Run mop_preprocess with Apple M1 chip

Question

Run mop_preprocess with Apple M1 chip

Closed this issue 2 years ago · 7 comments

Hi,

I am running the mop_preprocess workflow in a computer with an Apple M1 chip. I am getting an error related to it. Is there any way to circumvent it? The workflow is completed successfully when I include just a couple of input file, but it crashes when I include the entire set of files I need to analyze.

Thanks!
Jesús.

N E X T F L O W ~ version 22.04.0
Launching mop_preprocess.nf [sad_majorana] DSL2 - revision: ec40fe0af4

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║║║║ ║╠═╝ ╠═╝├┬┘├┤ ├─┘├┬┘│ ││ ├┤ └─┐└─┐
╩ ╩╚═╝╩ ╩ ┴└─└─┘┴ ┴└─└─┘└─┘└─┘└─┘└─┘

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

conffile. : /Users/j/MOP2/data/W/final_summary_FAR92050_1b93b532.txt

fast5 :
fastq : /Users/j/MOP2/data/W/fastq_pass/*.fastq.gz

reference : /Users/j/MOP2/anno/At.fa
annotation :

granularity. : 5

ref_type : transcriptome
pars_tools : drna_tool_splice_opt.tsv

output : /Users/j/MOP2/output/

GPU : ON

basecalling : NO
demultiplexing : NO
demulti_fast5 : NO

filtering : nanoq
mapping : minimap2

counting : nanocount
discovery : bambu

cram_conv : NO
subsampling_cram : NO

saveSpace : NO
email :

Skipping the email

----------------------CHECK TOOLS -----------------------------

basecalling will be skipped
demultiplexing will be skipped
mapping : minimap2
filtering : nanoq
counting : nanocount
discovery : bambu

[- ] process > preprocess_simple:FASTQC:fa... -

[- ] process > preprocess_simple:FASTQC:fa... -
[- ] process > preprocess_simple:MINIMAP2:map -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

[- ] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 20
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 10
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (2)
[f5/7a6bac] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 41
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 36
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (9)
[d9/74fd83] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 60
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 53
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 72
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 64
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 86
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 81
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 118
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 104
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 178
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 168
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 185
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 175
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 198
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 186
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 208
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 196
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 210
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 201
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 231
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 218
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 252
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 233
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 270
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 259
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 296
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 283
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (10)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 323
[- ] process > preprocess_simple:MINIMAP2:map [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (11)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 0%] 0 of 323
[fd/bc4a52] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (12)
[7f/54b157] process > preprocess_simple:FASTQC:fa... [ 0%] 2 of 323
[44/96cc2e] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (13)
[f2/0e9713] process > preprocess_simple:FASTQC:fa... [ 0%] 3 of 323
[a6/dc7f07] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (14)
[bf/fb552b] process > preprocess_simple:FASTQC:fa... [ 1%] 4 of 323
[80/aae8d2] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (15)
[7b/80748a] process > preprocess_simple:FASTQC:fa... [ 1%] 5 of 323
[df/14a7ec] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (16)
[f5/7a6bac] process > preprocess_simple:FASTQC:fa... [ 1%] 6 of 323
[98/1e7dce] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (17)
[f6/65194f] process > preprocess_simple:FASTQC:fa... [ 2%] 7 of 323
[f9/242a42] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (19)
[20/952b18] process > preprocess_simple:FASTQC:fa... [ 2%] 9 of 323
[8f/41e61d] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (20)
[b2/64f673] process > preprocess_simple:FASTQC:fa... [ 3%] 10 of 323
[bb/6366af] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -

executor > local (21)
[cf/17126d] process > preprocess_simple:FASTQC:fa... [ 3%] 10 of 323
[bb/6366af] process > preprocess_simple:MINIMAP2:... [ 0%] 0 of 323
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -
Error executing process > 'preprocess_simple:MINIMAP2:map (FAR92050_pass_1b93b532_287)'

Caused by:
Process preprocess_simple:MINIMAP2:map (FAR92050_pass_1b93b532_287) terminated with an error exit status (1)

Command executed:

minimap2 -t 1 -a -uf -ax splice -k14 At.fa FAR92050_pass_1b93b532_287.fastq.gz | samtools view -@ 1 -F4 -hSb - > FAR92050_pass_1b93b532_287.bam

Command exit status:
1

Command output:
(empty)

Command error:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
[M::mm_idx_gen::29.912*0.65] collected minimizers
[main_samview] fail to read the header from "-".

