[Errno 7] Argument list too long v 0.4.0

[Lucas-Maciel]

Hi, I'm trying to use ganon but I got an error when I tried to build the dataset

ganon build --db-prefix ganon_db -t 32 --input-files RefSeqCG_arc_bac/v1/files/*genomic.fna.gz

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(_	(_			(_)		_	v. 0.4.0

Downloading taxdump

• done in 5.72s.

Unpacking taxdump

• done in 6.61s.

Parsing taxonomy

• done in 4.71s.

Extracting sequence identifiers

• 44723 unique sequence headers successfully retrieved from 21442 input file(s)
• done in 2417.85s.

Retrieving sequence information from NCBI E-utils

• 44723 sequences successfully retrieved
• done in 639.22s.

Build: adding 44723 sequences

Calculating best bin length

• Approx. min. size possible: 68961.01MB
• bin length: 11707469bp (approx: 11269 bins / 103218.53MB)
• done in 6.24s. Building database files
• ganon_db.map
• ganon_db.tax
• ganon_db.gnn
• done in 1.00s.

Building index (ganon-build)

• max unique 19-mers: 11707451
• IBF calculated size with fp<=0.05: 110799.55MB (76435362 bits/bin 12160 optimal bins [12144 real bins]) The following command failed to run: Huge list of file* ~[Errno 7] Argument list too long: '/lucmac/miniconda3/bin/ganon-build' Error code: 0 Out: Error:

[pirovc]

Hi @Lucas-Maciel

Please check the following parameters:

  --input-directory     Directory containing input files
  --input-extension     Extension of files to use with --input-directory (provide it without * expansion, e.g. ".fna.gz")

the command would be something like: ganon build --db-prefix ganon_db -t 32 --input-directory "RefSeqCG_arc_bac/v1/files/" --input-extension "genomic.fna.gz"

[Lucas-Maciel]

@pirovc thanks for you fast reply, but changing the parameters as you suggested got me the same error

ganon build --db-prefix ganon_db -t 32 --input-directory "RefSeqCG_arc_bac/v1/files/" --input-extension "genomic.fna.gz"

Building index (ganon-build)

• max unique 19-mers: 11707451
• IBF calculated size with fp<=0.05: 110799.55MB (76435362 bits/bin * 12160 optimal bins [12144 real bins]) The following command failed to run: /lucmac/miniconda3/bin/ganon-build --seqid-bin-file ganon_db_tmp/acc_bin.txt --filter-size-bits 929454001920 --kmer-size 19 --hash-functions 3 --threads 32 --output-filter-file ganon_db.ibf --reference-files [files] --directory-reference-files RefSeqCG_arc_bac/v1/files/ --extension genomic.fna.gz

[Errno 7] Argument list too long: '/lucmac/miniconda3/bin/ganon-build' Error code: 0 Out: Error:

[pirovc]

Thanks for sharing again, there is indeed a bug causing this issue. I will provide a fix very soon.

In the meantime, please just concatenate your files together cat RefSeqCG_arc_bac/v1/files/*genomic.fna.gz > sequences.fna.gz and use it directly ganon build --db-prefix ganon_db -t 32 --input-files sequences.fna.gz