Malabady

RE: reads_to_ctg_map.py

10

Hi, the script "reads_to_ctg_map.py" fails at sam sort stage and give the following message" Convert SAM to BAM... Done. Time elapsed for SAM to BAM conversion: 0:03:52.958605 Sort BAM...Traceback (most...

RE: IsONclust on ONY; spot died with <Signals.SIGILL: 4>.

2

Hi I am running isONclust in a Conda environment and the spoa and medaka modules are loaded before the run. Here is my commands: ``` ml Miniconda3/4.10.3 source activate isonclust...

RE: annotate is not adding GO terms to the gbk file

1

Hello, I am running the following command `` funannotate annotate --gff Slycopersicum_225_iTAGv2.3.gene_exons.gff3 --fasta Slycopersicum_225_iTAGv2.40.fa -s 'Solanum lycopersicum' -o Sly --cpu 12 --iprscan iprscan.xml --database $FUNANNOTATE_DB --busco_db embryophyta`` Basically, I am...

RE: 4DTv and WGD

5

Hello Jefferson, My analysis includes my species of interest plus six other species. In my "comparisons_4DTv.txt", I listed single species as well as pairs of species, as follows: `` mySpecies...

assess_specific_genes is taking days

6

Hello, I am running the last workflow in the pipeline to assess four specific genes. My analysis included 10 plant species. the problem is that, this step is been running...

PloidyPlot: Something went wrong with command:

5

Hi, I am getting the following error: `` PloidyPlot: Something went wrong with command: Logex -T4 '.trim=A[12-]' Outdata/FastK_table `` my command is: ``PloidyPlot -e12 -k -v -T4 -oOutdata/kmerpairs Outdata/FastK_table`` Any...

HOGs

4

Hi, Is the expansion/contraction analysis based on the hierarchical orthogroups (HOGs from Phylogenetic_Hierarchical_Orthogroups/N.tsv), or only on the flat Orthogroups.tsv? thanks,

Hi, In the xyzzy.collinearity output file, the strand (plus or minus) is reported at the end of the alignment line. Is this strand pertinent to both chromosomes in the block...

Hi, I am using the following command: /RATTLE-1.0/rattle cluster --input all_fastq_pass_filtered.fq --threads 24 --iso --rna --output ./rattle_output the command gives these following messages: RNA mode: true Reading fasta file... Done...