[2023-03-18 08:17:17,750] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,750] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b35fbdb-5170-4331-998f-b18fc5539959/dqc_reference
[2023-03-18 08:17:18,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stgda646d94-f351-4d7d-ac04-05fbba2f065c/OceanDNA-b8985.fa | prodigal -d OceanDNA-b8985/cds.fna -a OceanDNA-b8985/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:27,242] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:27,243] [INFO] Task started: HMMsearch
[2023-03-18 08:17:27,243] [INFO] Running command: hmmsearch --tblout OceanDNA-b8985/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b35fbdb-5170-4331-998f-b18fc5539959/dqc_reference/reference_markers.hmm OceanDNA-b8985/protein.faa > /dev/null
[2023-03-18 08:17:27,455] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:27,455] [INFO] Found 6/6 markers.
[2023-03-18 08:17:27,465] [INFO] Query marker FASTA was written to OceanDNA-b8985/markers.fasta
[2023-03-18 08:17:27,465] [INFO] Task started: Blastn
[2023-03-18 08:17:27,465] [INFO] Running command: blastn -query OceanDNA-b8985/markers.fasta -db /var/lib/cwl/stg0b35fbdb-5170-4331-998f-b18fc5539959/dqc_reference/reference_markers.fasta -out OceanDNA-b8985/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:28,056] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:28,057] [INFO] Selected 28 target genomes.
[2023-03-18 08:17:28,057] [INFO] Target genome list was writen to OceanDNA-b8985/target_genomes.txt
[2023-03-18 08:17:28,072] [INFO] Task started: fastANI
[2023-03-18 08:17:28,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgda646d94-f351-4d7d-ac04-05fbba2f065c/OceanDNA-b8985.fa --refList OceanDNA-b8985/target_genomes.txt --output OceanDNA-b8985/fastani_result.tsv --threads 1
[2023-03-18 08:17:45,815] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:45,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b35fbdb-5170-4331-998f-b18fc5539959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:45,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b35fbdb-5170-4331-998f-b18fc5539959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:45,816] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:45,816] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:45,816] [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
--------------------------------------------------------------------------------
[2023-03-18 08:17:45,816] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8985/tc_result.tsv
[2023-03-18 08:17:45,816] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:45,816] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:45,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b35fbdb-5170-4331-998f-b18fc5539959/dqc_reference/checkm_data
[2023-03-18 08:17:45,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:45,822] [INFO] Task started: CheckM
[2023-03-18 08:17:45,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8985/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8985/checkm_input OceanDNA-b8985/checkm_result
[2023-03-18 08:18:11,721] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:11,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:11,723] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:11,723] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:11,723] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8985/markers.fasta)
[2023-03-18 08:18:11,723] [INFO] Task started: Blastn
[2023-03-18 08:18:11,723] [INFO] Running command: blastn -query OceanDNA-b8985/markers.fasta -db /var/lib/cwl/stg0b35fbdb-5170-4331-998f-b18fc5539959/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8985/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:12,730] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:12,731] [INFO] Selected 17 target genomes.
[2023-03-18 08:18:12,731] [INFO] Target genome list was writen to OceanDNA-b8985/target_genomes_gtdb.txt
[2023-03-18 08:18:12,855] [INFO] Task started: fastANI
[2023-03-18 08:18:12,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgda646d94-f351-4d7d-ac04-05fbba2f065c/OceanDNA-b8985.fa --refList OceanDNA-b8985/target_genomes_gtdb.txt --output OceanDNA-b8985/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:17,581] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:17,589] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:18:17,589] [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_002703065.1	s__MED-G14 sp002703065	97.628	272	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004321735.1	s__MED-G14 sp004321735	93.3154	320	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.77	95.40	0.78	0.75	4	-
GCA_902554655.1	s__MED-G14 sp902554655	78.4441	129	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.59	99.59	0.62	0.62	2	-
GCA_002693085.1	s__MED-G14 sp002693085	78.1831	131	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520835.1	s__MED-G14 sp902520835	78.1547	164	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457715.1	s__MED-G14 sp002457715	77.9092	132	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	98.34	98.31	0.91	0.89	3	-
GCA_002702385.1	s__MED-G14 sp002702385	77.7835	140	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574335.1	s__MED-G14 sp902574335	77.4417	68	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331885.1	s__MED-G14 sp003331885	76.9858	96	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
GCA_902515405.1	s__MED-G14 sp902515405	76.9156	101	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606555.1	s__MED-G14 sp902606555	76.4811	84	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586095.1	s__MED-G14 sp902586095	76.3502	63	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	76.0344	81	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCF_001975665.1	s__Polaribacter reichenbachii	75.5248	54	460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:17,589] [INFO] GTDB search result was written to OceanDNA-b8985/result_gtdb.tsv
[2023-03-18 08:18:17,590] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:17,591] [INFO] DFAST_QC result json was written to OceanDNA-b8985/dqc_result.json
[2023-03-18 08:18:17,591] [INFO] DFAST_QC completed!
[2023-03-18 08:18:17,591] [INFO] Total running time: 0h0m60s