCAACAACTGGGCCAAGGGTCATTACACAGAGGGTGCC
EGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCBBB XA:i:1 MD:Z:49T0 NM:i:1
XM:i:5
D00733:255:CB6DCANXX:7:1110:1992:2183 16 FBtr0086536_A6 392 255 50M * 0 0
AGTCGGGTGCCGGCAACAACTGGGCCAAGGGTCATTACACAGAGGGTGCC
EGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCBBB XA:i:1 MD:Z:49T0 NM:i:1
XM:i:5
D00733:255:CB6DCANXX:7:1110:1816:2200 16 FBtr0110818_A7 1089 255 50M * 0 0
TGGAAAACAATGGAAATGCAACAGGAAAACGAGACGGGAAGAGAAGGGGC
GGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGBB<BA XA:i:1 MD:Z:49T0 NM:i:1
XM:i:9
D00733:255:CB6DCANXX:7:1110:1816:2200 16 FBtr0110818_A6 1089 255 50M * 0 0
TGGAAAACAATGGAAATGCAACAGGAAAACGAGACGGGAAGAGAAGGGGC
GGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGBB<BA XA:i:1 MD:Z:49T0 NM:i:1
XM:i:9
D00733:255:CB6DCANXX:7:1110:1816:2200 16 FBtr0333850_A6 995 255 50M * 0 0
TGGAAAACAATGGAAATGCAACAGGAAAACGAGACGGGAAGAGAAGGGGC
GGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGBB<BA XA:i:1 MD:Z:49T0 NM:i:1
XM:i:9
D00733:255:CB6DCANXX:7:1110:1816:2200 16 FBtr0333850_A7 995 255 50M * 0 0
TGGAAAACAATGGAAATGCAACAGGAAAACGAGACGGGAAGAGAAGGGGC
GGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGBB<BA XA:i:1 MD:Z:49T0 NM:i:1
XM:i:9