Work dir:
/Users/j/MOP2/mop_preprocess/work/98/1e7dceeb1693b263391ae6cd69f897

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

Pipeline BIOCORE@CRG Master of Pore - preprocess completed!
Started at 2022-06-01T12:32:24.699108+02:00
Finished at 2022-06-01T12:34:35.078982+02:00
Time elapsed: 2m 10s
Execution status: failed
WARN: Killing running tasks (9)

executor > local (21)
[cf/17126d] process > preprocess_simple:FASTQC:fa... [ 3%] 10 of 323
[bb/6366af] process > preprocess_simple:MINIMAP2:... [ 1%] 4 of 322, failed: 4
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:SAMTOOLS_... -
[- ] process > preprocess_simple:bam2stats -
[- ] process > preprocess_simple:joinAlnStats -
[- ] process > preprocess_simple:NANOPLOT_... -
[- ] process > preprocess_simple:NANOCOUNT... -
[- ] process > preprocess_simple:AssignReads -
[- ] process > preprocess_simple:countStats -
[- ] process > preprocess_simple:joinCount... -
[- ] process > preprocess_simple:MULTIQC:m... -
Error executing process > 'preprocess_simple:MINIMAP2:map (FAR92050_pass_1b93b532_287)'

Caused by:
Process preprocess_simple:MINIMAP2:map (FAR92050_pass_1b93b532_287) terminated with an error exit status (1)

Command executed:

minimap2 -t 1 -a -uf -ax splice -k14 At.fa FAR92050_pass_1b93b532_287.fastq.gz | samtools view -@ 1 -F4 -hSb - > FAR92050_pass_1b93b532_287.bam

Command exit status:
1

Command output:
(empty)

Command error:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
[M::mm_idx_gen::29.912*0.65] collected minimizers
[main_samview] fail to read the header from "-".

Work dir:
/Users/jj/MOP2/mop_preprocess/work/98/1e7dceeb1693b263391ae6cd69f897

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

Answer 1 · 2022-06-07T16:56:37.000Z

Are you using docker? Here I found you can add an extra parameter:
https://stackoverflow.com/questions/66662820/m1-docker-preview-and-keycloak-images-platform-linux-amd64-does-not-match-th

--platform linux/amd64

You need to add it to the configuration file named local.config within local.config

    containerOptions = { workflow.containerEngine == "docker" ? '-u $(id -u):$(id -g) --platform linux/amd64': null}

Let me know if it works for you

L

Answer 2 · 2022-06-08T16:06:52.000Z

That solved the problem!

Thank you so much,
Jesús.

Answer 3 · 2022-06-09T10:33:43.000Z

Nice! I'll add to the documentation

Answer 4 · 2022-06-09T10:38:49.000Z

Even better, I added a new profile:

-profile m1mac

Answer 5 · 2023-04-12T08:34:44.000Z

Hi! I met the same problem.
However, my operational system is Ubuntu.
I use the solution you offer below, but it isn't work.
Any solution?
Thank you!

Answer 6 · 2023-04-12T09:26:32.000Z

Hi, which error do you have? I fear this is out of the scope of this project to support multiple CPU architectures since the original tool embedded are not written for this CPUs

Answer 7 · 2023-04-13T01:43:46.000Z

Hi!
The error is the same as below :" [main_samview] fail to read the header from "-".
I don't understand the multiple CPU you said. Is that mean the pipeline don't support multi CPU run? (to reach that I change local.config)
Thank you！

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

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