Jay

nhmmer failure: Error was 'Inappropriate ioctl for device' and return code '35584'

2

It looks like nhmmer fails on phyloFlash v3.4.2. I am running this command: ``` phyloFlash.pl -lib test_phyloflash -CPUs 32 -everything -read1 ../../data/interleave/JMF-2212-17-0001A.interleave.fastq.gz --interleaved -readlength 150 -clusterid 99 -dbhome /scratch/jmf/internal/Analyses_Jay/JMF_2212_17/results/138.1 ```...

libcfu/lib not included in code

8

I am running the standard install and it is not finding the libcfu/lib folder in the bundle. error from setup.py: checking for libcfu headers in /home/labuser/BamM/c/libcfu-0.03/include... found checking for libcfu...

Error: spades-hammer, OS return value: 1

5

### Description of bug Spades-hammer is terminating because of a segmentation fault while kmer-counting and reports an "OS return value: 1". Command line: ``` /lisc/scratch/jmf/internal/Analyses_Jay/JMF_2108_11/.snakemake/conda/0ae2b4a3475f1b8ec4109c90dec7e0d2_/bin/spades.py -t 48 -m 1000 -k...

Custom DB and custom taxonomy (GTDB or similar)

14

Is there a way to create a completely new database and non-NCBI taxonomy for that database? I am primarily interested in using something like GTDB, which has a genome download...

Counts from krona's generating using kreporto2krona are 3-7% lower than the total amount of reads in kraken. Is there a reason why? Code line: ``` python3 kreport2krona.py -r report.txt -o...

Minimum requirement to prep annotation for NCBI submission

1

I am hoping to annotate genomes before submitting them to NCBI or creating a bioproject/biosample for them. For this I need a fasta, generic yaml, and a metadata yaml. What...