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 (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