[2023-03-17 03:50:13,764] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:13,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:13,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e89716-120a-475d-b656-1946ff3f4a5f/dqc_reference
[2023-03-17 03:50:15,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:15,140] [INFO] Task started: Prodigal
[2023-03-17 03:50:15,140] [INFO] Running command: cat /var/lib/cwl/stg316f2e1a-ccbb-499a-937a-878eeafc694d/OceanDNA-b6757.fa | prodigal -d OceanDNA-b6757/cds.fna -a OceanDNA-b6757/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:30,445] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:30,445] [INFO] Task started: HMMsearch
[2023-03-17 03:50:30,445] [INFO] Running command: hmmsearch --tblout OceanDNA-b6757/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e89716-120a-475d-b656-1946ff3f4a5f/dqc_reference/reference_markers.hmm OceanDNA-b6757/protein.faa > /dev/null
[2023-03-17 03:50:30,626] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:30,627] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg316f2e1a-ccbb-499a-937a-878eeafc694d/OceanDNA-b6757.fa]
[2023-03-17 03:50:30,643] [INFO] Query marker FASTA was written to OceanDNA-b6757/markers.fasta
[2023-03-17 03:50:30,643] [INFO] Task started: Blastn
[2023-03-17 03:50:30,643] [INFO] Running command: blastn -query OceanDNA-b6757/markers.fasta -db /var/lib/cwl/stg20e89716-120a-475d-b656-1946ff3f4a5f/dqc_reference/reference_markers.fasta -out OceanDNA-b6757/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:31,249] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:31,249] [INFO] Selected 17 target genomes.
[2023-03-17 03:50:31,250] [INFO] Target genome list was writen to OceanDNA-b6757/target_genomes.txt
[2023-03-17 03:50:31,260] [INFO] Task started: fastANI
[2023-03-17 03:50:31,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg316f2e1a-ccbb-499a-937a-878eeafc694d/OceanDNA-b6757.fa --refList OceanDNA-b6757/target_genomes.txt --output OceanDNA-b6757/fastani_result.tsv --threads 1
[2023-03-17 03:50:42,264] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:42,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e89716-120a-475d-b656-1946ff3f4a5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:42,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e89716-120a-475d-b656-1946ff3f4a5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:42,274] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:42,275] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:50:42,275] [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
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	79.2813	372	854	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	79.2704	369	854	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	79.2674	377	854	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	79.2556	374	854	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	79.2137	378	854	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	79.038	349	854	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	79.0022	392	854	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.8934	383	854	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.8546	333	854	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.7295	338	854	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	78.3752	322	854	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.8433	241	854	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.5905	229	854	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	77.54	213	854	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.4732	180	854	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.4154	162	854	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	77.4116	197	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:42,275] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6757/tc_result.tsv
[2023-03-17 03:50:42,275] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:42,275] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:42,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e89716-120a-475d-b656-1946ff3f4a5f/dqc_reference/checkm_data
[2023-03-17 03:50:42,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:42,280] [INFO] Task started: CheckM
[2023-03-17 03:50:42,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6757/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6757/checkm_input OceanDNA-b6757/checkm_result
[2023-03-17 03:51:22,348] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:22,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:22,351] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:22,351] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:22,351] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6757/markers.fasta)
[2023-03-17 03:51:22,351] [INFO] Task started: Blastn
[2023-03-17 03:51:22,351] [INFO] Running command: blastn -query OceanDNA-b6757/markers.fasta -db /var/lib/cwl/stg20e89716-120a-475d-b656-1946ff3f4a5f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6757/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:23,295] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:23,296] [INFO] Selected 15 target genomes.
[2023-03-17 03:51:23,296] [INFO] Target genome list was writen to OceanDNA-b6757/target_genomes_gtdb.txt
[2023-03-17 03:51:23,350] [INFO] Task started: fastANI
[2023-03-17 03:51:23,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg316f2e1a-ccbb-499a-937a-878eeafc694d/OceanDNA-b6757.fa --refList OceanDNA-b6757/target_genomes_gtdb.txt --output OceanDNA-b6757/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:33,741] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:33,750] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:51:33,750] [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_900114265.1	s__Flaviramulus basaltis	80.1338	425	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.9281	373	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	79.5594	372	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	79.2766	301	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	79.2701	376	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	79.2553	378	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004791695.1	s__Flavivirga rizhaonensis	79.2513	371	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	79.2137	378	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	79.119	381	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.938	344	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900112395.1	s__Algibacter lectus	78.916	381	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_008033385.1	s__Algibacter pacificus	78.8671	332	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.526	342	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	78.3752	322	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	77.4899	179	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:33,750] [INFO] GTDB search result was written to OceanDNA-b6757/result_gtdb.tsv
[2023-03-17 03:51:33,750] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:33,752] [INFO] DFAST_QC result json was written to OceanDNA-b6757/dqc_result.json
[2023-03-17 03:51:33,752] [INFO] DFAST_QC completed!
[2023-03-17 03:51:33,752] [INFO] Total running time: 0h1m20s