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xiaochuanle / MECAT

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads
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problem with ‘failed to adjust overlap error rates’ #21

Open Mr-Inamn opened 7 years ago

Mr-Inamn commented 7 years ago

Hi，when I tried mecat to assemble PacBio reads. The same problem happened again. The mecat version which I used is v1.2. And the command is as follows.

date
mecat2pw -j 0 -d 00.data/Emu_F_Pacbio_Copenhagen_merge_all.fastq -w wk.dir -t 24 -o emu.fastq.pm.can -n 50 -a 2000 -k 4 -g 0 -x 0
date
mecat2cns -x 0 -i 0 -t 24 -p 100000 -r 0.9 -a 2000 -c 6 -l 7000 emu.fastq.pm.can 00.data/Emu_F_Pacbio_Copenhagen_merge_all.fastq emu.corrected.fa
date
mecat2canu -trim-assemble -d wk_result -p emu errorRate=0.015 genomeSize=1.3g maxMemory=200 maxThreads=24 useGrid=0 Overlapper=mecat2asmpw -pacbio-corrected emu.corrected.fa
date

But when it comes to mecat2canu step. Error appears that as follows. But there is no *.oea file in the directory. Could anyone give me some help. Many thanks.

61 overlap error adjustment jobs failed: /public/home/lijing/01.sd.project/01.genome/01.assembly/02.mecat/01.emu_copenhagen/wk_result/unitigging/3-overlapErrorAdjustment/0001.oea FAILED. ... Don't panic, but a mostly harmless error occurred and canu failed. canu failed with 'failed to adjust overlap error rates. Made 2 attempts, jobs still failed'.

Mr-Inamn commented 7 years ago

Did mecat need canu installed? My canu version is v1.4 right now.

Mr-Inamn commented 7 years ago

Moreover, I have tested ecoli pacbio reads with mecat. There is no problem. The only difference between ecoli pipeline and my pipeline is the third step. I did not extract sequence from the corrected reads generated in step 2. Instead, I used all the corrected reads for assembly? Does this matter?

Mr-Inamn commented 7 years ago

Then I tried MECAT step by step. The first 2 steps have no problem. And after that, I will get the corrected reads. But when I run the third step. Nothing result will be returned. The command is extract_sequences emu.corrected.fa emu.corrected.fa_40x 1300000000 40. And the log is as follows. Can anyone give me some help? Many thanks. @xiaochuanle

Sun Sep 24 13:58:59 CST 2017 step 1: convert fasta to fastq step 2: convert fastq to CA step 3

Starting file 'emu.corrected.fa.fastq.libname.frg'.

Processing SINGLE-ENDED SANGER QV encoding reads from: '/public/home/lijing/01.sd.project/01.genome/01.assembly/02.mecat/01.emu_copenhagen/emu.corrected.fa.fastq'

GKP finished with no alerts or errors.

step 4 Longest picked cutoff: 7637 Scanning store to find libraries used. Added 0 reads to maintain mate relationships. Dumping 0 fragments from unknown library (version 1 has these) Dumping 3675917 fragments from library IID 1 step 5 Longest picked cutoff: 7637 Scanning store to find libraries used and reads to dump. Added 0 reads to maintain mate relationships. Dumping 0 fragments from unknown library (version 1 has these) Dumping 3675917 fragments from library IID 1 Sun Sep 24 15:01:45 CST 2017

fhu2008-tio commented 6 years ago

i met the same problem as you met, run the extract_sequences command. there were no errors, no warnings, also no results file generated.

I write to the author a few weeks ago, no messages were received.