pditommaso
commented
5 years ago Ouch, the log is printed regularly without tower? may it be possible there's some println in the pipeline script breaking the ANSI rendering?
Open apeltzer opened 5 years ago
pditommaso
commented
5 years ago Ouch, the log is printed regularly without tower? may it be possible there's some println in the pipeline script breaking the ANSI rendering?
apeltzer
commented
5 years ago Yes, without tower it's not printed too often but I can check tomorrow morning! Will update here tomorrow morning!
pditommaso
commented
5 years ago not too often is suspect .. :)
apeltzer
commented
5 years ago Without tower:
nextflow run . -profile test,docker --skipQC -resume
N E X T F L O W ~ version 19.09.0-edge
Launching `./main.nf` [prickly_hopper] - revision: ebcf453221
Prefer GTF over GFF, so ignoring provided GFF in favor of GTF
[2m----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/rnaseq v1.4dev
----------------------------------------------------
Run Name : prickly_hopper
Reads : data/*{1,2}.fastq.gz
Data Type : Single-End
Gzipped Refs? : false
Strandedness : None
Trimming : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0
Aligner : STAR
Fasta Ref : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa
GTF Annotation : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf
GFF3 Annotation : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff
Biotype GTF field : gene_biotype
Save prefs : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No
Max Resources : 6 GB memory, 2 cpus, 2d time per job
Container : docker - nfcore/rnaseq:dev
Output dir : ./results
Launch dir : /Users/alexanderpeltzer/IDEA/nf-core/rnaseq
Working dir : /Users/alexanderpeltzer/IDEA/nf-core/rnaseq/work
Script dir : /Users/alexanderpeltzer/IDEA/nf-core/rnaseq
User : alexanderpeltzer
Config Profile : test,docker
Config Description: Minimal test dataset to check pipeline function
[2m----------------------------------------------------
executor > local (11)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
[13/cbd850] process > makeBED12 (genes.gtf) [100%] 1 of 1 ✔
executor > local (12)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
[13/cbd850] process > makeBED12 (genes.gtf) [100%] 1 of 1 ✔
executor > local (12)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
[13/cbd850] process > makeBED12 (genes.gtf) [100%] 1 of 1 ✔
executor > local (12)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
[13/cbd850] process > makeBED12 (genes.gtf) [100%] 1 of 1 ✔
executor > local (14)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
[13/cbd850] process > makeBED12 (genes.gtf) [100%] 1 of 1 ✔
[f7/0e21c1] process > makeSTARindex (genome.fa) [100%] 1 of 1 ✔
[- ] process > fastqc With tower:
N E X T F L O W ~ version 19.09.0-edge
Launching `./main.nf` [astonishing_feynman] - revision: ebcf453221
Prefer GTF over GFF, so ignoring provided GFF in favor of GTF
[2m----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/rnaseq v1.4dev
----------------------------------------------------
Run Name : astonishing_feynman
Reads : data/*{1,2}.fastq.gz
Data Type : Single-End
Gzipped Refs? : false
Strandedness : None
Trimming : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0
Aligner : STAR
Fasta Ref : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa
GTF Annotation : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf
GFF3 Annotation : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff
Biotype GTF field : gene_biotype
Save prefs : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No
Max Resources : 6 GB memory, 2 cpus, 2d time per job
Container : docker - nfcore/rnaseq:dev
Output dir : ./results
Launch dir : /Users/alexanderpeltzer/IDEA/nf-core/rnaseq
Working dir : /Users/alexanderpeltzer/IDEA/nf-core/rnaseq/work
Script dir : /Users/alexanderpeltzer/IDEA/nf-core/rnaseq
User : alexanderpeltzer
Config Profile : test,docker
Config Description: Minimal test dataset to check pipeline function
[2m----------------------------------------------------
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (12)
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (14)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (14)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (15)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (16)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (18)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (19)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (20)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (20)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (20)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (22)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (22)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (22)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (23)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/XXXXXX
executor > local (23)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
[a4/f62576] process > makeBED12 (genes.gtf) [100%] 1 of 1 ✔
[73/65e02d] process > makeSTARindex (genome.fa) [100%] 1 of 1 ✔
[- ] process > fastqc -
[51/e00082] process > trim_galore (SRR4238379) [100%] 4 of 4 ✔
[b4/2e0908] process > star (SRR4238355) [100%] 4 of 4 ✔
[- ] process > rseqc -
[- ] process > preseq -
[- ] process > markDuplicates -
[- ] process > qualimap -
[- ] process > dupradar -
[ed/773669] process > featureCounts (SRR4238355_subsampAlignedByCoord.out) [100%] 4 of 4 ✔yeah, but there's something wrong with the pipeline script. It should repeat these blocks:
executor > local (11)
[7e/475bae] process > get_software_versions [100%] 1 of 1 ✔
[13/cbd850] process > makeBED12 (genes.gtf) [100%] 1 of 1 ✔For example this.
I'm running some tests with tower and the
nf-core/rnaseqpipeline and have a lot of these messages in the nextflow log - not sure whether this is a problem with tower or Nextflow and/or intended:This is just an example, I typically see (depending on the pipeline) dozens of these entries. Running on OSX with
test,dockerand newest Edge Release of NXF.