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alekseyzimin / masurca

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errors at the begining of hybrid assembly using Masurca #239

Open Hedi65 opened 3 years ago

Hedi65 commented 3 years ago

Hi

im trying to make hybrid assembly for Ecoli using MiSeq and Nanopore data in Masurca. currently i m getting two errors marked in Bold bellow. my MinION fastq files should be OK, no idea why im getting such errors.

any helps would be appreciate.

/Downloads/MaSuRCA-4.0.3/bin/masurca -t 32 -i MiSeq_R1.fastq MiSeq_R2.fastq -r MinION.fastq

Verifying PATHS... jellyfish OK runCA OK createSuperReadsForDirectory.perl OK creating script file for the actions...done. execute assemble.sh to run assembly [fr. 04. juni 15:42:56 +0200 2021] Processing pe library reads [fr. 04. juni 15:42:56 +0200 2021] Average PE read length 250 [fr. 04. juni 15:42:56 +0200 2021] Using kmer size of 127 for the graph [fr. 04. juni 15:42:56 +0200 2021] MIN_Q_CHAR: 33 [fr. 04. juni 15:42:56 +0200 2021] Estimated genome size: 5058150 [fr. 04. juni 15:42:56 +0200 2021] Computing super reads from PE [fr. 04. juni 15:42:56 +0200 2021] Using CABOG from /Downloads/MaSuRCA-4.0.3/bin/../CA8/Linux-amd64/bin [fr. 04. juni 15:42:56 +0200 2021] Running mega-reads correction/assembly [fr. 04. juni 15:42:56 +0200 2021] Using mer size 17 for mapping, B=15, d=0.02 [fr. 04. juni 15:42:56 +0200 2021] Estimated Genome Size 5058150 [fr. 04. juni 15:42:56 +0200 2021] Estimated Ploidy 1 [fr. 04. juni 15:42:56 +0200 2021] Using 32 threads [fr. 04. juni 15:42:56 +0200 2021] Output prefix mr.41.17.15.0.02 [fr. 04. juni 15:42:56 +0200 2021] Pre-correction and initial filtering of the long reads [fr. 04. juni 15:42:57 +0200 2021] Failed to pre-correct MinION.fastq file, please check your data! [fr. 04. juni 15:42:57 +0200 2021] mega-reads exited before assembly

diogomilanesi commented 3 years ago

Same problem here. In an older 3.4.2 version no error appears, but newer ones always fail at this point.

ricardo-aaron commented 3 years ago

Same problem here with version 4.0.3 and nanopore reads.

FlintMitchell commented 3 years ago

Same problem here using v4.0.4 trying to do hybrid short+long assembly. Any update on this? I will try using a v3.x.x distribution.

eriled commented 3 years ago

Hi, I also seem to have the same issue. It seems to come from line 2 of this script: correct_with_k_unitigs.sh The problem is also mentioned in the file: create_mega-reads.err I get the message: command numactl not found

I am not sure how to fix it though.

valery-shap commented 3 years ago

The same error with 4.0.4 with Illumina and nanopore data Upd package numactl must be installed.