Closed olgabot closed 3 years ago
drpatelh
commented
3 years ago Hi @olgabot !! Apologies for the ridiculously late response.
The logic here looks ok no? If the user provides a STAR index you would have to assume they want to use that particula STAR index? For example, if you don't provide a STAR index and it is generated using --additional_fasta, then you can re-use that STAR index again whether you provide --additional_fasta or not?
drpatelh
commented
3 years ago Ping @olgabot ! Maybe I misunderstood something here? I will give you the chance to tell me I have before I close this!
RoganGrant
commented
3 years ago @drpatelh I think I agree with @olgabot on this one. Although your reasoning is correct, I think a lot of users (myself included) are going to black-box these low-level processing steps. I initially ran into the same error as @olgabot using a local hardcopy of my genome of interest, and was confused when I couldn't find counts for my transgenes in the final count matrix. I agree that a rebuild probably shouldn't be the default action, but a strong warning is probably merited here. Works beautifully with --star_index false though 😄
drpatelh
commented
3 years ago Ok. Warning it is 👍🏽 Will add it to the next release.
drpatelh
commented
3 years ago Warning below added in https://github.com/nf-core/rnaseq/pull/681
Check Documentation
I have checked the following places for your error:
Description of the bug
If
--additional_fastais provided, a new genome is not generated unless--star_indexis set to false.`--additional_fasta`, with `--star_index` but no new genome generated
This job fails because the `--star_index` was made with an older version of STAR and is incompatible wtih the current version of STAR. ``` Tue 26 Jan - 19:54 ~/nf-core--rnaseq-tower-test-awsbatch olga@lrrr sleep 5 && nextflow run nf-core/rnaseq \ -params-file nf-params-tb-v2.json \ -profile tower,awsbatch \ --custom_config_base /mnt/data_sm/home/olga/nextflow-configs \ --outdir "s3://czbiohub-cupcakes/nf-core/rnaseq/test/tb-data/$USER" N E X T F L O W ~ version 20.11.0-edge Pulling nf-core/rnaseq ... downloaded from https://github.com/nf-core/rnaseq.git Launching `nf-core/rnaseq` [silly_morse] - revision: 3643a94411 [master] ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/rnaseq v3.0 ------------------------------------------------------ Core Nextflow options revision : master runName : silly_morse containerEngine : docker launchDir : /home/olga/nf-core--rnaseq-tower-test-awsbatch workDir : /czb-nextflow/intermediates projectDir : /home/olga/.nextflow/assets/nf-core/rnaseq userName : olga profile : tower,awsbatch configFiles : /home/olga/.nextflow/assets/nf-core/rnaseq/nextflow.config Input/output options input : /home/olga/data_sm/tb_project__20201119_FS10000331_141_BPG61605-1919/samplesheets/mouse_tb_samplesheet_local_paths_mini_subset.csv outdir : s3://czbiohub-cupcakes/nf-core/rnaseq/test/tb-data/olga email : olga.botvinnik@czbiohub.org Reference genome options genome : gencode.vM19 fasta : s3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa gtf : s3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf additional_fasta : /mnt/data_sm/olga/tb_project__20201119_FS10000331_141_BPG61605-1919/additional_fastas/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.chromosome.Chromosome.fa star_index : s3://czbiohub-reference/gencode/mouse/vM21/STARIndex/ gencode : true save_reference : true igenomes_base : s3://czbiohub-reference/igenomes Alignment options seq_center : czbiohub Institutional config options custom_config_base : /mnt/data_sm/home/olga/nextflow-configs config_profile_description: Chan Zuckerberg Biohub AWS Batch profile provided by nf-core/configs. config_profile_contact : Olga Botvinnik (@olgabot) config_profile_url : https://www.czbiohub.org/ Max job request options max_cpus : 96 max_memory : 1.9 TB max_time : 10d Generic options tracedir : ./ ------------------------------------------------------ If you use nf-core/rnaseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.1400710 * The nf-core framework https://dx.doi.org/10.1038/s41587-020-0439-x