User: langziv

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langziv0
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Posts by langziv

<prev • 23 results • page 1 of 3 • next >
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Comment: C: mauve alignment results meaning
... The assembler we used was IDBA-UD. The genome size is about 1.4E9 (9 digits) bp. I read that the latest mauve version is suited for large genomes as well. ...
written 4 days ago by langziv0
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Comment: C: mauve alignment results meaning
... Thanks for the reply. It is an assembly. That's the amount of contigs we got after using programs such as cutadat, trimmomatic and bwa, among others. I don't know if it's normal or not. My PI seems ok with that. She's the experienced one in doing assemblies. All the programs we used ran fine. Ther ...
written 6 days ago by langziv0
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mauve alignment results meaning
... Hi. The alignment representation makes me think the 2 aligned genomes have no matching sequences, since I haven't seen such results when I searched for mauve results. The alignment results image: These two genomes are from 2 distinct samples that are of the same organism, so they are expected ...
progressivemauve mauve written 6 days ago by langziv0 • updated 6 days ago by zx87549.9k
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mauveAligner outputs empty .mauve files and no .alignment files
... Hi. I'm running mauveAligner with 2 genomes from the same species that might belong to 2 different strains. I'm also getting an error message: `Clust::SetLeafCount(0)`. /mauveAligner --output=genomes1_2.mauve \ --output-alignment=genomes1_2.alignment \ /output/mauve/genome1.fa /output/ ...
mauvealigner command-line mauve written 9 days ago by langziv0
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Comment: C: Getting "Floating point exception (core dumped)" when running mauveAligner
... The command I gave was inadequate. I didn't provide an sml file path. Once I did I managed to call mauve from a python script, but now I got a new issue. I'm getting the message: "*** ERROR *** Clust::SetLeafCount(0)" after mauve read the fasta files. The command is /mauveAligner --output=bwt ...
written 10 days ago by langziv0
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Comment: C: Getting "Floating point exception (core dumped)" when running mauveAligner
... Sorry about the delay. These are crazy days. Yes. I'm runnnig 2 assemblies in every run. I just thought about it again, and I realize I can run multiple genomes to align with another genome, but since those are very big files, maybe I should stay with 2 genomes in every run. The genomes' sizes are ...
written 10 days ago by langziv0
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Comment: C: Getting "Floating point exception (core dumped)" when running mauveAligner
... The data sets are of whole assemblies. I'm not sure if I can break them into smaller files. When I run the bash script there's no error file created. The error message I mentioned in the question appears when I run the command on a linux node. Actually, when I run the bash script an empty output fi ...
written 13 days ago by langziv0
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Comment: C: Getting "Floating point exception (core dumped)" when running mauveAligner
... I'm not sure. I'm adding the bash script in which there are various parameters, including memory usage. ...
written 13 days ago by langziv0
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Getting "Floating point exception (core dumped)" when running mauveAligner
... Hi. When I run the following command I get a "Floating point exception (core dumped)": `/linux-x64/mauveAligner --output=/mauve/output.mauve --output-alignment=/mauve/output.alignment`. The bash script that calls the relevant python script: #!/bin/bash #PBS -q name #PBS -N mauve ...
mauvealigner floating-point-exception mauve written 13 days ago by langziv0
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Comment: C: Running mauveAligner in Linux
... I installed mauve myself and now it runs. Thanks. ...
written 13 days ago by langziv0

Latest awards to langziv

Scholar 11 weeks ago, created an answer that has been accepted. For A: Getting irregular bam files when running bowtie2 with the -un-conc command

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