Error in NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE #312

alexmascension · 2024-02-05T13:29:21Z

Description of the bug

Im running the following command, using mirgenedb:

nextflow run nf-core/smrnaseq                                             
-r 2.2.4                                           
-profile docker                                             
-resume                                             
--max_cpus 9                                             
--max_memory 93.GB                                             
--max_time 500.h 
--skip_mirdeep 
--input work/test_human/samplesheets/SMRNASEQ_MIRGENE.csv 
--outdir results/test_human/SMRNASEQ_MIRGENE 
--genome GRCh38 
--mirgenedb 
--mirgenedb_gff database/smRNA/mirgenedb/hsa.gff 
--mirgenedb_mature $(pwd)/database/smRNA/mirgenedb/hsa.fas 
--mirgenedb_hairpin $(pwd)/database/smRNA/mirgenedb/hsa-pre.fas 
--fasta database/genomes/GRCh38/genome.fasta 
--bowtie_index database/indexes/GRCh38/BOWTIE

And I get the following error:

ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE'

Caused by:
  Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE` terminated with an error exit status (1)

Command executed:

  bowtie-build hsa.fas_igenome.fa_idx.fa fasta_bidx --threads 6
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE":
      bowtie: $(echo $(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  Settings:
    Output files: "fasta_bidx.*.ebwt"
    Line rate: 6 (line is 64 bytes)
    Lines per side: 1 (side is 64 bytes)
    Offset rate: 5 (one in 32)
    FTable chars: 10
    Strings: unpacked
    Max bucket size: default
    Max bucket size, sqrt multiplier: default
    Max bucket size, len divisor: 24
    Difference-cover sample period: 1024
    Endianness: little
    Actual local endianness: little
    Sanity checking: disabled
    Assertions: disabled
    Random seed: 0
    Sizeofs: void*:8, int:4, long:8, size_t:8
  Input files DNA, FASTA:
    hsa.fas_igenome.fa_idx.fa
  Reading reference sizes
    Time reading reference sizes: 00:00:00
  Total time for call to driver() for forward index: 00:00:00

Command error:
  Settings:
    Output files: "fasta_bidx.*.ebwt"
    Line rate: 6 (line is 64 bytes)
    Lines per side: 1 (side is 64 bytes)
    Offset rate: 5 (one in 32)
    FTable chars: 10
    Strings: unpacked
    Max bucket size: default
    Max bucket size, sqrt multiplier: default
    Max bucket size, len divisor: 24
    Difference-cover sample period: 1024
    Endianness: little
    Actual local endianness: little
    Sanity checking: disabled
    Assertions: disabled
    Random seed: 0
    Sizeofs: void*:8, int:4, long:8, size_t:8
  Input files DNA, FASTA:
    hsa.fas_igenome.fa_idx.fa
  Unable to read file magic number
  Reading reference sizes
  Warning: Empty input file
  Error: No unambiguous stretches of characters in the input.  Aborting...
    Time reading reference sizes: 00:00:00
  Total time for call to driver() for forward index: 00:00:00
  Command: bowtie-build --wrapper basic-0 --threads 6 hsa.fas_igenome.fa_idx.fa fasta_bidx 

Work dir:
  /data/Proyectos/NGS_pipeline/work/63/d9ebec3de933d7351832840280886b

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

The process works fine with mirtrace.

Command used and terminal output

No response

Relevant files

mirgene_db.zip
nextflow.log

System information

No response

Tasks

Give feedback

The text was updated successfully, but these errors were encountered:

apeltzer · 2024-02-08T13:32:38Z

Please try using the devversion for now, this should resolve a number of issues / bugs.

