[2023-03-15 10:56:32,980] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:56:32,980] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:56:32,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg35948818-3edc-489d-9938-9935534ec771/dqc_reference
[2023-03-15 10:56:34,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:56:34,072] [INFO] Task started: Prodigal
[2023-03-15 10:56:34,072] [INFO] Running command: cat /var/lib/cwl/stg001c5164-c8d1-4a9f-9f64-96bfcbc0c134/OceanDNA-b7481.fa | prodigal -d OceanDNA-b7481/cds.fna -a OceanDNA-b7481/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:56:55,490] [INFO] Task succeeded: Prodigal
[2023-03-15 10:56:55,490] [INFO] Task started: HMMsearch
[2023-03-15 10:56:55,490] [INFO] Running command: hmmsearch --tblout OceanDNA-b7481/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35948818-3edc-489d-9938-9935534ec771/dqc_reference/reference_markers.hmm OceanDNA-b7481/protein.faa > /dev/null
[2023-03-15 10:56:55,688] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:56:55,688] [INFO] Found 6/6 markers.
[2023-03-15 10:56:55,709] [INFO] Query marker FASTA was written to OceanDNA-b7481/markers.fasta
[2023-03-15 10:56:55,709] [INFO] Task started: Blastn
[2023-03-15 10:56:55,709] [INFO] Running command: blastn -query OceanDNA-b7481/markers.fasta -db /var/lib/cwl/stg35948818-3edc-489d-9938-9935534ec771/dqc_reference/reference_markers.fasta -out OceanDNA-b7481/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:56:56,318] [INFO] Task succeeded: Blastn
[2023-03-15 10:56:56,319] [INFO] Selected 18 target genomes.
[2023-03-15 10:56:56,319] [INFO] Target genome list was writen to OceanDNA-b7481/target_genomes.txt
[2023-03-15 10:56:56,331] [INFO] Task started: fastANI
[2023-03-15 10:56:56,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg001c5164-c8d1-4a9f-9f64-96bfcbc0c134/OceanDNA-b7481.fa --refList OceanDNA-b7481/target_genomes.txt --output OceanDNA-b7481/fastani_result.tsv --threads 1
[2023-03-15 10:57:06,876] [INFO] Task succeeded: fastANI
[2023-03-15 10:57:06,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35948818-3edc-489d-9938-9935534ec771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:57:06,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35948818-3edc-489d-9938-9935534ec771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:57:06,886] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 10:57:06,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 10:57:06,887] [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
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	96.11	994	1163	95	conclusive
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	79.034	493	1163	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	78.9827	448	1163	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	78.9808	492	1163	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	78.2919	385	1163	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	78.2583	386	1163	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	78.2219	402	1163	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.5967	76	1163	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	76.5391	101	1163	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	76.5353	101	1163	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.5214	77	1163	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	76.5014	112	1163	95	below_threshold
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	76.4826	113	1163	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.2505	82	1163	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.2505	82	1163	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	75.9136	77	1163	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.8684	75	1163	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:57:06,887] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7481/tc_result.tsv
[2023-03-15 10:57:06,887] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:57:06,887] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:57:06,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35948818-3edc-489d-9938-9935534ec771/dqc_reference/checkm_data
[2023-03-15 10:57:06,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:57:06,893] [INFO] Task started: CheckM
[2023-03-15 10:57:06,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7481/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7481/checkm_input OceanDNA-b7481/checkm_result
[2023-03-15 10:58:00,744] [INFO] Task succeeded: CheckM
[2023-03-15 10:58:00,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:58:00,747] [INFO] ===== Completeness check finished =====
[2023-03-15 10:58:00,747] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:58:00,747] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7481/markers.fasta)
[2023-03-15 10:58:00,748] [INFO] Task started: Blastn
[2023-03-15 10:58:00,748] [INFO] Running command: blastn -query OceanDNA-b7481/markers.fasta -db /var/lib/cwl/stg35948818-3edc-489d-9938-9935534ec771/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7481/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:58:01,595] [INFO] Task succeeded: Blastn
[2023-03-15 10:58:01,596] [INFO] Selected 14 target genomes.
[2023-03-15 10:58:01,596] [INFO] Target genome list was writen to OceanDNA-b7481/target_genomes_gtdb.txt
[2023-03-15 10:58:01,609] [INFO] Task started: fastANI
[2023-03-15 10:58:01,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg001c5164-c8d1-4a9f-9f64-96bfcbc0c134/OceanDNA-b7481.fa --refList OceanDNA-b7481/target_genomes_gtdb.txt --output OceanDNA-b7481/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:58:11,120] [INFO] Task succeeded: fastANI
[2023-03-15 10:58:11,127] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:58:11,128] [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_004104375.1	s__Leeuwenhoekiella aequorea	96.11	994	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	81.4021	754	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.465	458	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	79.034	493	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	78.9851	447	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	78.2582	386	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	78.2178	403	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	77.7387	287	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
GCF_003337215.1	s__Oceanihabitans sediminis	76.5679	77	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188275.1	s__Dokdonia pacifica	76.4826	113	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013151975.1	s__PRS1 sp013151975	76.2511	58	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.2505	82	1163	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-15 10:58:11,128] [INFO] GTDB search result was written to OceanDNA-b7481/result_gtdb.tsv
[2023-03-15 10:58:11,128] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:58:11,129] [INFO] DFAST_QC result json was written to OceanDNA-b7481/dqc_result.json
[2023-03-15 10:58:11,130] [INFO] DFAST_QC completed!
[2023-03-15 10:58:11,130] [INFO] Total running time: 0h1m38s