https://rdcu.be/b1GjZ * Software dependencies https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md ------------------------------------------------------ Uploading local `bin` scripts folder to s3://czb-nextflow/intermediates/tmp/75/7bfd07e4469989721ebaacb2a82e01/bin Monitor the execution with Nextflow Tower using this url http://nftower.czbiohub.org:8000/watch/9y6Z4Si94f12n executor > awsbatch (32) [10/c7540b] process > RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA (Mycobact... [100%] 1 of 1 ✔ [78/b9c53a] process > RNASEQ:PREPARE_GENOME:GTF2BED (gencode.vM19_Mycobact... [100%] 1 of 1 ✔ [5a/4cd775] process > RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER (gencode.vM19_... [100%] 1 of 1 ✔ [02/1d534c] process > RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRI... [100%] 1 of 1 ✔ [e4/c52722] process > RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (gencode.vM19_... [100%] 1 of 1 ✔ [5e/29cd5c] process > RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (mouse_tb_sampl... [100%] 1 of 1 ✔ [69/216791] process > RNASEQ:CAT_FASTQ (TBPOS_R2) [100%] 6 of 6 ✔ [e8/4509be] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (TBNEG_R1) [100%] 6 of 6 ✔ [fb/fd9d27] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (TBNEG_R3) [100%] 6 of 6 ✔ [c7/5cb65a] process > RNASEQ:ALIGN_STAR:STAR_ALIGN (TBNEG_R3) [100%] 6 of 6, failed: 6 ✔ [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOO... - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOO... - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOO... - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_MERGE_COUNTS - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SC... - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > RNASEQ:PRESEQ_LCEXTRAP - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAM... - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAM... - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAM... - [- ] process > RNASEQ:STRINGTIE - [- ] process > RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > RNASEQ:UCSC_BEDCLIP - [- ] process > RNASEQ:UCSC_BEDGRAPHTOBIGWIG - [- ] process > RNASEQ:QUALIMAP_RNASEQ - [- ] process > RNASEQ:DUPRADAR - [- ] process > RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [a4/3a8e87] process > RNASEQ:GET_SOFTWARE_VERSIONS [100%] 1 of 1 ✔ [61/41e108] process > RNASEQ:MULTIQC (1) [ 0%] 0 of 1 -[nf-core/rnaseq] Sent summary e-mail to olga.botvinnik@czbiohub.org (sendmail)- -[nf-core/rnaseq] Pipeline completed with errors- WARN: Killing pending tasks (1) Adieu ````--additional_fasta` with `--star_index` false --> new genome generated
``` ✘ Wed 27 Jan - 09:10 ~/nf-core--rnaseq-tower-test-awsbatch olga@lrrr sleep 5 && nextflow run nf-core/rnaseq \ -params-file nf-params-tb-v2.json \ -profile tower,awsbatch \ --custom_config_base /mnt/data_sm/home/olga/nextflow-configs \ --outdir "s3://czbiohub-cupcakes/nf-core/rnaseq/test/tb-data/$USER" N E X T F L O W ~ version 20.11.0-edge Launching `nf-core/rnaseq` [distraught_heisenberg] - revision: 3643a94411 [master] ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/rnaseq v3.0 ------------------------------------------------------ Core Nextflow options revision : master runName : distraught_heisenberg containerEngine : docker launchDir : /home/olga/nf-core--rnaseq-tower-test-awsbatch workDir : /czb-nextflow/intermediates projectDir : /home/olga/.nextflow/assets/nf-core/rnaseq userName : olga profile : tower,awsbatch configFiles : /home/olga/.nextflow/assets/nf-core/rnaseq/nextflow.config Input/output options input : /home/olga/data_sm/tb_project__20201119_FS10000331_141_BPG61605-1919/samplesheets/mouse_tb_samplesheet_local_paths_mini_subset.csv outdir : s3://czbiohub-cupcakes/nf-core/rnaseq/test/tb-data/olga email : olga.botvinnik@czbiohub.org Reference genome options genome : gencode.vM19 fasta : s3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa gtf : s3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf additional_fasta : /mnt/data_sm/olga/tb_project__20201119_FS10000331_141_BPG61605-1919/additional_fastas/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.chromosome.Chromosome.fa