[2023-03-16 01:12:29,290] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,292] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,292] [INFO] DQC Reference Directory: /var/lib/cwl/stg6292649e-30c8-40cc-92f4-061ad03d4112/dqc_reference
[2023-03-16 01:12:30,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,462] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stgc2be35fb-1427-4557-b5a9-133979a7fc05/OceanDNA-a2352.fa | prodigal -d OceanDNA-a2352/cds.fna -a OceanDNA-a2352/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:34,750] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:34,751] [INFO] Task started: HMMsearch
[2023-03-16 01:12:34,751] [INFO] Running command: hmmsearch --tblout OceanDNA-a2352/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6292649e-30c8-40cc-92f4-061ad03d4112/dqc_reference/reference_markers.hmm OceanDNA-a2352/protein.faa > /dev/null
[2023-03-16 01:12:34,896] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:34,896] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc2be35fb-1427-4557-b5a9-133979a7fc05/OceanDNA-a2352.fa]
[2023-03-16 01:12:34,908] [INFO] Query marker FASTA was written to OceanDNA-a2352/markers.fasta
[2023-03-16 01:12:34,911] [INFO] Task started: Blastn
[2023-03-16 01:12:34,911] [INFO] Running command: blastn -query OceanDNA-a2352/markers.fasta -db /var/lib/cwl/stg6292649e-30c8-40cc-92f4-061ad03d4112/dqc_reference/reference_markers.fasta -out OceanDNA-a2352/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:35,598] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:35,601] [INFO] Selected 0 target genomes.
[2023-03-16 01:12:35,601] [INFO] Target genome list was writen to OceanDNA-a2352/target_genomes.txt
[2023-03-16 01:12:35,601] [ERROR] File is empty. [OceanDNA-a2352/target_genomes.txt]
[2023-03-16 01:12:35,601] [ERROR] Task failed. No target genome found.
[2023-03-16 01:12:35,601] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:12:35,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6292649e-30c8-40cc-92f4-061ad03d4112/dqc_reference/checkm_data
[2023-03-16 01:12:35,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:12:35,817] [INFO] Task started: CheckM
[2023-03-16 01:12:35,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2352/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2352/checkm_input OceanDNA-a2352/checkm_result
[2023-03-16 01:12:59,774] [INFO] Task succeeded: CheckM
[2023-03-16 01:12:59,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.73%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 01:12:59,864] [INFO] ===== Completeness check finished =====
[2023-03-16 01:12:59,864] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:12:59,864] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2352/markers.fasta)
[2023-03-16 01:12:59,865] [INFO] Task started: Blastn
[2023-03-16 01:12:59,865] [INFO] Running command: blastn -query OceanDNA-a2352/markers.fasta -db /var/lib/cwl/stg6292649e-30c8-40cc-92f4-061ad03d4112/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2352/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:13:01,250] [INFO] Task succeeded: Blastn
[2023-03-16 01:13:01,254] [INFO] Selected 8 target genomes.
[2023-03-16 01:13:01,254] [INFO] Target genome list was writen to OceanDNA-a2352/target_genomes_gtdb.txt
[2023-03-16 01:13:01,325] [INFO] Task started: fastANI
[2023-03-16 01:13:01,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2be35fb-1427-4557-b5a9-133979a7fc05/OceanDNA-a2352.fa --refList OceanDNA-a2352/target_genomes_gtdb.txt --output OceanDNA-a2352/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:13:03,862] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:03,865] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:13:03,866] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018667575.1	s__MGIIa-L1 sp018667575	83.0866	209	255	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.28	99.11	0.90	0.88	4	-
GCA_002172355.2	s__MGIIa-L1 sp002172355	82.2905	170	255	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.37	98.74	0.95	0.91	3	-
GCA_002697705.1	s__MGIIa-L1 sp002697705	82.2566	176	255	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.07	99.07	0.77	0.77	2	-
GCA_003602575.1	s__MGIIa-L1 sp003602575	80.9887	210	255	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:13:03,869] [INFO] GTDB search result was written to OceanDNA-a2352/result_gtdb.tsv
[2023-03-16 01:13:03,871] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:13:03,875] [INFO] DFAST_QC result json was written to OceanDNA-a2352/dqc_result.json
[2023-03-16 01:13:03,875] [INFO] DFAST_QC completed!
[2023-03-16 01:13:03,875] [INFO] Total running time: 0h0m35s