[2023-03-19 03:50:07,851] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg23e07822-1245-450b-8351-e7dc1d78513f/dqc_reference
[2023-03-19 03:50:09,604] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,607] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,607] [INFO] Running command: cat /var/lib/cwl/stgbc8fc715-3173-4f22-84e2-15f413c79304/OceanDNA-b39.fa | prodigal -d OceanDNA-b39/cds.fna -a OceanDNA-b39/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:51:22,694] [INFO] Task succeeded: Prodigal
[2023-03-19 03:51:22,694] [INFO] Task started: HMMsearch
[2023-03-19 03:51:22,695] [INFO] Running command: hmmsearch --tblout OceanDNA-b39/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23e07822-1245-450b-8351-e7dc1d78513f/dqc_reference/reference_markers.hmm OceanDNA-b39/protein.faa > /dev/null
[2023-03-19 03:51:22,996] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:51:22,997] [INFO] Found 6/6 markers.
[2023-03-19 03:51:23,042] [INFO] Query marker FASTA was written to OceanDNA-b39/markers.fasta
[2023-03-19 03:51:23,042] [INFO] Task started: Blastn
[2023-03-19 03:51:23,042] [INFO] Running command: blastn -query OceanDNA-b39/markers.fasta -db /var/lib/cwl/stg23e07822-1245-450b-8351-e7dc1d78513f/dqc_reference/reference_markers.fasta -out OceanDNA-b39/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:23,574] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:23,574] [INFO] Selected 24 target genomes.
[2023-03-19 03:51:23,575] [INFO] Target genome list was writen to OceanDNA-b39/target_genomes.txt
[2023-03-19 03:51:23,587] [INFO] Task started: fastANI
[2023-03-19 03:51:23,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc8fc715-3173-4f22-84e2-15f413c79304/OceanDNA-b39.fa --refList OceanDNA-b39/target_genomes.txt --output OceanDNA-b39/fastani_result.tsv --threads 1
[2023-03-19 03:51:41,255] [INFO] Task succeeded: fastANI
[2023-03-19 03:51:41,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23e07822-1245-450b-8351-e7dc1d78513f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:51:41,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23e07822-1245-450b-8351-e7dc1d78513f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:51:41,264] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:51:41,264] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:51:41,264] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.094	77	2770	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	74.9258	63	2770	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	74.9193	70	2770	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	74.9129	53	2770	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	74.8559	97	2770	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	74.8496	164	2770	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	74.8388	50	2770	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	74.8044	117	2770	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	74.7831	157	2770	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	74.7663	124	2770	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	74.766	60	2770	95	below_threshold
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	74.7137	76	2770	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	74.6989	109	2770	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:51:41,265] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39/tc_result.tsv
[2023-03-19 03:51:41,265] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:51:41,265] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:51:41,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23e07822-1245-450b-8351-e7dc1d78513f/dqc_reference/checkm_data
[2023-03-19 03:51:41,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:51:41,274] [INFO] Task started: CheckM
[2023-03-19 03:51:41,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39/checkm_input OceanDNA-b39/checkm_result
[2023-03-19 03:54:36,821] [INFO] Task succeeded: CheckM
[2023-03-19 03:54:36,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:54:36,826] [INFO] ===== Completeness check finished =====
[2023-03-19 03:54:36,826] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:54:36,826] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39/markers.fasta)
[2023-03-19 03:54:36,827] [INFO] Task started: Blastn
[2023-03-19 03:54:36,827] [INFO] Running command: blastn -query OceanDNA-b39/markers.fasta -db /var/lib/cwl/stg23e07822-1245-450b-8351-e7dc1d78513f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:54:37,613] [INFO] Task succeeded: Blastn
[2023-03-19 03:54:37,614] [INFO] Selected 29 target genomes.
[2023-03-19 03:54:37,614] [INFO] Target genome list was writen to OceanDNA-b39/target_genomes_gtdb.txt
[2023-03-19 03:54:37,859] [INFO] Task started: fastANI
[2023-03-19 03:54:37,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc8fc715-3173-4f22-84e2-15f413c79304/OceanDNA-b39.fa --refList OceanDNA-b39/target_genomes_gtdb.txt --output OceanDNA-b39/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:54:56,210] [INFO] Task succeeded: fastANI
[2023-03-19 03:54:56,221] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:54:56,221] [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_003697015.1	s__J023 sp003697015	76.5068	369	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521815.1	s__JAAYLR01 sp012521815	75.9708	106	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	99.12	98.38	0.89	0.78	5	-
GCA_003388555.1	s__QQVD01 sp003388555	75.9117	208	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_009843505.1	s__WTGL01 sp009843505	75.8866	106	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_016699405.1	s__JAAYLR01 sp016699405	75.7927	148	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525365.1	s__WTGL01 sp011525365	75.7138	116	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	75.6985	123	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837885.1	s__WTGL01 sp009837885	75.6798	117	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.92	99.92	0.99	0.99	2	-
GCA_012270995.1	s__WTGL01 sp012270995	75.6602	100	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.6179	124	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837085.1	s__WTGL01 sp009837085	75.6119	116	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_017860005.1	s__JACTMI01 sp017860005	75.5824	127	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523565.1	s__WTGL01 sp011523565	75.5548	86	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883235.1	s__JADGNZ01 sp017883235	75.3011	63	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247495.1	s__JADGNZ01 sp019247495	75.1811	55	2770	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__JADGNZ01	95.0	99.75	99.65	0.94	0.93	3	-
GCF_003344635.1	s__Desertihabitans aurantiacus	74.9137	71	2770	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCA_016711215.1	s__JADJTL01 sp016711215	74.8224	59	2770	d__Bacteria;p__Myxococcota;c__Polyangia;o__GCA-2747355;f__GCA-2747355;g__JADJTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002068325.1	s__MVZH01 sp002068325	74.7708	56	2770	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__MVZH01;g__MVZH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:54:56,221] [INFO] GTDB search result was written to OceanDNA-b39/result_gtdb.tsv
[2023-03-19 03:54:56,221] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:54:56,223] [INFO] DFAST_QC result json was written to OceanDNA-b39/dqc_result.json
[2023-03-19 03:54:56,223] [INFO] DFAST_QC completed!
[2023-03-19 03:54:56,223] [INFO] Total running time: 0h4m48s