N E X T F L O W ~ version 22.10.7 Launching `mop_preprocess.nf` [extravagant_noether] DSL2 - revision: 5edc7cb039 ╔╦╗╔═╗╔═╗ ╔═╗┬─┐┌─┐┌─┐┬─┐┌─┐┌─┐┌─┐┌─┐┌─┐ ║║║║ ║╠═╝ ╠═╝├┬┘├┤ ├─┘├┬┘│ ││ ├┤ └─┐└─┐ ╩ ╩╚═╝╩ ╩ ┴└─└─┘┴ ┴└─└─┘└─┘└─┘└─┘└─┘ ==================================================== 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: ERROR : Unknown image format/type: /nfs/users/enovoa/ntodorov/nt_bin/MOP3/MoP3/mop_preprocess/../singularity/biocorecrg-mopprepr-0.7.img ABORT : Retval = 255  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)