N E X T F L O W ~ version 22.10.7
Launching `mop_preprocess.nf` [extravagant_noether] DSL2 - revision: 5edc7cb039
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====================================================
BIOCORE@CRG Master of Pores 2. Preprocessing - N F ~ version 2.0
====================================================
conffile : /no_backup_isis/enovoa/data/ont/raul_mendes_pAtail/RNA121192/RNA121192/20190910_1316_MN27184_FAL15400_ef2e3b1b/final_summaryv2.txt
fast5 : /no_backup_isis/enovoa/data/ont/raul_mendes_pAtail/RNA121192/RNA121192/20190910_1316_MN27184_FAL15400_ef2e3b1b/fast5/*.fast5
fastq :
reference : /no_backup_isis/enovoa/reference_fasta/mouse/gencode.vM24.transcripts.fa.gz
annotation :
granularity : 1
ref_type : transcriptome
pars_tools : /nfs/users/enovoa/ntodorov/nt_bin/MOP3/MoP3/mop_preprocess/tool_opts/drna_tool_splice_opt.tsv
barcodes :
output : /users/enovoa/ntodorov/tests_etc/MoP3_results
GPU : ON
basecalling : guppy
demultiplexing : deeplexicon
demulti_fast5 : YES
filtering : NO
mapping : minimap2
counting : nanocount
discovery : NO
cram_conv : YES
subsampling_cram : 50
saveSpace : NO
email : nikola.todorov@crg.es
Sending the email to nikola.todorov@crg.es
----------------------CHECK TOOLS -----------------------------
basecalling : guppy
demultiplexing : deeplexicon
mapping : minimap2
> filtering will be skipped
counting : nanocount
> discovery will be skipped
--------------------------------------------------------------
Pulling Singularity image docker://lpryszcz/deeplexicon:1.2.0-gpu [cache /nfs/users/enovoa/ntodorov/nt_bin/MOP3/MoP3/mop_preprocess/../singularity/lpryszcz-deeplexicon-1.2.0-gpu.img]
[f3/ffd449] Submitted process > preprocess_flow:checkRef (Checking gencode.vM24.transcripts.fa.gz)
[b4/663997] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---7)
[44/1e16f8] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---8)
[65/583fce] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---3)
[53/dfe92b] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---6)
[a7/e665b3] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---5)
[71/c50f6c] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---4)
[9e/1a3187] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---2)
[b8/ed1840] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---9)
[6f/8b6620] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---10)
[0f/74d8ac] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---1)
[65/72fa17] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---11)
[5b/aa318d] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---14)
[f2/0b8968] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---12)
[d0/8bd16f] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---15)
[63/152143] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---16)
[36/8f3ed8] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---17)
[85/47b9c6] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---13)
[c2/3f1ccc] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---18)
[4e/cba7d7] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---19)
[a3/691b47] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---20)
[df/30455b] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---21)
[4e/57d8f0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---23)
[b2/683ab3] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---22)
[09/455b74] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---24)
[50/50f6d5] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---28)
[34/2f715d] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---26)
[2b/b013f0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---30)
[a3/308d3d] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---32)
[2b/fdca41] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---29)
[f8/7fb0f1] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---27)
[99/67338a] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---25)
[bb/fdba7e] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---31)
[c9/792638] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---33)
[3f/554e34] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---34)
[63/f9c781] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---37)
[ed/684210] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---35)
[a2/3d344d] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---36)
[89/a1d47f] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---38)
[ac/b03934] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---39)
[26/694621] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---40)
[8c/04b2e6] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---42)
[29/2108aa] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---43)
[c0/2b436c] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---44)
[f5/565551] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---41)
[59/98c6af] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---46)
[57/fff1bb] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---47)
[b0/343487] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---45)
[16/b98346] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---50)
[0d/90bc42] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---48)
[c5/d78f07] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---53)
[3a/777405] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---54)
[07/fe777e] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---51)
[7f/2803b0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---49)
[5d/c3e9eb] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---52)
[da/b855c4] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---55)
[c1/c3a80a] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---58)
[a8/74b8a0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---56)
[e3/55e78f] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---57)
[d5/4bd7a3] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---60)
[40/303d3b] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---65)
[2b/67c7f0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---61)
[82/7f072d] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---66)
[5b/6d97ac] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---59)
[08/2765b3] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---68)
[1e/146c58] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---62)
[b4/d51a7b] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---63)
[a7/a2da11] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---64)
[c2/a5714b] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---67)
[45/097399] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---69)
[2b/0d8b61] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---70)
[bb/968e23] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---75)
[d3/92c36e] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---71)
[47/be2ff0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---73)
[6f/d40a06] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---80)
[1a/e35747] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---72)
[3b/5a4797] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---76)
[3b/2ba519] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---74)
[e5/ee508c] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---79)
[a2/436044] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---82)
[24/41c32d] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---77)
[58/20973a] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---81)
[96/39a27d] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---78)
[d7/dddd38] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---83)
[03/fcc025] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---87)
[c1/5599c3] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---90)
[98/980554] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---84)
[0d/cda364] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---89)
[99/881e0e] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---88)
[c3/942492] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---86)
[ba/2394c0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---85)
[5b/3a1081] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---96)
[44/f50df0] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---95)
[c5/19442b] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---98)
[60/60e356] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---91)
[e9/4d08b2] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---97)
[2b/93f93f] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---92)
[d5/ca951e] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---99)
[09/683d22] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---102)
[80/1461bb] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---94)
[04/049056] Submitted process > flow2:GUPPY_BASECALL:baseCall (fast5---105)
Error executing process > 'preprocess_flow:checkRef (Checking gencode.vM24.transcripts.fa.gz)'
Caused by:
Process `preprocess_flow:checkRef (Checking gencode.vM24.transcripts.fa.gz)` terminated with an error exit status (255)
Command executed:
if [ `echo gencode.vM24.transcripts.fa.gz | grep ".gz"` ]; then
zcat gencode.vM24.transcripts.fa.gz > reference.fa
else
ln -s gencode.vM24.transcripts.fa.gz reference.fa
fi
Command exit status:
255
Command output:
(empty)
Command error:
[91mERROR : Unknown image format/type: /nfs/users/enovoa/ntodorov/nt_bin/MOP3/MoP3/mop_preprocess/../singularity/biocorecrg-mopprepr-0.7.img
[0m[31mABORT : Retval = 255
[0m
Work dir:
/nfs/users/enovoa/ntodorov/nt_bin/MOP3/MoP3/mop_preprocess/work/f3/ffd449a39f9fcce8d9883c7ce5b826
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 2023-03-01T13:47:55.995176+01:00
Finished at 2023-03-01T13:48:51.179837+01:00
Time elapsed: 55.2s
Execution status: failed
Failed to invoke `workflow.onComplete` event handler
-- Check script 'mop_preprocess.nf' at line: 685 or see '.nextflow.log' file for more details
WARN: Killing running tasks (100)