[2023-03-18 05:35:37,308] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,309] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,309] [INFO] DQC Reference Directory: /var/lib/cwl/stga392e717-65f7-4d76-85c2-205c4e870a1c/dqc_reference
[2023-03-18 05:35:38,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,962] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,962] [INFO] Running command: cat /var/lib/cwl/stg7824f749-8162-494f-ab42-55b0781e1ab8/OceanDNA-b10534.fa | prodigal -d OceanDNA-b10534/cds.fna -a OceanDNA-b10534/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:49,035] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:49,035] [INFO] Task started: HMMsearch
[2023-03-18 05:35:49,035] [INFO] Running command: hmmsearch --tblout OceanDNA-b10534/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga392e717-65f7-4d76-85c2-205c4e870a1c/dqc_reference/reference_markers.hmm OceanDNA-b10534/protein.faa > /dev/null
[2023-03-18 05:35:49,219] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:49,219] [INFO] Found 6/6 markers.
[2023-03-18 05:35:49,255] [INFO] Query marker FASTA was written to OceanDNA-b10534/markers.fasta
[2023-03-18 05:35:49,256] [INFO] Task started: Blastn
[2023-03-18 05:35:49,256] [INFO] Running command: blastn -query OceanDNA-b10534/markers.fasta -db /var/lib/cwl/stga392e717-65f7-4d76-85c2-205c4e870a1c/dqc_reference/reference_markers.fasta -out OceanDNA-b10534/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:49,810] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:49,813] [INFO] Selected 33 target genomes.
[2023-03-18 05:35:49,814] [INFO] Target genome list was writen to OceanDNA-b10534/target_genomes.txt
[2023-03-18 05:35:49,833] [INFO] Task started: fastANI
[2023-03-18 05:35:49,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg7824f749-8162-494f-ab42-55b0781e1ab8/OceanDNA-b10534.fa --refList OceanDNA-b10534/target_genomes.txt --output OceanDNA-b10534/fastani_result.tsv --threads 1
[2023-03-18 05:36:08,714] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:08,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga392e717-65f7-4d76-85c2-205c4e870a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:08,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga392e717-65f7-4d76-85c2-205c4e870a1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:08,730] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:08,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:36:08,730] [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
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	76.7115	58	550	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.7098	57	550	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.5774	62	550	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.5373	92	550	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.498	57	550	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.4722	55	550	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	76.452	69	550	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.4433	63	550	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.3533	72	550	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.3458	66	550	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.3396	59	550	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.3101	60	550	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.2916	67	550	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2535	67	550	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	76.242	55	550	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.2146	79	550	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	76.154	70	550	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.0264	59	550	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.9382	65	550	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	75.9287	54	550	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	75.9045	55	550	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	75.808	63	550	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	75.7899	65	550	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	75.7889	62	550	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	75.7495	51	550	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.739	63	550	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.7169	71	550	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	75.3776	59	550	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:36:08,732] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10534/tc_result.tsv
[2023-03-18 05:36:08,733] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:08,733] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:08,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga392e717-65f7-4d76-85c2-205c4e870a1c/dqc_reference/checkm_data
[2023-03-18 05:36:08,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:08,739] [INFO] Task started: CheckM
[2023-03-18 05:36:08,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10534/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10534/checkm_input OceanDNA-b10534/checkm_result
[2023-03-18 05:36:38,911] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:38,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.72%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-03-18 05:36:38,915] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:38,915] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:38,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10534/markers.fasta)
[2023-03-18 05:36:38,916] [INFO] Task started: Blastn
[2023-03-18 05:36:38,916] [INFO] Running command: blastn -query OceanDNA-b10534/markers.fasta -db /var/lib/cwl/stga392e717-65f7-4d76-85c2-205c4e870a1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10534/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:39,694] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:39,696] [INFO] Selected 29 target genomes.
[2023-03-18 05:36:39,696] [INFO] Target genome list was writen to OceanDNA-b10534/target_genomes_gtdb.txt
[2023-03-18 05:36:39,735] [INFO] Task started: fastANI
[2023-03-18 05:36:39,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg7824f749-8162-494f-ab42-55b0781e1ab8/OceanDNA-b10534.fa --refList OceanDNA-b10534/target_genomes_gtdb.txt --output OceanDNA-b10534/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:52,953] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:52,967] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:36:52,967] [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_002684355.1	s__UBA3537 sp002684355	77.4948	119	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002690085.1	s__UBA3537 sp002690085	77.2951	101	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698705.1	s__UBA3537 sp002698705	77.2795	174	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709185.1	s__UBA3537 sp002709185	77.1496	81	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCF_003148645.1	s__Xanthomarina spongicola	77.0631	71	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516685.1	s__UBA3537 sp902516685	77.0299	77	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418085.1	s__Lacinutrix algicola	76.6688	57	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721175.1	s__SP29 sp002721175	76.6548	120	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SP29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725015.1	s__UBA3537 sp002725015	76.641	94	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCA_002162765.1	s__MAAR01 sp002162765	76.638	58	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	76.5344	56	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	76.5024	70	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	76.3537	72	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	76.3396	59	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.3241	96	550	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_002366675.1	s__Xanthomarina sp002366675	76.1808	75	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	76.0888	69	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	76.0328	73	550	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_018608625.1	s__Hel1-33-131 sp018608625	75.9524	84	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCF_003384935.1	s__Lutibacter oceani	75.9224	71	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001418105.1	s__Oceanihabitans himadriensis	75.888	64	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	75.8528	65	550	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	-
GCF_900312745.1	s__Aquimarina sp900312745	75.8222	59	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCA_002414705.1	s__Algorimicrobium sp002414705	75.6939	58	550	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:52,968] [INFO] GTDB search result was written to OceanDNA-b10534/result_gtdb.tsv
[2023-03-18 05:36:52,968] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:52,973] [INFO] DFAST_QC result json was written to OceanDNA-b10534/dqc_result.json
[2023-03-18 05:36:52,973] [INFO] DFAST_QC completed!
[2023-03-18 05:36:52,973] [INFO] Total running time: 0h1m16s