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STAR GenomeGenerate doesn't happen with --additional_fasta unless --star_index is false #556

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3 of 4 tasks
olgabot opened this issue Jan 27, 2021 · 5 comments
Closed
3 of 4 tasks

STAR GenomeGenerate doesn't happen with --additional_fasta unless --star_index is false #556

olgabot opened this issue Jan 27, 2021 · 5 comments
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@olgabot
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olgabot commented Jan 27, 2021 •
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Check Documentation

I have checked the following places for your error:

Description of the bug

If --additional_fasta is provided, a new genome is not generated unless --star_index is 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:

  1. Command line:
`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                                                           -
  • See error:

    • No error message, see logs above

    Expected behaviour

    I expected --additional_fasta to trigger a new genome build.

    Log files

    Have you provided the following extra information/files:

    • The command used to run the pipeline
    • The .nextflow.log file

    System

    • Hardware: Local
    • Executor: AWS Batch and local
    • OS: macOS
    • Version: 10.15.7

    Nextflow Installation

    • Version: 21.01.1-edge

    Container engine

    • Engine: Docker
    • version: v20.10.2
    • Image tag: The PREPARE_GENOME one?
    @olgabot olgabot added the bug Something isn't working label Jan 27, 2021
    @drpatelh
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    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
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    Ping @olgabot ! Maybe I misunderstood something here? I will give you the chance to tell me I have before I close this!

    @RoganGrant
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    @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
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    Ok. Warning it is 👍🏽 Will add it to the next release.

    drpatelh added a commit to drpatelh/nf-core-rnaseq that referenced this issue Jul 27, 2021
    @drpatelh
    Fix nf-core#556
    53fdef1
    @drpatelh
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    drpatelh commented Jul 27, 2021 •
    edited
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    Warning below added in #681

    image

    @drpatelh drpatelh mentioned this issue Jul 27, 2021
    Merged
    drpatelh added a commit that referenced this issue Jul 28, 2021
    @drpatelh
    Merge pull request #681 from drpatelh/updates
    5d3a3fb 
    FIx #556
    @drpatelh drpatelh mentioned this issue May 31, 2023
    Closed
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    @olgabot @RoganGrant @drpatelh