[2023-03-19 03:50:07,840] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg27ac626a-2597-47dd-997c-464655a02b5a/dqc_reference
[2023-03-19 03:50:09,604] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,605] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,605] [INFO] Running command: cat /var/lib/cwl/stgf53a5c1e-0bc0-41cc-9e3c-957665aceb7a/OceanDNA-b30115.fa | prodigal -d OceanDNA-b30115/cds.fna -a OceanDNA-b30115/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:34,412] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:34,412] [INFO] Task started: HMMsearch
[2023-03-19 03:50:34,413] [INFO] Running command: hmmsearch --tblout OceanDNA-b30115/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27ac626a-2597-47dd-997c-464655a02b5a/dqc_reference/reference_markers.hmm OceanDNA-b30115/protein.faa > /dev/null
[2023-03-19 03:50:34,689] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:34,690] [INFO] Found 6/6 markers.
[2023-03-19 03:50:34,724] [INFO] Query marker FASTA was written to OceanDNA-b30115/markers.fasta
[2023-03-19 03:50:34,724] [INFO] Task started: Blastn
[2023-03-19 03:50:34,724] [INFO] Running command: blastn -query OceanDNA-b30115/markers.fasta -db /var/lib/cwl/stg27ac626a-2597-47dd-997c-464655a02b5a/dqc_reference/reference_markers.fasta -out OceanDNA-b30115/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:35,553] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:35,554] [INFO] Selected 25 target genomes.
[2023-03-19 03:50:35,554] [INFO] Target genome list was writen to OceanDNA-b30115/target_genomes.txt
[2023-03-19 03:50:35,575] [INFO] Task started: fastANI
[2023-03-19 03:50:35,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53a5c1e-0bc0-41cc-9e3c-957665aceb7a/OceanDNA-b30115.fa --refList OceanDNA-b30115/target_genomes.txt --output OceanDNA-b30115/fastani_result.tsv --threads 1
[2023-03-19 03:50:56,644] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:56,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27ac626a-2597-47dd-997c-464655a02b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:56,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27ac626a-2597-47dd-997c-464655a02b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:56,661] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 03:50:56,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 03:50:56,661] [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
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	97.0881	1199	1242	95	conclusive
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	81.3537	729	1242	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	81.2181	744	1242	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	79.5618	696	1242	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	79.5167	673	1242	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	79.4693	678	1242	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	79.4327	596	1242	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.9024	519	1242	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.8978	525	1242	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.4186	441	1242	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.3597	500	1242	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.2438	455	1242	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	78.0465	408	1242	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.9534	382	1242	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	77.6025	386	1242	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.5004	385	1242	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.4806	354	1242	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.4479	326	1242	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.3386	337	1242	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0641	286	1242	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.0533	251	1242	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	76.8898	244	1242	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	76.8567	245	1242	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6744	243	1242	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.2171	125	1242	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:50:56,662] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30115/tc_result.tsv
[2023-03-19 03:50:56,662] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:56,662] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:56,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27ac626a-2597-47dd-997c-464655a02b5a/dqc_reference/checkm_data
[2023-03-19 03:50:56,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:56,669] [INFO] Task started: CheckM
[2023-03-19 03:50:56,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30115/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30115/checkm_input OceanDNA-b30115/checkm_result
[2023-03-19 03:51:58,984] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:58,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:58,987] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:58,987] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:58,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30115/markers.fasta)
[2023-03-19 03:51:58,988] [INFO] Task started: Blastn
[2023-03-19 03:51:58,988] [INFO] Running command: blastn -query OceanDNA-b30115/markers.fasta -db /var/lib/cwl/stg27ac626a-2597-47dd-997c-464655a02b5a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30115/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:52:00,595] [INFO] Task succeeded: Blastn
[2023-03-19 03:52:00,596] [INFO] Selected 7 target genomes.
[2023-03-19 03:52:00,596] [INFO] Target genome list was writen to OceanDNA-b30115/target_genomes_gtdb.txt
[2023-03-19 03:52:00,603] [INFO] Task started: fastANI
[2023-03-19 03:52:00,603] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53a5c1e-0bc0-41cc-9e3c-957665aceb7a/OceanDNA-b30115.fa --refList OceanDNA-b30115/target_genomes_gtdb.txt --output OceanDNA-b30115/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:52:07,472] [INFO] Task succeeded: fastANI
[2023-03-19 03:52:07,477] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:52:07,477] [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_000768555.3	s__Roseovarius mucosus	97.0881	1199	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.95	96.93	0.91	0.89	3	conclusive
GCA_018066915.1	s__Roseovarius sp018066915	90.2696	925	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_002080415.1	s__Roseovarius mucosus_A	87.8326	1095	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCF_000152845.1	s__Roseovarius sp000152845	85.6706	977	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.99	97.99	0.83	0.83	2	-
GCF_000744325.1	s__Roseovarius sp000744325	83.9173	959	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	81.3574	729	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842985.1	s__Roseovarius sp002842985	80.4202	627	1242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:52:07,477] [INFO] GTDB search result was written to OceanDNA-b30115/result_gtdb.tsv
[2023-03-19 03:52:07,477] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:52:07,479] [INFO] DFAST_QC result json was written to OceanDNA-b30115/dqc_result.json
[2023-03-19 03:52:07,479] [INFO] DFAST_QC completed!
[2023-03-19 03:52:07,480] [INFO] Total running time: 0h1m60s