bs3 killed and no output

[AdrianS85]

Hello!

Im trying to use BS-seeker3 for my experiment. Unfortunately, I am getting an error "Loading index from directory... Killed" and also no output is produced despite successful (?) alignment. I know that others have raised this issue, but I figured my case may be a bit different.

SOME RELEVANT INFORMATION:

• ps3_build seemed to work well, without any problems.
• My reads are paired, around 75 bp of length.
• I am working on Singularity-Ubuntu:18.04
• Seed size is 16.
• I have about 200GB RAM available
• Command that I used:

python ./bs3-align.py --snap-t 10 -1 ../read1.fq_trimmed.fq.gz -2 ../read2.fq_trimmed.fq.gz -g mm10ucsc.fa -f sam -o ./FullBS3test.sam -d reference_genome/

THE OUTPUT:

     BS-Seeker3 beta

Welcome to SNAP version 1.0dev.97.

Loading index from directory... Welcome to SNAP version 1.0dev.97.

Loading index from directory... Welcome to SNAP version 1.0dev.97.

Loading index from directory... Welcome to SNAP version 1.0dev.97.

Loading index from directory... Welcome to SNAP version 1.0dev.97.

Loading index from directory... Welcome to SNAP version 1.0dev.97.

Loading index from directory... Welcome to SNAP version 1.0dev.97.

Loading index from directory... Welcome to SNAP version 1.0dev.97.

Loading index from directory... Killed
Killed
625s.  1166842752 bases, seed size 16
436s.  1166842752 bases, seed size 16
562s.  1166842752 bases, seed size 16
688s.  1166842752 bases, seed size 16
Aligning.
Aligning.
Aligning.
Aligning.
Killed
619s.  1166842752 bases, seed size 16
668s.  1166842752 bases, seed size 16
Aligning.
Aligning.
Killed
619s.  1166842752 bases, seed size 16
668s.  1166842752 bases, seed size 16
Aligning.
Aligning.
Killed
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns  %Pairs    Reads/s   Time in Aligner (s)
4,800,256      2,927,452 (60.99%)     543,465 (11.32%)       582,544 (12.14%)       746,795 (15.56%)       29.40%    1,414     3,394
(None, None)
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns  %Pairs    Reads/s   Time in Aligner (s)
6,400,000      3,905,781 (61.03%)     722,389 (11.29%)       778,360 (12.16%)       993,470 (15.52%)       29.39%    1,550     4,126
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns  %Pairs    Reads/s   Time in Aligner (s)
6,400,000      3,887,135 (60.74%)     725,278 (11.33%)       776,962 (12.14%)       1,010,625 (15.79%)     29.07%    1,549     4,132
Total Reads    Aligned, MAPQ >= 10    Aligned, MAPQ < 10     Unaligned              Too Short/Too Many Ns  %Pairs    Reads/s   Time in Aligner (s)
6,400,000      3,902,420 (60.98%)     724,141 (11.31%)       778,564 (12.17%)       994,875 (15.54%)       29.51%    1,634     3,916
(None, None)
(None, None)
(None, None)
(None, None)
(None, None)
(None, None)
(None, None)

        BS-seeker3 Result

        Final Alignment Report
================================================

Number of reads in total: 49600256
Number of unique-hits reads (before post-filtering): 0
Number of reads mapped after post-filtering 0

Alignment Time: 5107.08876896secs

        Final Cytosine Report
================================================

Total Number of Cytosines: 0
Total Number of Cs in CpG context: 0
Total Number of Cs in CHG context: 0
Total Number of Cs in CHH context: 0

Rate of Methylation
 mCG  0.000%
 mCHG  0.000%
 mCHH  0.000%

I will be thankful for response!

Best
Adrian

[whirlsyu]

I encountered the same issue, which give me empty results with 0 Cytosine site