[2023-03-15 17:46:31,735] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,735] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1b79ac8-d84d-4a4f-8cc2-3492b7239921/dqc_reference
[2023-03-15 17:46:32,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,857] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,857] [INFO] Running command: cat /var/lib/cwl/stgf1b9c1e9-27b6-45f4-bf9a-519e395e68eb/OceanDNA-b46297.fa | prodigal -d OceanDNA-b46297/cds.fna -a OceanDNA-b46297/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:47:09,743] [INFO] Task succeeded: Prodigal
[2023-03-15 17:47:09,743] [INFO] Task started: HMMsearch
[2023-03-15 17:47:09,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b46297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1b79ac8-d84d-4a4f-8cc2-3492b7239921/dqc_reference/reference_markers.hmm OceanDNA-b46297/protein.faa > /dev/null
[2023-03-15 17:47:09,962] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:47:09,963] [INFO] Found 6/6 markers.
[2023-03-15 17:47:09,995] [INFO] Query marker FASTA was written to OceanDNA-b46297/markers.fasta
[2023-03-15 17:47:09,996] [INFO] Task started: Blastn
[2023-03-15 17:47:09,996] [INFO] Running command: blastn -query OceanDNA-b46297/markers.fasta -db /var/lib/cwl/stgb1b79ac8-d84d-4a4f-8cc2-3492b7239921/dqc_reference/reference_markers.fasta -out OceanDNA-b46297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:10,641] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:10,643] [INFO] Selected 27 target genomes.
[2023-03-15 17:47:10,643] [INFO] Target genome list was writen to OceanDNA-b46297/target_genomes.txt
[2023-03-15 17:47:10,659] [INFO] Task started: fastANI
[2023-03-15 17:47:10,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1b9c1e9-27b6-45f4-bf9a-519e395e68eb/OceanDNA-b46297.fa --refList OceanDNA-b46297/target_genomes.txt --output OceanDNA-b46297/fastani_result.tsv --threads 1
[2023-03-15 17:47:37,438] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:37,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1b79ac8-d84d-4a4f-8cc2-3492b7239921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:37,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1b79ac8-d84d-4a4f-8cc2-3492b7239921/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:37,446] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:37,446] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:47:37,446] [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
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	74.916	58	1284	95	below_threshold
Streptomyces varsoviensis	strain=NRRL ISP-5346	GCA_000718635.1	67373	67373	type	True	74.9159	58	1284	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	74.9031	62	1284	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	74.8962	56	1284	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	74.8962	56	1284	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.8802	82	1284	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	74.8733	52	1284	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.8667	61	1284	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.7909	65	1284	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:47:37,446] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46297/tc_result.tsv
[2023-03-15 17:47:37,446] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:37,446] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:37,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1b79ac8-d84d-4a4f-8cc2-3492b7239921/dqc_reference/checkm_data
[2023-03-15 17:47:37,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:37,553] [INFO] Task started: CheckM
[2023-03-15 17:47:37,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46297/checkm_input OceanDNA-b46297/checkm_result
[2023-03-15 17:49:10,108] [INFO] Task succeeded: CheckM
[2023-03-15 17:49:10,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:49:10,112] [INFO] ===== Completeness check finished =====
[2023-03-15 17:49:10,112] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:49:10,112] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46297/markers.fasta)
[2023-03-15 17:49:10,114] [INFO] Task started: Blastn
[2023-03-15 17:49:10,114] [INFO] Running command: blastn -query OceanDNA-b46297/markers.fasta -db /var/lib/cwl/stgb1b79ac8-d84d-4a4f-8cc2-3492b7239921/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:49:11,446] [INFO] Task succeeded: Blastn
[2023-03-15 17:49:11,447] [INFO] Selected 27 target genomes.
[2023-03-15 17:49:11,447] [INFO] Target genome list was writen to OceanDNA-b46297/target_genomes_gtdb.txt
[2023-03-15 17:49:11,575] [INFO] Task started: fastANI
[2023-03-15 17:49:11,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1b9c1e9-27b6-45f4-bf9a-519e395e68eb/OceanDNA-b46297.fa --refList OceanDNA-b46297/target_genomes_gtdb.txt --output OceanDNA-b46297/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:49:36,226] [INFO] Task succeeded: fastANI
[2023-03-15 17:49:36,238] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:49:36,238] [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_003695015.1	s__J093 sp003695015	76.1211	63	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__J093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	75.9948	66	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779125.1	s__GCA-2715965 sp016779125	75.9747	74	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__GCA-2715965;g__GCA-2715965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219875.1	s__JACRJZ01 sp016219875	75.9233	79	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJZ01;g__JACRJZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235585.1	s__JACRJY01 sp016235585	75.9188	117	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJY01;g__JACRJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871675.1	s__VHCN01 sp016871675	75.8575	92	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__VHCN01;g__VHCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863315.1	s__SXTU01 sp903863315	75.8566	114	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916195.1	s__CAIVQB01 sp903916195	75.8503	96	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.38	98.88	0.92	0.89	6	-
GCA_016871715.1	s__VHCO01 sp016871715	75.7838	68	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__VHCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695395.1	s__SXTU01 sp009695395	75.679	68	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235545.1	s__SXTU01 sp016235545	75.6657	103	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791875.1	s__SXTU01 sp005791875	75.6461	110	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.67	99.31	0.92	0.90	5	-
GCA_011327785.1	s__DSVZ01 sp011327785	75.5746	63	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075445.1	s__DSVZ01 sp015075445	75.4614	81	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933025.1	s__UBA6176 sp008933025	75.4384	72	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872345.1	s__UBA11358 sp903872345	75.4065	51	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	100.00	100.00	0.99	0.99	3	-
GCA_009695285.1	s__SIBH01 sp009695285	75.3756	60	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SIBH01;g__SIBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935555.1	s__JAFGQR01 sp016935555	75.3718	60	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JAFGQR01;g__JAFGQR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195385.1	s__JACPZS01 sp016195385	75.3297	64	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACPZS01;g__JACPZS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525685.1	s__WYBW01 sp011525685	75.3006	75	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__WYBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930565.1	s__CAIXFN01 sp903930565	75.1371	52	1284	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Pedosphaeraceae;g__CAIXFN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:49:36,239] [INFO] GTDB search result was written to OceanDNA-b46297/result_gtdb.tsv
[2023-03-15 17:49:36,239] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:49:36,240] [INFO] DFAST_QC result json was written to OceanDNA-b46297/dqc_result.json
[2023-03-15 17:49:36,241] [INFO] DFAST_QC completed!
[2023-03-15 17:49:36,241] [INFO] Total running time: 0h3m5s