mihinduk

Here is the log you asked for: [2020-12-23 09:15:03.933246] ERROR: DIAMOND finished abnormally. # CAT v5.0.4. CAT is running. Protein prediction, alignment, and contig classification are carried out. Rarw! Supplied...

I have solved the problem for PE data by setting -T 2 and requesting more memory based on the stats generated by running /usr/bin/time -v . For SE data, if...

I would try increasing the amount of memory you request: Dataset | tissue | samples | Cores | time | Max mem MSBB | BM10 | 325 | 2 |...

The second error is on SE data. It takes more memory and time than the PE data. I was able to get this to run locally, but not yet on...

Hi Tobias, Do you have any idea why this would run locally: /usr/bin/time -v DCC @/40/Public_Data/bulkRNASeq/201812_MSBB/Gene_Expression/02.-ProcessedData/06.-circRNA/Hg19/BM44/DCC/DCC_InputFiles/samplesheet -mt1 @/40/Public_Data/bulkRNASeq/201812_MSBB/Gene_Expression/02.-ProcessedData/06.-circRNA/Hg19/BM44/DCC/DCC_InputFiles/read -T 4 -D -N -R /40/pipelines/RNAseq/circRNA/hg19_Repeats_RepeatMasker_SimpleRepeats.gtf -an /40/pipelines/RNAseq/circRNA/Hg19_gencodev19_spikein/gencode.v19.annotation.spike-in.gtf -F -M -Nr 1...

I found the problem: When you specify a TSV file, e.g. hecatomb run --reads samples.tsv, Hecatomb expects a 3-column tab separated file with the first column specifying the sample name,...

I was trying to make a helper script to pull reads from a family of interest, so a shell script but could do it differently.

Hi Mike, [Uploading 2021_05_18_Viral_Baltimore_full_classification_table_ICTV2020.txt…]() I just created an updated taxonomy database with Baltimore classification, which I am having trouble uploading here. This is the latest ICTV release. I will email...

Here are some additional families (added to ICTV after the attached file was made). Family Host Adintoviridae Eukaryotes Aliusviridae Insects Crepuscuviridae Insects Curvulaviridae Fungi Guelinviridae Bacteria Kolmioviridae Vertebrates icluding humans...

I was thinking that the column should be called "Known_hosts" to emphasize that additional hosts could be discovered