SoWhat1001 · 2024-02-08T15:33:11Z

I am running into the same problem even though I am using the dev version

apeltzer · 2024-02-08T17:02:33Z

Mirgenedb isn't clear to me. Looks like the input fastas are empty ?

alexmascension · 2024-02-09T09:47:37Z

Hi! I get this error just by changing to dev:

ERROR ~ No such variable: index

The log says more specifically:

Feb-09 10:46:33.250 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: index for class: nextflow.script.WorkflowBinding

apeltzer · 2024-02-09T12:46:39Z

Weird, apart from that no changes to what you described in your first posting? We should probably add a test case I fear :-(

alexmascension · 2024-02-09T13:26:58Z

Yeap, nothing else has changed.

christopher-mohr · 2024-02-09T13:37:17Z

Is there more in the nextflow.log on the error? Could you share that?

alexmascension · 2024-02-09T14:06:18Z

Sure!

nextflow.log

christopher-mohr · 2024-02-14T10:33:27Z

Hi @alexmascension, I cannot reproduce the error you posted five days ago using dev. I get the error you posted initially. Can you confirm this?

alexmascension · 2024-02-14T11:00:03Z

Hi, I'm running the code again and I get the second error again.

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/smrnaseq v2.3.0-g18ae224
------------------------------------------------------
Core Nextflow options
  revision           : dev
  runName            : nauseous_curie
  containerEngine    : docker
  launchDir          : /data/Proyectos/NGS_pipeline
  workDir            : /data/Proyectos/NGS_pipeline/work
  projectDir         : /home/nanoneuro/.nextflow/assets/nf-core/smrnaseq
  userName           : nanoneuro
  profile            : docker
  configFiles        : 

Input/output options
  input              : work/test_human/samplesheets/SMRNASEQ_MIRGENE.csv
  outdir             : results/test_human/SMRNASEQ_MIRGENE

Reference genome options
  genome             : GRCh38
  mirgenedb          : true
  mirtrace_species   : hsa
  fasta              : database/genomes/GRCh38/genome.fasta
  mirgenedb_gff      : database/smRNA/mirgenedb/hsa.gff
  mirgenedb_mature   : /data/Proyectos/NGS_pipeline/database/smRNA/mirgenedb/hsa.fas
  mirgenedb_hairpin  : /data/Proyectos/NGS_pipeline/database/smRNA/mirgenedb/hsa-pre.fas
  bowtie_index       : database/indexes/GRCh38/BOWTIE

Trimming options
  clip_r1            : 0
  three_prime_clip_r1: 0

Skipping pipeline steps
  skip_mirdeep       : true

Max job request options
  max_cpus           : 9
  max_memory         : 84.GB
  max_time           : 500.h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/smrnaseq for your analysis please cite:

* The pipeline
  https://zenodo.org/badge/latestdoi/140590861

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/smrnaseq/blob/master/CITATIONS.md

ERROR ~ No such variable: index

 -- Check script '/home/nanoneuro/.nextflow/assets/nf-core/smrnaseq/./workflows/smrnaseq.nf' at line: 165 or see '.nextflow.log' file for more details

nextflow.log

However, nf-core continues if I remove the variable --bowtie_index database/indexes/GRCh38/BOWTIE, but it stops with the error I began with.

ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE'

Caused by:
  Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE` terminated with an error exit status (1)

Command executed:

  bowtie-build hsa.fas_igenome.fa_idx.fa fasta_bidx --threads 6
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE":
      bowtie: $(echo $(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  Settings:
    Output files: "fasta_bidx.*.ebwt"
    Line rate: 6 (line is 64 bytes)
    Lines per side: 1 (side is 64 bytes)
    Offset rate: 5 (one in 32)
    FTable chars: 10
    Strings: unpacked
    Max bucket size: default
    Max bucket size, sqrt multiplier: default
    Max bucket size, len divisor: 24
    Difference-cover sample period: 1024
    Endianness: little
    Actual local endianness: little
    Sanity checking: disabled
    Assertions: disabled
    Random seed: 0
    Sizeofs: void*:8, int:4, long:8, size_t:8
  Input files DNA, FASTA:
    hsa.fas_igenome.fa_idx.fa
  Reading reference sizes
    Time reading reference sizes: 00:00:00
  Total time for call to driver() for forward index: 00:00:00

