IMP issueshttps://git-r3lab.uni.lu/IMP/IMP/-/issues2017-12-19T09:20:54+01:00https://git-r3lab.uni.lu/IMP/IMP/-/issues/13Handling multiple fastq files2017-12-19T09:20:54+01:00Shaman NarayanasamyHandling multiple fastq filesSometimes `fastq` files may not exist as a single pair of R1 and R2 files. They may exist as multiple pairs of fastq pairs. This is a potential request when we eventually release IMP to the public.
This may require a major refactor.
Sometimes `fastq` files may not exist as a single pair of R1 and R2 files. They may exist as multiple pairs of fastq pairs. This is a potential request when we eventually release IMP to the public.
This may require a major refactor.
https://git-r3lab.uni.lu/IMP/IMP/-/issues/104MissingInputException2017-07-12T09:30:20+02:00jingzhejiangMissingInputExceptionHi!
I have installed and finished 'impy init' on AWS instance, then save it as a AMI.
when I start a new instance (c4.8*large) with this AMI, and run:
```
impy run -t DYL1.fq.gz -t DYL2.fq.gz -o ~/DYL-IMP-default-Output --single-om...Hi!
I have installed and finished 'impy init' on AWS instance, then save it as a AMI.
when I start a new instance (c4.8*large) with this AMI, and run:
```
impy run -t DYL1.fq.gz -t DYL2.fq.gz -o ~/DYL-IMP-default-Output --single-omics
Executing IMP command:
docker run --rm --name home_ubuntu_DYL_IMP_default_Output -v /home/ubuntu/DYL-rawdata/imp-db:/home/imp/databases -v /home/ubuntu/DYL-IMP-default-Output:/home/imp/output -v /home/ubuntu/DYL-rawdata:/home/imp/data -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" -e IMP_BINNING_METHOD="maxbin" -e MEMTOTAL="8" -e MEMCORE="2" -e THREADS="4" -e MG="" -e MT="/home/imp/data/DYL1.fq.gz /home/imp/data/DYL2.fq.gz" -e IMP_ASSEMBLER="idba" -e IMP_STEPS="preprocessing assembly analysis binning report" docker-r3lab.uni.lu/imp/imp:1.4.1 snakemake -s /home/imp/code/Snakefile
usermod: no changes
MissingInputException in line 1 of /home/imp/code/rules/Preprocessing/trimming.rules:
Missing input files for rule trimming:
/home/imp/databases/adapters/adapters.done
```
What is the problem?
Thank you!https://git-r3lab.uni.lu/IMP/IMP/-/issues/118Automate for samples with multiple runs in sequencing2017-10-03T17:04:56+02:00Shaman NarayanasamyAutomate for samples with multiple runs in sequencingSome samples are run on separate sequencing runs. Usually, users would want to pool such samples and perform analysis as if it were a single sample.
-Shaman-Some samples are run on separate sequencing runs. Usually, users would want to pool such samples and perform analysis as if it were a single sample.
-Shaman-https://git-r3lab.uni.lu/IMP/IMP/-/issues/135Read preprocessing using fastp2018-10-08T16:32:54+02:00Cedric LacznyRead preprocessing using fastpMaybe [fastp](https://github.com/OpenGene/fastp) could be integrated as a preprocessing step.
According to its documentation is is (supposedly)
>like FASTQC but faster and more informative
and it integrates trimming etc. while automati...Maybe [fastp](https://github.com/OpenGene/fastp) could be integrated as a preprocessing step.
According to its documentation is is (supposedly)
>like FASTQC but faster and more informative
and it integrates trimming etc. while automatically detecting the adapters as well as
>trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq data