[2023-03-18 22:34:59,283] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:34:59,283] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:34:59,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg23dcf47c-4962-47ff-9993-f55aaf99e525/dqc_reference
[2023-03-18 22:35:00,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:35:00,409] [INFO] Task started: Prodigal
[2023-03-18 22:35:00,409] [INFO] Running command: cat /var/lib/cwl/stg67b250e9-bdca-48fe-b89c-035926df6e4c/OceanDNA-b38975.fa | prodigal -d OceanDNA-b38975/cds.fna -a OceanDNA-b38975/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:35:20,318] [INFO] Task succeeded: Prodigal
[2023-03-18 22:35:20,318] [INFO] Task started: HMMsearch
[2023-03-18 22:35:20,318] [INFO] Running command: hmmsearch --tblout OceanDNA-b38975/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23dcf47c-4962-47ff-9993-f55aaf99e525/dqc_reference/reference_markers.hmm OceanDNA-b38975/protein.faa > /dev/null
[2023-03-18 22:35:20,535] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:35:20,536] [INFO] Found 6/6 markers.
[2023-03-18 22:35:20,557] [INFO] Query marker FASTA was written to OceanDNA-b38975/markers.fasta
[2023-03-18 22:35:20,559] [INFO] Task started: Blastn
[2023-03-18 22:35:20,559] [INFO] Running command: blastn -query OceanDNA-b38975/markers.fasta -db /var/lib/cwl/stg23dcf47c-4962-47ff-9993-f55aaf99e525/dqc_reference/reference_markers.fasta -out OceanDNA-b38975/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:35:21,225] [INFO] Task succeeded: Blastn
[2023-03-18 22:35:21,226] [INFO] Selected 25 target genomes.
[2023-03-18 22:35:21,226] [INFO] Target genome list was writen to OceanDNA-b38975/target_genomes.txt
[2023-03-18 22:35:21,243] [INFO] Task started: fastANI
[2023-03-18 22:35:21,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b250e9-bdca-48fe-b89c-035926df6e4c/OceanDNA-b38975.fa --refList OceanDNA-b38975/target_genomes.txt --output OceanDNA-b38975/fastani_result.tsv --threads 1
[2023-03-18 22:35:38,017] [INFO] Task succeeded: fastANI
[2023-03-18 22:35:38,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23dcf47c-4962-47ff-9993-f55aaf99e525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:35:38,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23dcf47c-4962-47ff-9993-f55aaf99e525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:35:38,031] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:35:38,031] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:35:38,031] [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
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.1233	408	1074	95	below_threshold
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	79.0939	403	1074	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	78.8953	436	1074	95	below_threshold
Marinobacter daqiaonensis	strain=CGMCC 1.9167	GCA_900115285.1	650891	650891	type	True	78.8636	418	1074	95	below_threshold
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	78.7849	426	1074	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	78.7576	296	1074	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.6679	256	1074	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	78.5658	309	1074	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	78.5509	308	1074	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	78.5261	290	1074	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.5178	290	1074	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	78.4904	252	1074	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	78.4738	257	1074	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	78.4251	282	1074	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.4128	240	1074	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	78.3797	322	1074	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.3778	283	1074	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	78.3659	290	1074	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	78.252	259	1074	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.1887	295	1074	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.1804	313	1074	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	78.1674	284	1074	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	78.0111	227	1074	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	77.4376	190	1074	95	below_threshold
Marinobacter fonticola	strain=CS412	GCA_008122265.1	2603215	2603215	type	True	77.4	201	1074	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:35:38,032] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38975/tc_result.tsv
[2023-03-18 22:35:38,032] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:35:38,033] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:35:38,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23dcf47c-4962-47ff-9993-f55aaf99e525/dqc_reference/checkm_data
[2023-03-18 22:35:38,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:35:38,039] [INFO] Task started: CheckM
[2023-03-18 22:35:38,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38975/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38975/checkm_input OceanDNA-b38975/checkm_result
[2023-03-18 22:36:29,428] [INFO] Task succeeded: CheckM
[2023-03-18 22:36:29,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:36:29,431] [INFO] ===== Completeness check finished =====
[2023-03-18 22:36:29,431] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:36:29,431] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38975/markers.fasta)
[2023-03-18 22:36:29,433] [INFO] Task started: Blastn
[2023-03-18 22:36:29,433] [INFO] Running command: blastn -query OceanDNA-b38975/markers.fasta -db /var/lib/cwl/stg23dcf47c-4962-47ff-9993-f55aaf99e525/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38975/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:36:30,511] [INFO] Task succeeded: Blastn
[2023-03-18 22:36:30,513] [INFO] Selected 26 target genomes.
[2023-03-18 22:36:30,513] [INFO] Target genome list was writen to OceanDNA-b38975/target_genomes_gtdb.txt
[2023-03-18 22:36:30,552] [INFO] Task started: fastANI
[2023-03-18 22:36:30,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b250e9-bdca-48fe-b89c-035926df6e4c/OceanDNA-b38975.fa --refList OceanDNA-b38975/target_genomes_gtdb.txt --output OceanDNA-b38975/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:36:47,370] [INFO] Task succeeded: fastANI
[2023-03-18 22:36:47,384] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:36:47,384] [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_900111555.1	s__Marinobacter segnicrescens	79.1051	402	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	78.9005	435	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115285.1	s__Marinobacter daqiaonensis	78.8427	420	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002258215.1	s__Marinobacter vinifirmus	78.7703	295	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_003315345.1	s__Marinobacter pelagius_A	78.7228	297	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	78.6882	308	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	78.6473	256	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	78.5658	309	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	78.5455	309	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	78.5085	288	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_000170835.1	s__Marinobacter algicola	78.4904	252	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	78.482	251	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	78.48	256	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	78.3998	276	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_001045555.1	s__Marinobacter subterrani	78.3797	322	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_003007685.1	s__Marinobacter halophilus	78.3659	290	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018402255.1	s__Marinobacter sp018402255	78.3507	253	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_900114155.1	s__Marinobacter persicus	78.3441	272	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014201735.1	s__Marinobacter oulmenensis	78.2388	260	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617755.1	s__Marinobacter salsuginis	78.2263	292	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCA_003030785.1	s__Marinobacter sp003030785	78.2249	206	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427555.1	s__Marinobacter litoralis_A	78.145	168	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	78.1387	219	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	78.0732	299	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_001981305.1	s__Marinobacter lutaoensis	78.0551	274	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCA_014859525.1	s__Marinobacter sp014859525	78.023	224	1074	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:36:47,384] [INFO] GTDB search result was written to OceanDNA-b38975/result_gtdb.tsv
[2023-03-18 22:36:47,384] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:36:47,387] [INFO] DFAST_QC result json was written to OceanDNA-b38975/dqc_result.json
[2023-03-18 22:36:47,387] [INFO] DFAST_QC completed!
[2023-03-18 22:36:47,387] [INFO] Total running time: 0h1m48s