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Hello,
I am running Masurca 4.1.0 with Illumina and ONT reads, but after the "Joining" step I get the below errors. Masurca correctly estimates the genome size but can't seem to join the mega-reads. Any ideas if these errors are fixable?
MaSuRCA-4.1.0/bin/masurca -t 80 -i RawIllumina/Bio2242476_1_trimmed.fastq.gz,RawIllumina/Bio2242476_2_trimmed.fastq.gz -r Nanopore/HMminionreads.fastq
Verifying PATHS...
jellyfish OK
runCA OK
createSuperReadsForDirectory.perl OK
creating script file for the actions...done.
execute assemble.sh to run assembly
[Thu 23 Nov 2023 11:00:29 AM AST] Processing pe library reads
[Thu 23 Nov 2023 11:00:29 AM AST] Average PE read length 148
[Thu 23 Nov 2023 11:00:29 AM AST] Using kmer size of 49 for the graph
[Thu 23 Nov 2023 11:00:30 AM AST] MIN_Q_CHAR: 33
WARNING: JF_SIZE set too low, increasing JF_SIZE to at least 5705008487, this automatic increase may be not enough!
[Thu 23 Nov 2023 11:00:30 AM AST] Estimated genome size: 2028949031
[Thu 23 Nov 2023 11:00:30 AM AST] Computing super reads from PE
[Thu 23 Nov 2023 11:00:30 AM AST] Using CABOG from /home/mcrg/MaSuRCA-4.1.0/bin/../CA8/Linux-amd64/bin
[Thu 23 Nov 2023 11:00:30 AM AST] Running mega-reads correction/assembly
[Thu 23 Nov 2023 11:00:30 AM AST] Using mer size 17 for mapping, B=15, d=0.02
[Thu 23 Nov 2023 11:00:30 AM AST] Estimated Genome Size 2028949031
[Thu 23 Nov 2023 11:00:30 AM AST] Estimated Ploidy 2
[Thu 23 Nov 2023 11:00:30 AM AST] Using 80 threads
[Thu 23 Nov 2023 11:00:30 AM AST] Output prefix mr.49.17.15.0.02
[Thu 23 Nov 2023 11:00:30 AM AST] Computing allowed merges
[Thu 23 Nov 2023 11:00:30 AM AST] Joining
read sequence for not found
[Thu 23 Nov 2023 11:00:51 AM AST] mega-reads joining failed
[Thu 23 Nov 2023 11:00:51 AM AST] mega-reads exited before assembly
The text was updated successfully, but these errors were encountered:
Hello,
I am running Masurca 4.1.0 with Illumina and ONT reads, but after the "Joining" step I get the below errors. Masurca correctly estimates the genome size but can't seem to join the mega-reads. Any ideas if these errors are fixable?
MaSuRCA-4.1.0/bin/masurca -t 80 -i RawIllumina/Bio2242476_1_trimmed.fastq.gz,RawIllumina/Bio2242476_2_trimmed.fastq.gz -r Nanopore/HMminionreads.fastq
Verifying PATHS...
jellyfish OK
runCA OK
createSuperReadsForDirectory.perl OK
creating script file for the actions...done.
execute assemble.sh to run assembly
[Thu 23 Nov 2023 11:00:29 AM AST] Processing pe library reads
[Thu 23 Nov 2023 11:00:29 AM AST] Average PE read length 148
[Thu 23 Nov 2023 11:00:29 AM AST] Using kmer size of 49 for the graph
[Thu 23 Nov 2023 11:00:30 AM AST] MIN_Q_CHAR: 33
WARNING: JF_SIZE set too low, increasing JF_SIZE to at least 5705008487, this automatic increase may be not enough!
[Thu 23 Nov 2023 11:00:30 AM AST] Estimated genome size: 2028949031
[Thu 23 Nov 2023 11:00:30 AM AST] Computing super reads from PE
[Thu 23 Nov 2023 11:00:30 AM AST] Using CABOG from /home/mcrg/MaSuRCA-4.1.0/bin/../CA8/Linux-amd64/bin
[Thu 23 Nov 2023 11:00:30 AM AST] Running mega-reads correction/assembly
[Thu 23 Nov 2023 11:00:30 AM AST] Using mer size 17 for mapping, B=15, d=0.02
[Thu 23 Nov 2023 11:00:30 AM AST] Estimated Genome Size 2028949031
[Thu 23 Nov 2023 11:00:30 AM AST] Estimated Ploidy 2
[Thu 23 Nov 2023 11:00:30 AM AST] Using 80 threads
[Thu 23 Nov 2023 11:00:30 AM AST] Output prefix mr.49.17.15.0.02
[Thu 23 Nov 2023 11:00:30 AM AST] Computing allowed merges
[Thu 23 Nov 2023 11:00:30 AM AST] Joining
read sequence for not found
[Thu 23 Nov 2023 11:00:51 AM AST] mega-reads joining failed
[Thu 23 Nov 2023 11:00:51 AM AST] mega-reads exited before assembly
The text was updated successfully, but these errors were encountered: