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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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truncated output, with no errors in log #118

Closed swomics closed 5 years ago

swomics commented 5 years ago

Hi,

I downloaded the latest version with git clone (Version: 2.4.1 (20190603)) and had no problems compiling. However when I ran the first step the output appeared truncated and no errors had been indicated in the program log. I used a colleagues older version, which so far seems to have run with no problems (Version: 2.4 (20190312))

Output files from Version: 2.4.1 (20190603): dbg2.1.dot.gz dbg2.1.nodes dbg2.1.reads dbg2.2.dot.gz dbg2.alignments.gz dbg2.binkmer dbg2.closed_bins dbg2.clps dbg2.events dbg2.kmerdep

Output files from Version: 2.4 (20190312): dbg3.1.dot.gz dbg3.1.nodes dbg3.1.reads dbg3.2.dot.gz dbg3.3.dot.gz dbg3.alignments.gz dbg3.binkmer dbg3.closed_bins dbg3.clps dbg3.ctg.dot.gz dbg3.ctg.lay.gz dbg3.events dbg3.frg.dot.gz dbg3.frg.nodes dbg3.kmerdep dbg3.raw.fa

ruanjue commented 5 years ago

Could you paste the log message just start from aligning, like this

** PROC_STAT(0) **: real 12.441 sec, user 60.050 sec, sys 6.820 sec, maxrss 1235264.0 kB, maxvsize 2619364.0 kB
[Mon Jun 17 17:50:36 2019] Done
13727 reads|total hits 141255
...
swomics commented 5 years ago

Sure, no problem

PROC_STAT(0) : real 1212.565 sec, user 32861.680 sec, sys 1496.460 sec, maxrss 143411248.0 kB, maxvsize 188739692.0 kB [Sun Jun 16 00:09:27 2019] Done 1115003 reads|total hits 637435622 PROC_STAT(0) : real 31996.932 sec, user 1856597.060 sec, sys 29821.320 sec, maxrss 173516960.0 kB, maxvsize 234157660.0 kB [Sun Jun 16 08:42:31 2019] sorting rdhits ... Done [Sun Jun 16 08:42:40 2019] clipping ... 15.00% bases [Sun Jun 16 08:42:43 2019] generating regs ... 3227759326 [Sun Jun 16 08:47:37 2019] sorting regs ... Done [Sun Jun 16 08:49:18 2019] generating intervals ... 43100040 intervals [Sun Jun 16 08:49:47 2019] selecting important intervals from 43100040 intervals [Sun Jun 16 09:01:37 2019] Intervals: kept 2403709, discarded 40696331 PROC_STAT(0) : real 33142.716 sec, user 1861639.000 sec, sys 30703.800 sec, maxrss 173516960.0 kB, maxvsize 245222452.0 kB [Sun Jun 16 09:01:37 2019] Done, 2403709 nodes [Sun Jun 16 09:01:37 2019] output "dbg2.1.nodes". Done. [Sun Jun 16 09:01:52 2019] median node depth = 6 [Sun Jun 16 09:01:52 2019] masked 5437 high coverage nodes (>200 or <3) [Sun Jun 16 09:01:56 2019] masked 50128 repeat-like nodes by local subgraph analysis [Sun Jun 16 09:01:56 2019] generating edges [Sun Jun 16 09:04:15 2019] Done, 72424897 edges [Sun Jun 16 09:04:15 2019] output "dbg2.1.reads". Done. [Sun Jun 16 09:04:36 2019] output "dbg2.1.dot.gz". Done. [Sun Jun 16 09:06:01 2019] graph clean [Sun Jun 16 09:06:05 2019] rescued 106849 low cov edges [Sun Jun 16 09:06:09 2019] deleted 2562 binary edges [Sun Jun 16 09:06:10 2019] deleted 505982 isolated nodes [Sun Jun 16 09:06:17 2019] cut 122740 transitive edges [Sun Jun 16 09:06:18 2019] output "dbg2.2.dot.gz". Done.

ruanjue commented 5 years ago

I am afraid it was cause by recently introduced function rescue_high_cov_edges_graph. I will fix it and notice you. Thanks for bug reporting.

ruanjue commented 5 years ago

Please have a try with https://github.com/ruanjue/wtdbg2/commit/6f76ff1fac7bb8b45f81a11859283fd2bda45046 .

swomics commented 5 years ago

Hi,

All the output files seem to be present and the output log looks complete. Thanks for the quick fix!

dbg4.1.dot.gz dbg4.1.nodes dbg4.1.reads dbg4.2.dot.gz dbg4.3.dot.gz dbg4.alignments.gz dbg4.binkmer dbg4.closed_bins dbg4.clps dbg4.ctg.dot.gz dbg4.ctg.lay.gz dbg4.events dbg4.frg.dot.gz dbg4.frg.nodes dbg4.kmerdep