[2023-03-15 05:51:32,068] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,069] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg56b4a54f-fef5-4042-9cf2-69bafd36963c/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stgfbcf882f-8a6b-4fa9-a876-3a08817af84e/OceanDNA-b38942.fa | prodigal -d OceanDNA-b38942/cds.fna -a OceanDNA-b38942/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:55,873] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:55,873] [INFO] Task started: HMMsearch
[2023-03-15 05:51:55,873] [INFO] Running command: hmmsearch --tblout OceanDNA-b38942/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56b4a54f-fef5-4042-9cf2-69bafd36963c/dqc_reference/reference_markers.hmm OceanDNA-b38942/protein.faa > /dev/null
[2023-03-15 05:51:56,088] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:56,088] [INFO] Found 6/6 markers.
[2023-03-15 05:51:56,110] [INFO] Query marker FASTA was written to OceanDNA-b38942/markers.fasta
[2023-03-15 05:51:56,112] [INFO] Task started: Blastn
[2023-03-15 05:51:56,112] [INFO] Running command: blastn -query OceanDNA-b38942/markers.fasta -db /var/lib/cwl/stg56b4a54f-fef5-4042-9cf2-69bafd36963c/dqc_reference/reference_markers.fasta -out OceanDNA-b38942/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:56,825] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:56,827] [INFO] Selected 25 target genomes.
[2023-03-15 05:51:56,828] [INFO] Target genome list was writen to OceanDNA-b38942/target_genomes.txt
[2023-03-15 05:51:56,846] [INFO] Task started: fastANI
[2023-03-15 05:51:56,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbcf882f-8a6b-4fa9-a876-3a08817af84e/OceanDNA-b38942.fa --refList OceanDNA-b38942/target_genomes.txt --output OceanDNA-b38942/fastani_result.tsv --threads 1
[2023-03-15 05:52:13,938] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:13,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56b4a54f-fef5-4042-9cf2-69bafd36963c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:52:13,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56b4a54f-fef5-4042-9cf2-69bafd36963c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:52:13,951] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 05:52:13,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 05:52:13,951] [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
Hydrocarboniclastica marina	strain=soil36-7	GCA_004851605.1	2259620	2259620	type	True	98.6708	1165	1214	95	conclusive
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	77.2349	135	1214	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	77.1559	138	1214	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	77.1487	121	1214	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	77.0499	123	1214	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	77.0256	112	1214	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	77.0036	137	1214	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	76.947	118	1214	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	76.9373	142	1214	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	76.9132	136	1214	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.8972	130	1214	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	76.8928	126	1214	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.8878	117	1214	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	76.8857	115	1214	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	76.8485	127	1214	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	76.8247	111	1214	95	below_threshold
Marinobacter mobilis	strain=CGMCC 1.7059	GCA_900106945.1	488533	488533	type	True	76.7812	101	1214	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	76.6649	164	1214	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.051	71	1214	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.9109	75	1214	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:52:13,952] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38942/tc_result.tsv
[2023-03-15 05:52:13,952] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:52:13,952] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:52:13,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56b4a54f-fef5-4042-9cf2-69bafd36963c/dqc_reference/checkm_data
[2023-03-15 05:52:13,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:52:13,961] [INFO] Task started: CheckM
[2023-03-15 05:52:13,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38942/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38942/checkm_input OceanDNA-b38942/checkm_result
[2023-03-15 05:53:09,753] [INFO] Task succeeded: CheckM
[2023-03-15 05:53:09,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:53:09,771] [INFO] ===== Completeness check finished =====
[2023-03-15 05:53:09,771] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:53:09,771] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38942/markers.fasta)
[2023-03-15 05:53:09,772] [INFO] Task started: Blastn
[2023-03-15 05:53:09,772] [INFO] Running command: blastn -query OceanDNA-b38942/markers.fasta -db /var/lib/cwl/stg56b4a54f-fef5-4042-9cf2-69bafd36963c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38942/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:11,000] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:11,002] [INFO] Selected 25 target genomes.
[2023-03-15 05:53:11,002] [INFO] Target genome list was writen to OceanDNA-b38942/target_genomes_gtdb.txt
[2023-03-15 05:53:11,023] [INFO] Task started: fastANI
[2023-03-15 05:53:11,023] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbcf882f-8a6b-4fa9-a876-3a08817af84e/OceanDNA-b38942.fa --refList OceanDNA-b38942/target_genomes_gtdb.txt --output OceanDNA-b38942/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:53:27,024] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:27,036] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:53:27,036] [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_004851605.1	s__Hydrocarboniclastica marina	98.6708	1165	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Hydrocarboniclastica	95.0	98.61	98.58	0.90	0.89	3	conclusive
GCF_002258215.1	s__Marinobacter vinifirmus	77.1851	135	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_900115175.1	s__Marinobacter gudaonensis	77.1706	120	1214	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	77.11	121	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCF_900114925.1	s__Marinobacter pelagius	77.0252	134	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	76.9961	135	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCA_018623515.1	s__Marinobacter sp018623515	76.9738	103	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114155.1	s__Marinobacter persicus	76.9708	114	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	76.9575	140	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860425.1	s__Marinobacter sp018860425	76.9117	94	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933275.1	s__Marinobacter maroccanus	76.8701	123	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364845.1	s__Marinobacter_A nanhaiticus	76.8485	127	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188315.1	s__Marinobacter sp900188315	76.8337	119	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	76.8292	138	1214	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	76.8137	102	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_900106945.1	s__Marinobacter mobilis	76.8065	99	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001981305.1	s__Marinobacter lutaoensis	76.7428	133	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCF_004327985.1	s__Marinobacter_A halodurans	76.6758	162	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692645.1	s__REBR01 sp007692645	76.3906	76	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__REBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521985.1	s__Pseudomonas_E khazarica	76.0303	66	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_001457615.1	s__Pseudomonas aeruginosa	75.9482	74	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
--------------------------------------------------------------------------------
[2023-03-15 05:53:27,038] [INFO] GTDB search result was written to OceanDNA-b38942/result_gtdb.tsv
[2023-03-15 05:53:27,038] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:53:27,042] [INFO] DFAST_QC result json was written to OceanDNA-b38942/dqc_result.json
[2023-03-15 05:53:27,042] [INFO] DFAST_QC completed!
[2023-03-15 05:53:27,042] [INFO] Total running time: 0h1m55s