gencode : true save_reference : true igenomes_base : s3://czbiohub-reference/igenomes Alignment options seq_center : czbiohub Institutional config options custom_config_base : /mnt/data_sm/home/olga/nextflow-configs config_profile_description: Chan Zuckerberg Biohub AWS Batch profile provided by nf-core/configs. config_profile_contact : Olga Botvinnik (@olgabot) config_profile_url : https://www.czbiohub.org/ Max job request options max_cpus : 96 max_memory : 1.9 TB max_time : 10d Generic options tracedir : ./ ------------------------------------------------------ If you use nf-core/rnaseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.1400710 * The nf-core framework https://dx.doi.org/10.1038/s41587-020-0439-x https://rdcu.be/b1GjZ * Software dependencies https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md ------------------------------------------------------ Uploading local `bin` scripts folder to s3://czb-nextflow/intermediates/tmp/0a/505309db362f3e6e70388db257caff/bin Monitor the execution with Nextflow Tower using this url http://nftower.czbiohub.org:8000/watch/2BOj8waqJgqSSg executor > awsbatch (2) [c0/fbfcd5] process > RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA (Mycobact... [ 0%] 0 of 1 [- ] process > RNASEQ:PREPARE_GENOME:GTF2BED - [- ] process > RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER - [- ] process > RNASEQ:PREPARE_GENOME:RSEM_PREPAREREFERENCE_TRANSCRIPTS - [- ] process > RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES - [- ] process > RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE - <------ this task wasn't here before [55/695511] process > RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (mouse_tb_sampl... [ 0%] 0 of 1 [- ] process > RNASEQ:CAT_FASTQ - [- ] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC - [- ] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE - [- ] process > RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOO... - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOO... - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOO... - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_MERGE_COUNTS - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SC... - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > RNASEQ:PRESEQ_LCEXTRAP - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAM... - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAM... - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAM... - [- ] process > RNASEQ:STRINGTIE - [- ] process > RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > RNASEQ:UCSC_BEDCLIP - [- ] process > RNASEQ:UCSC_BEDGRAPHTOBIGWIG - [- ] process > RNASEQ:QUALIMAP_RNASEQ - [- ] process > RNASEQ:DUPRADAR - [- ] process > RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [- ] process > RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > RNASEQ:MULTIQC - ```Steps to reproduce
Steps to reproduce the behaviour:
`nextflow run nf-core/rnaseq -profile test,docker` --> no new genome generated
Produces: ``` executor > local (10) [cd/1d07be] process > RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz) [100%] 1 of 1, cached: 1 ✔ [ba/820437] process > RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz) [100%] 1 of 1, cached: 1 ✔ [77/7b11bf] process > RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA (gfp.fa) [100%] 1 of 1 ✔ [ae/c8f83b] process > RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf) [100%] 1 of 1 ✔ [70/5eb451] process > RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome_gfp.fasta) [100%] 1 of 1 ✔ [35/2cfe29] process > RNASEQ:PREPARE_GENOME:UNTAR_STAR_INDEX (star.tar.gz) [100%] 1 of 1, cached: 1 ✔ [ac/fcdffa] process > RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz) [100%] 1 of 1, cached: 1 ✔ [60/cc04ca] process > RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔ [76/8ff46d] process > RNASEQ:CAT_FASTQ (WT_R2) [100%] 5 of 5, cached: 5 ✔ [49/7fc81d] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_R2) [100%] 5 of 5, cached: 5 ✔ [10/17fc52] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_R2) [100%] 5 of 5, cached: 