Error in tabulation of example

[jvhaarst]

I have tried running the example through bwa-meth, but I fail at the tabulation step, any idea what goes wrong ?

jvh@host:/location_on_disk/bwa-meth/example$ ../bwameth.py index ref.fa
converting c2t in ref.fa to ref.fa.bwameth.c2t
indexing: ref.fa.bwameth.c2t
jvh@host:/location_on_disk/bwa-meth/example$ ../bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz -t 12
running: bwa mem -T 40 -B 3 -L 25 -CM -U 100 -p -R '@RG ID:t_R  SM:t_R' -t 12  ref.fa.bwameth.c2t '</usr/bin/python ../bwameth.py c2t t_R1.fastq.gz t_R2.fastq.gz'
writing to:
samtools view -bS - | samtools sort -@3 - bwa-meth
converting reads in t_R1.fastq.gz,t_R2.fastq.gz
[M::main_mem] read 92726 sequences (9365326 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44884, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (109, 137, 175)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 307)
[M::mem_pestat] mean and std.dev: (145.08, 48.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 373)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[main] Version: 0.7.6a-dev-r434
[main] CMD: bwa mem -T 40 -B 3 -L 25 -CM -U 100 -p -R @RG       ID:t_R  SM:t_R -t 12 ref.fa.bwameth.c2t </usr/bin/python ../bwameth.py c2t t_R1.fastq.gz t_R2.fastq.gz
[main] Real time: 9.615 sec; CPU: 16.204 sec
running: samtools index bwa-meth.bam
[E::hts_idx_push] chromosome blocks not continuous
jvh@host:/location_on_disk/bwa-meth/example$ samtools flagstat bwa-meth.bam
92791 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
92723 + 0 mapped (99.93%:-nan%)
92791 + 0 paired in sequencing
46399 + 0 read1
46392 + 0 read2
92276 + 0 properly paired (99.44%:-nan%)
92652 + 0 with itself and mate mapped
71 + 0 singletons (0.08%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
jvh@host:/location_on_disk/bwa-meth/example$ ../bwameth.py tabulate  --trim 3,3 --map-q 60 --bissnp $BISSNP --prefix ex -t 12 --reference ref.fa bwa-meth.bam
Traceback (most recent call last):
  File "../bwameth.py", line 500, in <module>
    main(sys.argv[1:])
  File "../bwameth.py", line 475, in main
    sys.exit(tabulate_main(args[1:]))
  File "../bwameth.py", line 407, in tabulate_main
    % a.reference)
AssertionError: run samtools faidx ref.fa

[brentp]

Yes, you need to run

samtools faidx ref.fa

before calling tabulate. I will make this error more explicit.

[brentp]

@jvhaarst did this resolve it for you?

[jvhaarst]

Yes. I just tested the example, and I got exactly the same result.

On Thu, Feb 20, 2014 at 9:37 PM, Brent Pedersen - Bioinformatics < notifications@github.com> wrote:

@jvhaarst https://github.com/jvhaarst did this resolve it for you?

— Reply to this email directly or view it on GitHubhttps://github.com/brentp/bwa-meth/issues/1#issuecomment-35666050 .

Dag, Jan

[brentp]

closing this. if you have further problems, please re-open.