Dmitry Mylarshchikov

I also have the same problem with version 1.1.0. Based on the traceback, the culprit is this line: https://github.com/open2c/pairtools/blob/8c41a26b3f3a3905e307f3baa4b547203394dca1/pairtools/lib/dedup.py#L9 It does seem to be a circular import.

But this advice > You have to PIP install from source after installing the dependencies: > > ``` > git clone -b "v1.1.0" https://github.com/open2c/pairtools.git > cd pairtools && pip install...

The command I run is similar to this: ``` nextflow -bg run nf-core/nascent -r 2.2.0 -profile cbe -work-dir $NXF_WRK -params-file params.json ``` My samplesheet looks like this: ``` sample,fastq_1,fastq_2 SAMPLE_REP1,path/to/reads.fq.gz,...

Just tried running `dev` version, it also fails with the same error.

> Is there anyway I could get the exact command, not just similar? I replaced unnecessary details of my local paths preserving the conceptual structure. I'm not sure if knowledge...

Okay, `samtools index` works on `2.2.0` but not on `dev`.

I ran the pipeline `dev` version with samplesheet: ``` sample,fastq_1,fastq_2 REP1,./sortmerna/SRR1693611/out/other.fq.gz, REP2,./sortmerna/SRR1693612/out/other.fq.gz, ``` The sample names are different in this case, since I cannot run latest version with the same...

I renamed samples to "replicate1" and "replicate2", and I still get the same error from GROHMM_PARAMETERTUNING.