blasr skipping reads

[yunfeiguo]

Hi,

I just tried longislnd, it was running nicely!

However, I had an issue with blasr skipping about half of the simulated reads when I used blasr to align simulated reads to EColi genome. Here are the commands:

$./download_and_align.sh
$ cat learn_and_simulate.sh
#!/usr/bin/env bash

#$ -cwd
#$ -V
#$ -S /bin/bash
#$ -l h_vmem=40g
#$ -e ecoli_longislnd.e
#$ -o ecoli_longislnd.o
#$ -q bina.q

longislnd_sample.py --model_dir model --flank 3 --reference polished_assembly.fasta --input_suffix fofn.cmp.h5
longislnd_simulate.py --model_dir model --fasta polished_assembly.fasta --coverage 1
$qsub learn_and_simulate.sh
#after it was done
$cd out
$blasr -bam $PWD/m160923_095320_00000_cclrbam_p6_s1_p0.bam $PWD/../polished_assembly.fasta -out $PWD/simulated_on_ecoli.bam
manpath: warning: $MANPATH set, ignoring /etc/man_db.conf
/home/users/guoy28/.bashrc: line 45: bind: warning: line editing not enabled
[INFO] 2016-09-23T14:18:02 [blasr] started.
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/10/0_5224
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/10/5269_7062
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/12/0_11455
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/12/11500_16318
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/14/0_2814
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/14/2859_5675
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/14/5720_8550
...
Skipping an invalid read m160923_095320_00000_cclrbam_p6_s1_p0/379/28172_30169
[INFO] 2016-09-23T14:19:19 [blasr] ended.

Thanks.

Best, Yunfei

[bayolau]

Dear @yunfeiguo,

Thank you for your interest and also trying it out. Please try out v0.9.3 and let us know if it fits your needs. Note that you don't have to rebuild the sampling_example directory. If you're using the binary release, you can simply copy the jar file over from the target directory. If you're using a checkout, simply git pull from the master branch then execute mvn package.

[yunfeiguo]

It's working perfectly now! Thanks!