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alekseyzimin / masurca

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Error correct PE & Failed to pre-correct long reads #259

Open minjinhan opened 2 years ago

minjinhan commented 2 years ago

Hi, I tried to use MaSuRCA-4.0.5 to assemble a insect genome(~500Mb) on centos 8 system with 512 G Mem. We have 30x Illumina PE reads and 60x pacbio reads. But I encounter error correct PE and Failed to pre-correct long reads (please see below).

[02:31:36 CST] Processing pe library reads [02:37:53 CST] Average PE read length 150 [02:37:53 CST] Using kmer size of 99 for the graph [02:37:54 CST] MIN_Q_CHAR: 33 [02:37:54 CST] Creating mer database for Quorum [02:45:02 CST] Error correct PE [03:02:06 CST] Estimating genome size [03:05:03 CST] Estimated genome size: 410539653 [03:05:03 CST] Creating k-unitigs with k=99 [03:12:00 CST] Computing super reads from PE flye 1 [03:38:10 CST] Using Flye from /home/user01/tools/MaSuRCA-4.0.5/bin/../Flye/bin [03:38:10 CST] Running mega-reads correction/assembly [03:38:10 CST] Using mer size 17 for mapping, B=15, d=0.02 [03:38:10 CST] Estimated Genome Size 410539653 [03:38:10 CST] Estimated Ploidy 1 [03:38:10 CST] Using 150 threads [03:38:10 CST] Output prefix mr.99.17.15.0.02 [03:38:10 CST] Creating k-unitigs for k=19 [03:42:39 CST] Pre-correcting long reads [03:46:19 CST] Failed to pre-correct long reads, please check your input files /data2/Pacbio_reads.fasta and pe.cor.fa and the other parameters [03:46:19 CST] Failed to pre-correct /data2/Pacbio_reads.fasta file, please check your data! [03:46:19 CST] Assembly with flye failed, see files under flye/

dlavrov commented 2 years ago

I got the same error. Apparently, you need to install/load numactl. Masurca is running again. Fingers crossed.

vanessa63104 commented 1 year ago

Bonjour Je suis novice dans le domaine....Pouvez vous m'aider? Je bloque toujours à cette étape: [mercredi 4 janvier 2023, 11:15:33 (UTC+0100)] Output prefix mr.99.17.15.0.02 [mercredi 4 janvier 2023, 11:15:33 (UTC+0100)] Creating k-unitigs for k=19 [mercredi 4 janvier 2023, 11:21:21 (UTC+0100)] Pre-correcting long reads [mercredi 4 janvier 2023, 11:40:09 (UTC+0100)] Failed to pre-correct /data/MaSuRCA-4.0.9/bin/xx.fastq file, please check your data! [mercredi 4 janvier 2023, 11:40:09 (UTC+0100)] Assembly with flye failed, see files under flye/

J'ai installé numactl et j'ai relancé assemble.sh mais j'ai toujours le même problème.