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alekseyzimin / masurca

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mega_reads_assemble_cluster2.sh failed to run flye #282

Open Jung19911124 opened 2 years ago

Jung19911124 commented 2 years ago

Hi, I used MaSuRCA 4.0.8 on my Ubuntu 20.04 LTS system to assemble an insect genome (approximately 460Mb). illumina short reads (x100) and Nanopore long reads (x100) were submitted to the pipeline, but I got the error at the flye stage.

I have two questions.

  1. What is possible explanation for this situation?
  2. Is it possible to resume the assembly process from the flye stage?

Any advice would be appreciated. Thanks in advance!

[Sun Apr 10 17:01:27 JST 2022] Processing pe library reads [Sun Apr 10 17:30:04 JST 2022] Average PE read length 149 [Sun Apr 10 17:30:04 JST 2022] Using kmer size of 99 for the graph [Sun Apr 10 17:30:05 JST 2022] MIN_Q_CHAR: 33 [Sun Apr 10 17:30:05 JST 2022] Creating mer database for Quorum [Sun Apr 10 18:01:49 JST 2022] Error correct PE [Mon Apr 11 01:17:28 JST 2022] Estimating genome size [Mon Apr 11 02:04:27 JST 2022] Estimated genome size: 352628472 [Mon Apr 11 02:04:27 JST 2022] Creating k-unitigs with k=99 [Mon Apr 11 13:05:50 JST 2022] Computing super reads from PE [Mon Apr 11 17:58:47 JST 2022] Using Flye from /path/to/MaSuRCA-4.0.8/bin/../Flye/bin [Mon Apr 11 17:58:48 JST 2022] Running mega-reads correction/assembly [Mon Apr 11 17:58:48 JST 2022] Using mer size 17 for mapping, B=15, d=0.02 [Mon Apr 11 17:58:48 JST 2022] Estimated Genome Size 352628472 [Mon Apr 11 17:58:48 JST 2022] Estimated Ploidy 1 [Mon Apr 11 17:58:48 JST 2022] Using 60 threads [Mon Apr 11 17:58:48 JST 2022] Output prefix mr.99.17.15.0.02 [Mon Apr 11 17:58:48 JST 2022] Creating k-unitigs for k=19 [Mon Apr 11 18:43:54 JST 2022] Pre-correcting long reads [Tue Apr 12 23:21:36 JST 2022] Pre-corrected reads are in longest_reads.25x.fa [Tue Apr 12 23:21:56 JST 2022] Computing mega-reads [Tue Apr 12 23:21:57 JST 2022] Running locally in 1 batch [Sat Apr 16 00:14:36 JST 2022] Refining alignments [Sat Apr 16 00:44:47 JST 2022] Computing allowed merges [Sat Apr 16 00:45:40 JST 2022] Joining [Sat Apr 16 01:02:15 JST 2022] Gap consensus [Sat Apr 16 01:37:03 JST 2022] Running assembly with Flye /path/to/MaSuRCA-4.0.8/bin/mega_reads_assemble_cluster2.sh: line 654: cd: flye.mr.99.17.15.0.02: No such file or directory [Sat Apr 16 01:37:03 JST 2022] Assembly with flye failed, see files under flye/

andrzej-grz commented 2 years ago

I have just experienced similar issue. Check please in flye.log whether it is an issue of python version. In my case a solution was to restart ./assembly.sh under environment with python 2.7.