User: rioualen

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rioualen190
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Posts by rioualen

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Answer: A: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... In case someone else is running into this issue, using shortcuts for params names avoids the problem: `-q` instead of `--qual-threshold` and `-l` instead of `--length-threshold`, specifically. So in my case the problem was not related to my VM, but to the fact that my VM was using another version ...
written 12 days ago by rioualen190
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... I'm sorry but I'm not the one who wrote Sickle, that's why I actually need help... ...
written 3 months ago by rioualen190
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... case 'q': single_qual_threshold = atoi(optarg); if (single_qual_threshold < 0) { fprintf(stderr, "Quality threshold must be >= 0\n"); return EXIT_FAILURE; } break; case 'l': single_leng ...
written 3 months ago by rioualen190
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... int single_qual_threshold = 20; int single_length_threshold = 20; static struct option single_long_options[] = { {"fastq-file", required_argument, 0, 'f'}, {"output-file", required_argument, 0, 'o'}, {"qual-type", required_argument, 0, 't'}, {"qual-th ...
written 3 months ago by rioualen190
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... They look normal, and again I've ran this tool on these specific files lots of times before. ...
written 3 months ago by rioualen190
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Comment: C: "Segmentation fault (core dumped)" using sickle for trimming, depending on optio
... The VM has 4 CPUs and 8Go of RAM, and I've ran it successfully in smaller VMs before. Also, I don't get why just changing the name of the parameter is generating this type of error. ...
written 3 months ago by rioualen190
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"Segmentation fault (core dumped)" using sickle for trimming, depending on options used
... Hello, I'm running into "Segmentation fault (core dumped)" error when running a workflow with (or without) snakemake. I've used the same data, same tools and same parameters on several machines without a problem before. Now the problem arises on a Ubuntu 14.04 virtual machine (4 CPU, 8Go RAM), w ...
trimming virtual-machine sickle written 3 months ago by rioualen190
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Comment: C: Using the Homer suite with conda
... Thank you, that's the kind of plan I have for the future, but I have dozens of Snakemake rules and my workflows are available publicly, so it's gonna take a while until I do all of this properly. Like I said, I'm a total newbie with Conda and many of the software I'm using don't have Conda recipes. ...
written 4 months ago by rioualen190
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Comment: C: Using the Homer suite with conda
... I'm using python 3.5 cause I'm using snakemake, but I understand it is not possible to use both python versions in one environment? ...
written 4 months ago by rioualen190
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Comment: C: Using the Homer suite with conda
... Oh thanks, I'll look into that! Eventually my point is to use many peak-calling tools, and that includes Homer... Besides, I wanted to use Macs2 but it raises conflict with python 2 and 3! I've also tried other peak-callers outside Conda but they're super annoying to install and they definitely a ...
written 4 months ago by rioualen190

Latest awards to rioualen

Scholar 12 days ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Student 5 months ago, asked a question with at least 3 up-votes. For Differences between trimming tools: cutadapt, bbduk and sickle
Popular Question 15 months ago, created a question with more than 1,000 views. For Get chromosome sizes from fasta file
Scholar 20 months ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans
Scholar 2.2 years ago, created an answer that has been accepted. For A: Get chromosome name from RefSeq format for C.elegans

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