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First real issue was cutadapt. It was trying to load a python2 module that I don't know how to get.
Original Makefile:
```
include config.mk
include ../utils.mk
## Based on the official instr…
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So, I forgot that we have a `qsub` tool on C4 that emulates Torque/PBS `qsub`. However, it does _not_ support CLI option `-d ` which set the working directory. The LG3 Pipeline uses it solely(*) as …
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```
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are requ…
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FYI, I've created lg3 [2021-10-08](https://github.com/UCSF-Costello-Lab/LG3_Pipeline/tree/2021-10-08), which is a fork of the previous release [2020-05-26](https://github.com/UCSF-Costello-Lab/LG3_Pip…
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I see that [you disabled](https://github.com/UCSF-Costello-Lab/LG3_Pipeline/commit/85abc1440dc387f661fe7f129c1d4815f69b83e2#diff-1615c06ff867567fde8b4caed7973fae157a4e384ebb043edc20cd2dd3a67bb1) the `…
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```sh
$ grep -E "^SAMTOOLS=" -r --include="*.sh"
scripts/Merge_QC.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
scripts/Recal_step.sh:SAMTOOLS=${LG3_HOME}/tools/samtools-0.1.18/samtools
s…
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I've looked through all the script/*.R scripts, I'm 99.9% certain that they work with any version of R. In other words, we should be able to drop the fixed location /opt/R/R-latest/bin/ and rely on R …
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@ivan108 wrote:
Hi Henrik,
I am trying to run Costello-PSCN-Seq pipeline, the frozen version Stephanie was using before she left.
However, the hardcoded symbolic link
annotationData -> /cb…
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I am getting an error when trying to run 1.mpileup.R, which is the first step of the pipeline.
>module load CBC r/3.4.4
>cd /home/jocostello/repositories/HenrikBengtsson/Costello-PSCN-Seq
>Rscri…
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Stephanie and I are experiencing the same error last few days:
```
[...]
Processing incomplete BAMs (i.e. missing one or more chromosomes)...done
Collect and resolve all futures...
A 'liste…