[2023-03-16 18:00:27,870] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:00:27,870] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:00:27,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eb3bfa4-43a7-4f06-b3ad-14e949d9bafb/dqc_reference
[2023-03-16 18:00:28,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:00:28,967] [INFO] Task started: Prodigal
[2023-03-16 18:00:28,967] [INFO] Running command: cat /var/lib/cwl/stg861e1fc8-16c9-46fe-a2fe-1a546fb6e3de/OceanDNA-b10594.fa | prodigal -d OceanDNA-b10594/cds.fna -a OceanDNA-b10594/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:00:38,062] [INFO] Task succeeded: Prodigal
[2023-03-16 18:00:38,062] [INFO] Task started: HMMsearch
[2023-03-16 18:00:38,062] [INFO] Running command: hmmsearch --tblout OceanDNA-b10594/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eb3bfa4-43a7-4f06-b3ad-14e949d9bafb/dqc_reference/reference_markers.hmm OceanDNA-b10594/protein.faa > /dev/null
[2023-03-16 18:00:38,228] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:00:38,228] [INFO] Found 6/6 markers.
[2023-03-16 18:00:38,240] [INFO] Query marker FASTA was written to OceanDNA-b10594/markers.fasta
[2023-03-16 18:00:38,241] [INFO] Task started: Blastn
[2023-03-16 18:00:38,241] [INFO] Running command: blastn -query OceanDNA-b10594/markers.fasta -db /var/lib/cwl/stg3eb3bfa4-43a7-4f06-b3ad-14e949d9bafb/dqc_reference/reference_markers.fasta -out OceanDNA-b10594/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:00:38,799] [INFO] Task succeeded: Blastn
[2023-03-16 18:00:38,800] [INFO] Selected 37 target genomes.
[2023-03-16 18:00:38,800] [INFO] Target genome list was writen to OceanDNA-b10594/target_genomes.txt
[2023-03-16 18:00:38,868] [INFO] Task started: fastANI
[2023-03-16 18:00:38,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg861e1fc8-16c9-46fe-a2fe-1a546fb6e3de/OceanDNA-b10594.fa --refList OceanDNA-b10594/target_genomes.txt --output OceanDNA-b10594/fastani_result.tsv --threads 1
[2023-03-16 18:01:02,855] [INFO] Task succeeded: fastANI
[2023-03-16 18:01:02,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eb3bfa4-43a7-4f06-b3ad-14e949d9bafb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:01:02,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eb3bfa4-43a7-4f06-b3ad-14e949d9bafb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:01:02,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:01:02,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:01:02,856] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-16 18:01:02,856] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10594/tc_result.tsv
[2023-03-16 18:01:02,857] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:01:02,857] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:01:02,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eb3bfa4-43a7-4f06-b3ad-14e949d9bafb/dqc_reference/checkm_data
[2023-03-16 18:01:02,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:01:03,029] [INFO] Task started: CheckM
[2023-03-16 18:01:03,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10594/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10594/checkm_input OceanDNA-b10594/checkm_result
[2023-03-16 18:01:43,931] [INFO] Task succeeded: CheckM
[2023-03-16 18:01:43,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:01:43,936] [INFO] ===== Completeness check finished =====
[2023-03-16 18:01:43,936] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:01:43,936] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10594/markers.fasta)
[2023-03-16 18:01:43,937] [INFO] Task started: Blastn
[2023-03-16 18:01:43,937] [INFO] Running command: blastn -query OceanDNA-b10594/markers.fasta -db /var/lib/cwl/stg3eb3bfa4-43a7-4f06-b3ad-14e949d9bafb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10594/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:01:45,011] [INFO] Task succeeded: Blastn
[2023-03-16 18:01:45,012] [INFO] Selected 30 target genomes.
[2023-03-16 18:01:45,012] [INFO] Target genome list was writen to OceanDNA-b10594/target_genomes_gtdb.txt
[2023-03-16 18:01:45,203] [INFO] Task started: fastANI
[2023-03-16 18:01:45,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg861e1fc8-16c9-46fe-a2fe-1a546fb6e3de/OceanDNA-b10594.fa --refList OceanDNA-b10594/target_genomes_gtdb.txt --output OceanDNA-b10594/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:02:07,280] [INFO] Task succeeded: fastANI
[2023-03-16 18:02:07,287] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:02:07,287] [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
GCF_001735715.1	s__GCA001735715 sp001735715	80.2037	222	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_002684355.1	s__UBA3537 sp002684355	77.0885	85	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002709185.1	s__UBA3537 sp002709185	76.8048	62	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	76.71	83	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725015.1	s__UBA3537 sp002725015	76.6034	59	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	76.4996	73	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690085.1	s__UBA3537 sp002690085	76.4333	66	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	76.3676	63	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698705.1	s__UBA3537 sp002698705	76.1552	69	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	76.1225	64	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	76.0588	59	354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:02:07,288] [INFO] GTDB search result was written to OceanDNA-b10594/result_gtdb.tsv
[2023-03-16 18:02:07,288] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:02:07,290] [INFO] DFAST_QC result json was written to OceanDNA-b10594/dqc_result.json
[2023-03-16 18:02:07,290] [INFO] DFAST_QC completed!
[2023-03-16 18:02:07,290] [INFO] Total running time: 0h1m39s