Hi again! Sorry for all my issue requests, but I am learning bioinformatics as a hobby with RNAseq, therefore, my knowledge on code is very limited!!

So I wanted to run the pipeline on my own time with my laptop, but I am having issues with docker; thus I do not know if I installed Nextflow + Docker + Guppy correctly and I was hoping if anyone had written up a documentation of running MOP2 on an Apple laptop! It would be super helpful to me!

attached is the error I am currently seeing while running mop_preprocess with test configurations!

N E X T F L O W ~ version 21.10.6 Launching mop_preprocess.nf [scruffy_wing] - revision: ecf5447b25

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==================================================== BIOCORE@CRG Master of Pores 2. Preprocessing - N F ~ version 2.0

conffile : final_summary_01.txt

fast5 : /Users/anaescobedo/MOP2/mop_preprocess/../data/*/.fast5 fastq :

reference : /Users/anaescobedo/MOP2/mop_preprocess/../anno/yeast_rRNA_ref.fa.gz annotation :

granularity : 1

ref_type : transcriptome pars_tools : drna_tool_splice_opt.tsv

output : /Users/anaescobedo/MOP2/mop_preprocess/output

GPU : OFF

basecalling : guppy demultiplexing : NO demulti_fast5 : NO

filtering : nanoq mapping : graphmap

counting : nanocount discovery : NO

cram_conv : YES subsampling_cram : 50

saveSpace : NO

email : lucacozzuto@crg.es

Sending the email to lucacozzuto@crg.es

----------------------CHECK TOOLS ----------------------------- basecalling : guppy

demultiplexing will be skipped mapping : graphmap filtering : nanoq counting : nanocount discovery will be skipped

[- ] process > flow1:GUPPY_BASECALL:baseCall - [- ] process > flow1:NANOQ_FILTER:filter - [- ] process > preprocess_flow:MinIONQC - [- ] process > preprocess_flow:RNA2DNA - [- ] process > preprocess_flow:GRAPHMAP:map - [- ] process > preprocess_flow:SAMTOOLS_CAT:catAln - [- ] process > preprocess_flow:SAMTOOLS_SORT:sortAln - [- ] process > preprocess_flow:SAMTOOLS_INDEX:indexBam - [- ] process > preprocess_flow:checkRef - [- ] process > preprocess_flow:bam2Cram - [- ] process > preprocess_flow:bam2stats - [- ] process > preprocess_flow:joinAlnStats - [- ] process > preprocess_flow:NANOPLOT_QC:MOP_nanoPlot - [- ] process > preprocess_flow:concatenateFastQFiles - [- ] process > preprocess_flow:FASTQC:fastQC - [- ] process > preprocess_flow:NANOCOUNT:nanoCount - [- ] process > preprocess_flow:AssignReads -

executor > local (1) [0c/aafd62] process > flow1:GUPPY_BASECALL:baseCall (wt---2) [ 0%] 0 of 2 [- ] process > flow1:NANOQ_FILTER:filter - [- ] process > preprocess_flow:MinIONQC - [- ] process > preprocess_flow:RNA2DNA - [- ] process > preprocess_flow:GRAPHMAP:map - [- ] process > preprocess_flow:SAMTOOLS_CAT:catAln - [- ] process > preprocess_flow:SAMTOOLS_SORT:sortAln - [- ] process > preprocess_flow:SAMTOOLS_INDEX:indexBam - [- ] process > preprocess_flow:checkRef [ 0%] 0 of 1 [- ] process > preprocess_flow:bam2Cram - [- ] process > preprocess_flow:bam2stats - [- ] process > preprocess_flow:joinAlnStats - [- ] process > preprocess_flow:NANOPLOT_QC:MOP_nanoPlot - [- ] process > preprocess_flow:concatenateFastQFiles - [- ] process > preprocess_flow:FASTQC:fastQC - [- ] process > preprocess_flow:NANOCOUNT:nanoCount - [- ] process > preprocess_flow:AssignReads - [- ] process > preprocess_flow:countStats - [- ] process > preprocess_flow:joinCountStats - [- ] process > preprocess_flow:MULTIQC:makeReport -

