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biosustain / dsp_nf-metagenomics

Shotgun metagenomics pipeline to process microbiome samples
GNU General Public License v3.0
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Testing the pipeline #3

Open marcoreverenna opened 6 months ago

marcoreverenna commented 6 months ago

Considering these parameters:

host_genome  : az://metanfnewsample/orange_genome/host_genome/GCF_022201045.2_DVS_A1.0_genomic.fna
reads        : az://metanfnewsample/data/*_{1,2}.fq.gz
genomedir    : az://metanfnewsample/orange_genome/host_genome
metaphlan_db : az://metanfnewsample/databases/metaphlan_db
outdir       : az://metanfnewsample/results

The pipeline breaks in the kneddata process.

Uploading local `bin` scripts folder to az://results/tmp/a8/bc9f8851d939e7c80287c7b03f381f/bin
[O1, [/metanfnewsample/data/O1_1.fq.gz, /metanfnewsample/data/O1_2.fq.gz]]
[bc/7762c0] Submitted process > QC (Kneaddata on O1)
[e0/d873b2] Submitted process > FASTQC (FASTQC on O1)
ERROR ~ Error executing process > 'QC (Kneaddata on O1)'

kneaddata -i1 O1_1.fq.gz -i2 O1_2.fq.gz     --threads 8     --output .  --bypass-trim

  mkdir -p kneaddata_logs
  mv O1_1_kneaddata.log kneaddata_logs/