Dave Carlson

After Collect stage, some output files not found

8

I ran the Preprocess and Collect steps according the ReadMe with no apparent errors. However, it seems like some expected output was not produced because when I run the Assembly...

No queries aligned when running diamond in distributed mode

3

I'm trying to do an all-against-all blastp search of several proteomes. When running this with diamond on a single node, there are many hits as would be expected. However, when...

Compile error

1

Hi All, I'm trying to compile the latest version of Igrec on Centos 7, but I keep hitting errors. I'm using: gcc 7.4.0 cmake 3.15.3 python 2.7.15 Here are the...

TEMP_Insertion.sh produces empty output

5

Hi Jiali, I'm having some trouble getting TEMP to work properly. Most of the output files that are produced are empty (or empty except for the headers). No error messages...

Pipeline test is failing

2

### Description of the bug The test profile for the pipeline is failing to run on my HPC cluster. This does not happen with other nf-core pipelines (e.g., rnaseq). The...

### Description of the bug I tried running the pipeline using my own fasta and gff files, but instead of converting the gff to gtf, the human GRCh38 gtf file...

MultiQC report is missing fastQC results on the dev branch

10

### Description of the bug When running the rnaseq pipeline using the dev branch, the fastQC results are no longer included in the MultiQC report, even though the fastqc zip...

Salmon 1.10.3 build failure

1

**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?** This is related to salmon. **Describe the bug** When building Salmon 1.10.3 from source, I'm seeing the...

Assembly size seems to double between contigger and polishing stage

4

I'm assembling a somewhat low coverage (~20x) human genome using ONT R10.4.1 reads with flye v2.9.5-b1801. During the contigger stage, the `contigs.fasta` file was ~2.9 GB in size. However, the...