N E X T F L O W  ~  version 23.10.1
Launching `mop_preprocess.nf` [compassionate_franklin] DSL2 - revision: ec40fe0af4


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

conffile.                 : final_summary_01.txt

fast5                     : 
fastq                     : /Users/didemdkn/Downloads/strvs45fastq3/**/*.fastq

reference                 : /Users/didemdkn/Downloads/Homo_sapiens.GRCh37.cdna.fa
annotation                : /Users/didemdkn/Downloads/Homo_sapiens.GRCh37.gtf

granularity.              : 1

ref_type                  : transcriptome
pars_tools                : drna_tool_splice_opt.tsv

output                    : /Users/didemdkn/Downloads/strvs45fastqpreprocess

GPU                       : OFF

basecalling               : guppy 
demultiplexing            : NO 
demulti_fast5             : NO

filtering                 : nanoq
mapping                   : minimap2

counting                  : nanocount
discovery                 : NO

cram_conv           	  : YES
subsampling_cram          : 50


saveSpace                 : YES
email                     : 

Skipping the email

----------------------CHECK TOOLS -----------------------------
> basecalling will be skipped
> demultiplexing will be skipped
mapping : minimap2
filtering : nanoq
counting : nanocount
> discovery will be skipped
--------------------------------------------------------------
[ed/f494fe] Submitted process > preprocess_simple:MINIMAP2:map (combined_str)
[e9/71a653] Submitted process > preprocess_simple:MINIMAP2:map (combined_45e2)
[b1/63d26f] Submitted process > preprocess_simple:FASTQC:fastQC (combined_str.fastq)
[e3/6197e0] Submitted process > preprocess_simple:FASTQC:fastQC (combined_45e2.fastq)
[96/7ab8f4] Submitted process > preprocess_simple:checkRef (Checking Homo_sapiens.GRCh37.cdna.fa)
ERROR ~ Error executing process > 'preprocess_simple:MINIMAP2:map (combined_45e2)'

Caused by:
  Process `preprocess_simple:MINIMAP2:map (combined_45e2)` terminated with an error exit status (1)

Command executed:

  minimap2 -t 1 -a -uf -ax splice -k14 Homo_sapiens.GRCh37.cdna.fa combined_45e2.fastq | samtools view -@ 1 -F4 -hSb - > combined_45e2.bam

Command exit status:
  1

Command output:
  (empty)

Command error:
  [M::mm_idx_gen::846.637*0.05] collected minimizers
  [main_samview] fail to read the header from "-".

Work dir:
  /Users/didemdkn/MOP2/MOP2/mop_preprocess/work/e9/71a6531c04a2fad2db9a8aea07d149

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

 -- Check '.nextflow.log' file for details
Pipeline BIOCORE@CRG Master of Pore - preprocess completed!
Started at  2024-03-14T23:27:26.508464+03:00
Finished at 2024-03-14T23:42:13.621084+03:00
Time elapsed: 14m 47s
Execution status: failed
WARN: Killing running tasks (3)