Suspect that that conda environment is not being created within the docker profile

[DanBeaton]

Suspect that that conda environment is not being created within the docker profile

[DanBeaton]

Additional information: after running NanoRTax using the conda profile I get the following error

Caused by:
java.nio.channels.OverlappingFileLockException

Creating the conda environment manually still produces the error. Running the fastp code on its own does work.

I suspect that the conda environment is not being created under either the docker or the conda profile.

[vicho33]

I have a similar problem:

Launching main.nf [soggy_gilbert] DSL1 - revision: 3ef505f614
WARN: Access to undefined parameter multiqc_config -- Initialise it to a default value eg. params.multiqc_config = some_value
WARN: Access to undefined parameter reads_rt -- Initialise it to a default value eg. params.reads_rt = some_value
WARN: Access to undefined parameter kraken -- Initialise it to a default value eg. params.kraken = some_value
WARN: Access to undefined parameter centrifuge -- Initialise it to a default value eg. params.centrifuge = some_value
WARN: Access to undefined parameter blast -- Initialise it to a default value eg. params.blast = some_value

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/rtnanopipeline v1.0dev

Run Name : soggy_gilbert
Reads : /Users/vicentearriagada/Documents/prueba_segunda_bar/Segunda_seq_16s/fastq_pass/barcode01/FAT29459_pass_barcode01_0ae29989_0.fastq
Max Resources : 128 GB memory, 16 cpus, 10d time per job
Output dir : /Users/vicentearriagada/centrigufe/results_seg_bar
Launch dir : /Users/vicentearriagada/centrigufe/NanoRTax
Working dir : /Users/vicentearriagada/centrigufe/NanoRTax/work
Script dir : /Users/vicentearriagada/centrigufe/NanoRTax
User : vicentearriagada
Config Profile : conda

WARN: Access to undefined parameter hostnames -- Initialise it to a default value eg. params.hostnames = some_value
executor > local (2)
executor > local (2)
[5f/3b9906] process > QC (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > qc_reporting -
[- ] process > read_binning_kraken -
[- ] process > agg_kraken -
[- ] process > kraken_push -
[- ] process > agg_kraken_diversity -
[57/a71840] process > output_documentation [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rtnanopipeline] Pipeline completed with errors-
WARN: There's no process matching config selector: get_software_versions
Error executing process > 'QC (1)'

Caused by:
Process QC (1) terminated with an error exit status (127)

Command executed:

barcode=$(basename $(dirname /Users/vicentearriagada/Documents/prueba_segunda_bar/Segunda_seq_16s/fastq_pass/barcode01/FAT29459_pass_barcode01_0ae29989_0.fastq))
fastp -i /Users/vicentearriagada/Documents/prueba_segunda_bar/Segunda_seq_16s/fastq_pass/barcode01/FAT29459_pass_barcode01_0ae29989_0.fastq -q 8 -l 1400 --length_limit 1700 -o $barcode_qced_reads.fastq --json $barcode_qc_report.txt
head -n30 $barcode_qc_report.txt | sed '30s/,/\n}/' > $barcode_qc_report.json
echo "}" >> $barcode_qc_report.json

Command exit status:
127

Command output:
(empty)

Command error:
.command.sh: line 3: fastp: command not found

Work dir:
/Users/vicentearriagada/centrigufe/NanoRTax/work/5f/3b99062b898c54cdc215c80464c3fb

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
I don't know that to do