[2023-03-15 11:09:10,825] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,825] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b252d11-13fc-41d9-a87c-31e97b948b4d/dqc_reference
[2023-03-15 11:09:12,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,122] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,122] [INFO] Running command: cat /var/lib/cwl/stgaa896c2e-e5fe-4cdc-bde3-ce4c9435992b/OceanDNA-b6485.fa | prodigal -d OceanDNA-b6485/cds.fna -a OceanDNA-b6485/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:29,164] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:29,165] [INFO] Task started: HMMsearch
[2023-03-15 11:09:29,165] [INFO] Running command: hmmsearch --tblout OceanDNA-b6485/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b252d11-13fc-41d9-a87c-31e97b948b4d/dqc_reference/reference_markers.hmm OceanDNA-b6485/protein.faa > /dev/null
[2023-03-15 11:09:29,421] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:29,422] [INFO] Found 6/6 markers.
[2023-03-15 11:09:29,440] [INFO] Query marker FASTA was written to OceanDNA-b6485/markers.fasta
[2023-03-15 11:09:29,440] [INFO] Task started: Blastn
[2023-03-15 11:09:29,440] [INFO] Running command: blastn -query OceanDNA-b6485/markers.fasta -db /var/lib/cwl/stg2b252d11-13fc-41d9-a87c-31e97b948b4d/dqc_reference/reference_markers.fasta -out OceanDNA-b6485/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:30,061] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:30,062] [INFO] Selected 15 target genomes.
[2023-03-15 11:09:30,062] [INFO] Target genome list was writen to OceanDNA-b6485/target_genomes.txt
[2023-03-15 11:09:30,069] [INFO] Task started: fastANI
[2023-03-15 11:09:30,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa896c2e-e5fe-4cdc-bde3-ce4c9435992b/OceanDNA-b6485.fa --refList OceanDNA-b6485/target_genomes.txt --output OceanDNA-b6485/fastani_result.tsv --threads 1
[2023-03-15 11:09:40,423] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:40,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b252d11-13fc-41d9-a87c-31e97b948b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:40,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b252d11-13fc-41d9-a87c-31e97b948b4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:40,432] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:40,432] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:40,432] [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 marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	81.2272	600	917	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	80.01	523	917	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	80.0071	521	917	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	79.9997	524	917	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	79.8618	544	917	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	79.8458	488	917	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	79.8264	537	917	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.8038	425	917	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.3684	330	917	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.8644	355	917	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.826	309	917	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	77.5897	245	917	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.4527	314	917	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.3046	198	917	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.9686	194	917	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:40,433] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6485/tc_result.tsv
[2023-03-15 11:09:40,433] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:40,433] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:40,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b252d11-13fc-41d9-a87c-31e97b948b4d/dqc_reference/checkm_data
[2023-03-15 11:09:40,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:40,439] [INFO] Task started: CheckM
[2023-03-15 11:09:40,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6485/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6485/checkm_input OceanDNA-b6485/checkm_result
[2023-03-15 11:10:24,798] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:24,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:24,800] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:24,800] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:24,800] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6485/markers.fasta)
[2023-03-15 11:10:24,801] [INFO] Task started: Blastn
[2023-03-15 11:10:24,801] [INFO] Running command: blastn -query OceanDNA-b6485/markers.fasta -db /var/lib/cwl/stg2b252d11-13fc-41d9-a87c-31e97b948b4d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6485/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:25,711] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:25,712] [INFO] Selected 14 target genomes.
[2023-03-15 11:10:25,712] [INFO] Target genome list was writen to OceanDNA-b6485/target_genomes_gtdb.txt
[2023-03-15 11:10:25,723] [INFO] Task started: fastANI
[2023-03-15 11:10:25,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa896c2e-e5fe-4cdc-bde3-ce4c9435992b/OceanDNA-b6485.fa --refList OceanDNA-b6485/target_genomes_gtdb.txt --output OceanDNA-b6485/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:35,414] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:35,422] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:10:35,423] [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_905480415.1	s__Algibacter_B sp905480415	99.1249	753	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003143755.1	s__Algibacter_B sp003143755	81.2498	598	917	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_014202225.1	s__Algibacter_B amylolyticus	80.0046	522	917	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_900114265.1	s__Flaviramulus basaltis	79.9555	530	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	79.8422	488	917	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_900141715.1	s__Arenitalea lutea	79.842	545	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013001275.1	s__Flaviramulus sp013001275	79.3989	427	917	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	79.17	476	917	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	79.0472	426	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	78.8667	455	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	78.5502	402	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.6575	286	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418085.1	s__Lacinutrix algicola	77.6153	243	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	77.5363	259	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:35,423] [INFO] GTDB search result was written to OceanDNA-b6485/result_gtdb.tsv
[2023-03-15 11:10:35,423] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:35,424] [INFO] DFAST_QC result json was written to OceanDNA-b6485/dqc_result.json
[2023-03-15 11:10:35,425] [INFO] DFAST_QC completed!
[2023-03-15 11:10:35,425] [INFO] Total running time: 0h1m25s