5 ✔ [c9/e8af8d] process > RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_R2) [ 0%] 0 of 5 [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_MERGE_COUNTS - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > RNASEQ:PRESEQ_LCEXTRAP - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > RNASEQ:STRINGTIE - [- ] process > RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > RNASEQ:UCSC_BEDCLIP - [- ] process > RNASEQ:UCSC_BEDGRAPHTOBIGWIG - [- ] process > RNASEQ:QUALIMAP_RNASEQ - [- ] process > RNASEQ:DUPRADAR - [- ] process > RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [64/e10b14] process > RNASEQ:QUANTIFY_SALMON:SALMON_QUANT (RAP1_IAA_30M_R1) [ 80%] 4 of 5 [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_MERGE_COUNTS - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > RNASEQ:DESEQ2_QC_SALMON - [- ] process > RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > RNASEQ:MULTIQC - ````nextflow run nf-core/rnaseq -profile test,docker --star_index false` --> new genome generated
``` executor > local (4) [cd/1d07be] process > RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes.gtf.gz) [100%] 1 of 1, cached: 1 ✔ [ba/820437] process > RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz) [100%] 1 of 1, cached: 1 ✔ [77/7b11bf] process > RNASEQ:PREPARE_GENOME:CAT_ADDITIONAL_FASTA (gfp.fa) [100%] 1 of 1, cached: 1 ✔ [ae/c8f83b] process > RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf) [100%] 1 of 1, cached: 1 ✔ [70/5eb451] process > RNASEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome_gfp.fasta) [100%] 1 of 1, cached: 1 ✔ [b4/7cc5d3] process > RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta) [ 0%] 0 of 1 <----- This exists now!! [ac/fcdffa] process > RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz) [100%] 1 of 1, cached: 1 ✔ [60/cc04ca] process > RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1, cached: 1 ✔ [51/8eb14a] process > RNASEQ:CAT_FASTQ (WT_R1) [100%] 5 of 5, cached: 5 ✔ [a0/9dd458] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_R1) [100%] 5 of 5, cached: 5 ✔ [10/17fc52] process > RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_R2) [100%] 5 of 5, cached: 5 ✔ [- ] process > RNASEQ:ALIGN_STAR:STAR_ALIGN - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > RNASEQ:ALIGN_STAR:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_MERGE_COUNTS - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED - [- ] process > RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > RNASEQ:DESEQ2_QC_STAR_SALMON - [- ] process > RNASEQ:MULTIQC_CUSTOM_FAIL_MAPPED - [- ] process > RNASEQ:PRESEQ_LCEXTRAP - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT - [- ] process > RNASEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS - [- ] process > RNASEQ:STRINGTIE - [- ] process > RNASEQ:SUBREAD_FEATURECOUNTS - [- ] process > RNASEQ:MULTIQC_CUSTOM_BIOTYPE - [- ] process > RNASEQ:BEDTOOLS_GENOMECOV - [- ] process > RNASEQ:UCSC_BEDCLIP - [- ] process > RNASEQ:UCSC_BEDGRAPHTOBIGWIG - [- ] process > RNASEQ:QUALIMAP_RNASEQ - [- ] process > RNASEQ:DUPRADAR - [- ] process > RNASEQ:RSEQC:RSEQC_BAMSTAT - [- ] process > RNASEQ:RSEQC:RSEQC_INNERDISTANCE - [- ] process > RNASEQ:RSEQC:RSEQC_INFEREXPERIMENT - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONANNOTATION - [- ] process > RNASEQ:RSEQC:RSEQC_JUNCTIONSATURATION - [- ] process > RNASEQ:RSEQC:RSEQC_READDISTRIBUTION - [- ] process > RNASEQ:RSEQC:RSEQC_READDUPLICATION - [- ] process > RNASEQ:MULTIQC_CUSTOM_STRAND_CHECK - [19/e9f944] process > RNASEQ:QUANTIFY_SALMON:SALMON_QUANT (WT_R2) [100%] 5 of 5, cached: 4 ✔ [ec/0eab58] process > RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE (genome_gfp.gtf) [100%] 1 of 1 ✔ [c2/1da96d] process > RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT (WT_R2) [ 0%] 0 of 5 [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_MERGE_COUNTS - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED - [- ] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT - [- ] process > RNASEQ:DESEQ2_QC_SALMON - [- ] process > RNASEQ:GET_SOFTWARE_VERSIONS - [- ] process > RNASEQ:MULTIQC - ```