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Socket timeout while opening Blueprint FTP links.
E.g. try `ftp://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_progenitor_methylomes/rna/RNA_D1_CLP_100.bw`
Not clear why it happening. But the p…
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Using GATK jar /usr/local/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_writ…
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Hi there,
1. Does exomiser support only certain vcf file format and above?
2. Exomiser v14.0.0 is not recognizing unstructured key meta-information line with key as “##META” as a valid header line…
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This my command:
`java -Xmx1000g -jar /.../abra2-2.24-0/abra2.jar --sa --cons --amq 32 --in in.bam --out out.bam --ref ~/.../XENLA_9.2_genome.fa --threads 50 --targets /.../X9.2_opt_SORTED.bed --tm…
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This is related a bit with #520 (which I'm still looking forward to be approve by the maintainers), but it could still be done in the current API status. My idea is that while importing HTSJDK for a p…
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Anywhere in fgbio we need to access FASTA for reference genomes or similar we end up using HTSJDK's `ReferenceSequenceFile` and related classes (`ReferenceSequenceFileFactory`, `ReferenceSequence`). …
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There's quite a lot of business logic in `VCFOutput` around [here](https://github.com/hammerlab/guacamole/blob/master/src/main/scala/org/hammerlab/guacamole/commands/jointcaller/VCFOutput.scala#L135) …
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Hi,
I'd like to view VCFs from the 1000 Genomes Project in IGV (version 2.17.4 with Java included) but a couple of them won't load, with an error message:
"Error loading [URL]: Unable to parse h…
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Here's the cryptic error message when we try and run `RevertSam` with `I=/dev/stdin`. Full command line:
```
RevertSam INPUT=/dev/stdin OUTPUT=/dev/stdout SORT_ORDER=queryname RESTORE_ORIGINAL_Q…
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File `/Users/Oleg.Shpynov/Desktop/2021_comparative_analysis/fdr0.05/H1_H3K79me2_2_1__broad0.05_peaks.broadPeak` is zero bytes long.
```
[Aug 24, 2021 14:12:45] ERROR TrackViewLoader Cannot load Tr…
olegs updated
3 years ago