Command error:
  Settings:
    Output files: "fasta_bidx.*.ebwt"
    Line rate: 6 (line is 64 bytes)
    Lines per side: 1 (side is 64 bytes)
    Offset rate: 5 (one in 32)
    FTable chars: 10
    Strings: unpacked
    Max bucket size: default
    Max bucket size, sqrt multiplier: default
    Max bucket size, len divisor: 24
    Difference-cover sample period: 1024
    Endianness: little
    Actual local endianness: little
    Sanity checking: disabled
    Assertions: disabled
    Random seed: 0
    Sizeofs: void*:8, int:4, long:8, size_t:8
  Input files DNA, FASTA:
    hsa.fas_igenome.fa_idx.fa
  Unable to read file magic number
  Reading reference sizes
  Warning: Empty input file
  Error: No unambiguous stretches of characters in the input.  Aborting...
  Command: bowtie-build --wrapper basic-0 --threads 6 hsa.fas_igenome.fa_idx.fa fasta_bidx 
    Time reading reference sizes: 00:00:00
  Total time for call to driver() for forward index: 00:00:00

Work dir:
  /data/Proyectos/NGS_pipeline/work/bf/a41903d3122c5f446a98faf0b75611

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details

nexflow.2.log

The contents of the folder are genome.1.ebwt genome.2.ebwt genome.3.ebwt genome.4.ebwt genome.rev.1.ebwt genome.rev.2.ebwt

If I change --bowtie_index database/indexes/GRCh38/BOWTIE with --bowtie_index database/indexes/GRCh38/BOWTIE/genome I get the same error.

christopher-mohr · 2024-02-14T11:10:40Z

Okay, I think we might need a separate issue for the --bowtie_index error. Could you try running it again without --bowtie_index but add the following to your call --mirgenedb_species "Hsa" please.

alexmascension · 2024-02-14T12:53:42Z

Hi!

With --mirgenedb_species "Hsa" the program works fine!

Do I open a new issue for the --bowtie_index error?

Thanks!

christopher-mohr · 2024-02-14T13:02:39Z

Yes please, I will also leave this issue open and close it with a PR where I add a check to make sure the --mirgenedb_species parameter is set.

alexmascension · 2024-02-14T13:23:50Z

Fine!

apeltzer · 2024-02-22T12:41:33Z

Dev fixes this issue now, thanks for reporting @alexmascension

alexmascension added the bug Something isn't working label Feb 5, 2024

christopher-mohr added enhancement New feature or request and removed bug Something isn't working labels Feb 14, 2024

christopher-mohr mentioned this issue Feb 14, 2024

add check if mirgene_db_species is set if mirgene_db #315

Merged

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apeltzer closed this as completed Feb 22, 2024

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Error in NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE #312

Error in NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE #312

alexmascension commented Feb 5, 2024 •

edited by apeltzer

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apeltzer commented Feb 8, 2024

SoWhat1001 commented Feb 8, 2024

apeltzer commented Feb 8, 2024

alexmascension commented Feb 9, 2024

apeltzer commented Feb 9, 2024

alexmascension commented Feb 9, 2024

christopher-mohr commented Feb 9, 2024

alexmascension commented Feb 9, 2024

christopher-mohr commented Feb 14, 2024

alexmascension commented Feb 14, 2024

christopher-mohr commented Feb 14, 2024

alexmascension commented Feb 14, 2024

christopher-mohr commented Feb 14, 2024

alexmascension commented Feb 14, 2024

apeltzer commented Feb 22, 2024

Error in NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE #312

Error in NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE #312

Comments

alexmascension commented Feb 5, 2024 • edited by apeltzer Loading

Description of the bug

Command used and terminal output

Relevant files

System information

Tasks

apeltzer commented Feb 8, 2024

SoWhat1001 commented Feb 8, 2024

apeltzer commented Feb 8, 2024

alexmascension commented Feb 9, 2024

apeltzer commented Feb 9, 2024

alexmascension commented Feb 9, 2024

christopher-mohr commented Feb 9, 2024

alexmascension commented Feb 9, 2024

christopher-mohr commented Feb 14, 2024

alexmascension commented Feb 14, 2024

christopher-mohr commented Feb 14, 2024

alexmascension commented Feb 14, 2024

christopher-mohr commented Feb 14, 2024

alexmascension commented Feb 14, 2024

apeltzer commented Feb 22, 2024

alexmascension commented Feb 5, 2024 •

edited by apeltzer

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