executor > local (2) [0c/aafd62] process > flow1:GUPPY_BASECALL:baseCall (wt---2) [- ] process > flow1:NANOQ_FILTER:filter [- ] process > preprocess_flow:MinIONQC [- ] process > preprocess_flow:RNA2DNA [- ] process > preprocess_flow:GRAPHMAP:map [- ] process > preprocess_flow:SAMTOOLS_CAT:catAln [- ] process > preprocess_flow:SAMTOOLS_SORT:sortAln [- ] process > preprocess_flow:SAMTOOLS_INDEX:indexBam [e7/f9cd7c] process > preprocess_flow:checkRef [- ] process > preprocess_flow:bam2Cram [- ] process > preprocess_flow:bam2stats [- ] process > preprocess_flow:joinAlnStats [- ] process > preprocess_flow:NANOPLOT_QC:MOP_nanoPlot [- ] process > preprocess_flow:concatenateFastQFiles [- ] process > preprocess_flow:FASTQC:fastQC [- ] process > preprocess_flow:NANOCOUNT:nanoCount [- ] process > preprocess_flow:AssignReads [- ] process > preprocess_flow:countStats [- ] process > preprocess_flow:joinCountStats [- ] process > preprocess_flow:MULTIQC:makeReport [ 0%] 0 of 2 - - - - - - - (Checking yeast_rRNA_ref.fa.gz) [ 0%] 0 of 1 - - - - - - - - - - -

executor > local (2) [0c/aafd62] process > flow1:GUPPY_BASECALL:baseCall (wt---2) [ 0%] 0 of 2 [- ] process > flow1:NANOQ_FILTER:filter - [- ] process > preprocess_flow:MinIONQC - [- ] process > preprocess_flow:RNA2DNA - [- ] process > preprocess_flow:GRAPHMAP:map - [- ] process > preprocess_flow:SAMTOOLS_CAT:catAln - [- ] process > preprocess_flow:SAMTOOLS_SORT:sortAln - [- ] process > preprocess_flow:SAMTOOLS_INDEX:indexBam - [e7/f9cd7c] process > preprocess_flow:checkRef (Checking yeast_rRNA_ref.fa.gz) [ 0%] 0 of 1 [- ] process > preprocess_flow:bam2Cram - [- ] process > preprocess_flow:bam2stats - [- ] process > preprocess_flow:joinAlnStats - [- ] process > preprocess_flow:NANOPLOT_QC:MOP_nanoPlot - [- ] process > preprocess_flow:concatenateFastQFiles - [- ] process > preprocess_flow:FASTQC:fastQC - [- ] process > preprocess_flow:NANOCOUNT:nanoCount - [- ] process > preprocess_flow:AssignReads - [- ] process > preprocess_flow:countStats - [- ] process > preprocess_flow:joinCountStats - [- ] process > preprocess_flow:MULTIQC:makeReport - Error executing process > 'flow1:GUPPY_BASECALL:baseCall (wt---2)'

Caused by: Process flow1:GUPPY_BASECALL:baseCall (wt---2) terminated with an error exit status (125)

Command executed:

guppy_basecaller --fast5_out --flowcell FLO-MIN106 --kit SQK-RNA002 -i ./ --save_path ./wt---2_out --gpu_runners_per_device 1 --cpu_threads_per_caller 1 --num_callers 8 cat wt---2_out/.fastq >> wt---2.fastq rm wt---2_out/.fastq gzip wt---2.fastq

Command exit status: 125

Command output: (empty)

Command error: docker: Error response from daemon: Range of CPUs is from 0.01 to 4.00, as there are only 4 CPUs available. See 'docker run --help'.

Work dir: /Users/anaescobedo/MOP2/mop_preprocess/work/0c/aafd6231abadda45a3e00e0446f905

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Pipeline BIOCORE@CRG Master of Pore - preprocess completed! Started at 2022-04-06T17:17:10.093-04:00 Finished at 2022-04-06T17:17:24.933-04:00 Time elapsed: 14.8s Execution status: failed

biocorecrg / MOP2

Running mop_preprocess on MacbookPro/macOS Monterey #18

==================================================== BIOCORE@CRG Master of Pores 2. Preprocessing - N F ~ version 2.0

demultiplexing will be skipped mapping : graphmap filtering : nanoq counting : nanocount discovery will be skipped