[2023-03-18 23:44:06,343] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,344] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bfc874b-846f-4e54-bb80-1dd8c4103188/dqc_reference
[2023-03-18 23:44:07,515] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,515] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,515] [INFO] Running command: cat /var/lib/cwl/stgdd63e4f0-8245-4361-8fb6-61d0dd90d085/OceanDNA-b3677.fa | prodigal -d OceanDNA-b3677/cds.fna -a OceanDNA-b3677/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:34,642] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:34,642] [INFO] Task started: HMMsearch
[2023-03-18 23:44:34,642] [INFO] Running command: hmmsearch --tblout OceanDNA-b3677/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bfc874b-846f-4e54-bb80-1dd8c4103188/dqc_reference/reference_markers.hmm OceanDNA-b3677/protein.faa > /dev/null
[2023-03-18 23:44:34,851] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:34,852] [INFO] Found 6/6 markers.
[2023-03-18 23:44:34,883] [INFO] Query marker FASTA was written to OceanDNA-b3677/markers.fasta
[2023-03-18 23:44:34,884] [INFO] Task started: Blastn
[2023-03-18 23:44:34,884] [INFO] Running command: blastn -query OceanDNA-b3677/markers.fasta -db /var/lib/cwl/stg6bfc874b-846f-4e54-bb80-1dd8c4103188/dqc_reference/reference_markers.fasta -out OceanDNA-b3677/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:35,508] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:35,509] [INFO] Selected 28 target genomes.
[2023-03-18 23:44:35,509] [INFO] Target genome list was writen to OceanDNA-b3677/target_genomes.txt
[2023-03-18 23:44:35,528] [INFO] Task started: fastANI
[2023-03-18 23:44:35,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd63e4f0-8245-4361-8fb6-61d0dd90d085/OceanDNA-b3677.fa --refList OceanDNA-b3677/target_genomes.txt --output OceanDNA-b3677/fastani_result.tsv --threads 1
[2023-03-18 23:44:56,618] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:56,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bfc874b-846f-4e54-bb80-1dd8c4103188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:56,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bfc874b-846f-4e54-bb80-1dd8c4103188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:56,632] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:56,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:56,633] [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
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	75.7685	102	1206	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.7559	103	1206	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	75.5897	67	1206	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	75.5193	58	1206	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.431	72	1206	95	below_threshold
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	75.1352	63	1206	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	74.963	72	1206	95	below_threshold
Hymenobacter nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	74.8954	57	1206	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.8912	213	1206	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	74.8861	153	1206	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	74.8615	61	1206	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	74.8343	180	1206	95	below_threshold
Thermaurantiacus tibetensis	strain=SYSU G02173	GCA_015354055.1	2759035	2759035	type	True	74.8137	62	1206	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	74.7761	116	1206	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	74.7433	191	1206	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	74.7251	134	1206	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	74.7228	192	1206	95	below_threshold
Propionibacterium acidifaciens	strain=DSM 21887	GCA_000426605.1	556499	556499	type	True	74.7187	85	1206	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	74.6868	183	1206	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	74.6749	191	1206	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	74.6698	82	1206	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	74.6514	104	1206	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	74.6373	115	1206	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:56,634] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3677/tc_result.tsv
[2023-03-18 23:44:56,635] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:56,635] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:56,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bfc874b-846f-4e54-bb80-1dd8c4103188/dqc_reference/checkm_data
[2023-03-18 23:44:56,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:56,650] [INFO] Task started: CheckM
[2023-03-18 23:44:56,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3677/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3677/checkm_input OceanDNA-b3677/checkm_result
[2023-03-18 23:46:00,865] [INFO] Task succeeded: CheckM
[2023-03-18 23:46:00,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:46:00,868] [INFO] ===== Completeness check finished =====
[2023-03-18 23:46:00,868] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:46:00,869] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3677/markers.fasta)
[2023-03-18 23:46:00,869] [INFO] Task started: Blastn
[2023-03-18 23:46:00,870] [INFO] Running command: blastn -query OceanDNA-b3677/markers.fasta -db /var/lib/cwl/stg6bfc874b-846f-4e54-bb80-1dd8c4103188/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3677/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:01,809] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:01,810] [INFO] Selected 28 target genomes.
[2023-03-18 23:46:01,810] [INFO] Target genome list was writen to OceanDNA-b3677/target_genomes_gtdb.txt
[2023-03-18 23:46:01,835] [INFO] Task started: fastANI
[2023-03-18 23:46:01,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd63e4f0-8245-4361-8fb6-61d0dd90d085/OceanDNA-b3677.fa --refList OceanDNA-b3677/target_genomes_gtdb.txt --output OceanDNA-b3677/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:46:19,410] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:19,418] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:46:19,418] [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_003390915.1	s__Lewinella_A sp003390915	75.9352	109	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490175.1	s__WFYJ01 sp015490175	75.8765	97	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	75.7429	104	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002934605.1	s__Lewinella_A xylanilytica	75.5005	59	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803465.1	s__Lewinella_A litorea	75.4174	73	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713875.1	s__PHOS-HE28 sp016713875	75.3425	51	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.66	99.38	0.97	0.94	4	-
GCA_016788285.1	s__PHOS-HE28 sp016788285	75.1876	51	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360395.1	s__PHOS-HE28 sp013360395	75.1478	51	1206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.56	99.56	0.97	0.97	2	-
GCF_002283365.1	s__Rubrivirga marina	74.8992	217	1206	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792765.1	s__SBBV01 sp016792765	74.772	102	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838755.1	s__Brevilactibacter sp012838755	74.7496	63	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653785.1	s__Promicromonospora soli	74.7123	140	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:46:19,418] [INFO] GTDB search result was written to OceanDNA-b3677/result_gtdb.tsv
[2023-03-18 23:46:19,418] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:46:19,420] [INFO] DFAST_QC result json was written to OceanDNA-b3677/dqc_result.json
[2023-03-18 23:46:19,420] [INFO] DFAST_QC completed!
[2023-03-18 23:46:19,420] [INFO] Total running time: 0h2m13s