[2023-03-16 10:46:24,344] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:46:24,344] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:46:24,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg1925d937-db2b-4738-964e-a2183a46acf6/dqc_reference
[2023-03-16 10:46:25,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:46:25,498] [INFO] Task started: Prodigal
[2023-03-16 10:46:25,498] [INFO] Running command: cat /var/lib/cwl/stg4f5c354c-268a-48f9-b393-2070d21b2bfa/OceanDNA-b46299.fa | prodigal -d OceanDNA-b46299/cds.fna -a OceanDNA-b46299/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:47:38,554] [INFO] Task succeeded: Prodigal
[2023-03-16 10:47:38,555] [INFO] Task started: HMMsearch
[2023-03-16 10:47:38,555] [INFO] Running command: hmmsearch --tblout OceanDNA-b46299/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1925d937-db2b-4738-964e-a2183a46acf6/dqc_reference/reference_markers.hmm OceanDNA-b46299/protein.faa > /dev/null
[2023-03-16 10:47:38,833] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:47:38,833] [INFO] Found 6/6 markers.
[2023-03-16 10:47:38,876] [INFO] Query marker FASTA was written to OceanDNA-b46299/markers.fasta
[2023-03-16 10:47:38,904] [INFO] Task started: Blastn
[2023-03-16 10:47:38,904] [INFO] Running command: blastn -query OceanDNA-b46299/markers.fasta -db /var/lib/cwl/stg1925d937-db2b-4738-964e-a2183a46acf6/dqc_reference/reference_markers.fasta -out OceanDNA-b46299/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:47:39,513] [INFO] Task succeeded: Blastn
[2023-03-16 10:47:39,513] [INFO] Selected 24 target genomes.
[2023-03-16 10:47:39,514] [INFO] Target genome list was writen to OceanDNA-b46299/target_genomes.txt
[2023-03-16 10:47:39,802] [INFO] Task started: fastANI
[2023-03-16 10:47:39,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5c354c-268a-48f9-b393-2070d21b2bfa/OceanDNA-b46299.fa --refList OceanDNA-b46299/target_genomes.txt --output OceanDNA-b46299/fastani_result.tsv --threads 1
[2023-03-16 10:47:58,325] [INFO] Task succeeded: fastANI
[2023-03-16 10:47:58,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1925d937-db2b-4738-964e-a2183a46acf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:47:58,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1925d937-db2b-4738-964e-a2183a46acf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:47:58,329] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:47:58,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:47:58,329] [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
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	74.9719	57	2256	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:47:58,329] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46299/tc_result.tsv
[2023-03-16 10:47:58,329] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:47:58,329] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:47:58,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1925d937-db2b-4738-964e-a2183a46acf6/dqc_reference/checkm_data
[2023-03-16 10:47:58,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:47:58,352] [INFO] Task started: CheckM
[2023-03-16 10:47:58,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46299/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46299/checkm_input OceanDNA-b46299/checkm_result
[2023-03-16 10:51:17,187] [INFO] Task succeeded: CheckM
[2023-03-16 10:51:17,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:51:17,192] [INFO] ===== Completeness check finished =====
[2023-03-16 10:51:17,192] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:51:17,192] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46299/markers.fasta)
[2023-03-16 10:51:17,194] [INFO] Task started: Blastn
[2023-03-16 10:51:17,194] [INFO] Running command: blastn -query OceanDNA-b46299/markers.fasta -db /var/lib/cwl/stg1925d937-db2b-4738-964e-a2183a46acf6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46299/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:51:18,058] [INFO] Task succeeded: Blastn
[2023-03-16 10:51:18,059] [INFO] Selected 29 target genomes.
[2023-03-16 10:51:18,059] [INFO] Target genome list was writen to OceanDNA-b46299/target_genomes_gtdb.txt
[2023-03-16 10:51:18,145] [INFO] Task started: fastANI
[2023-03-16 10:51:18,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5c354c-268a-48f9-b393-2070d21b2bfa/OceanDNA-b46299.fa --refList OceanDNA-b46299/target_genomes_gtdb.txt --output OceanDNA-b46299/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:51:51,297] [INFO] Task succeeded: fastANI
[2023-03-16 10:51:51,308] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:51:51,308] [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_002715965.1	s__GCA-2715965 sp002715965	77.3524	370	2256	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_016779125.1	s__GCA-2715965 sp016779125	76.221	211	2256	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_903863315.1	s__SXTU01 sp903863315	75.9987	140	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009922615.1	s__SXTU01 sp009922615	75.8793	133	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.88	99.88	0.94	0.94	2	-
GCA_016871675.1	s__VHCN01 sp016871675	75.8133	112	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__VHCN01;g__VHCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773355.1	s__SXTU01 sp009773355	75.7391	191	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.99	99.99	0.98	0.97	3	-
GCA_009695395.1	s__SXTU01 sp009695395	75.6679	86	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842505.1	s__UBA6176 sp903842505	75.6259	66	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__UBA6176	95.0	99.72	99.54	0.92	0.90	4	-
GCA_003695015.1	s__J093 sp003695015	75.6111	56	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__J093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858275.1	s__UBA11358 sp903858275	75.5882	50	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.00	98.19	0.88	0.83	3	-
GCA_903922735.1	s__UBA11358 sp903922735	75.548	57	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871615.1	s__SXXZ01 sp016871615	75.5374	67	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844265.1	s__CAIMTB01 sp903844265	75.528	55	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIMTB01;g__CAIMTB01	95.0	99.52	99.41	0.88	0.83	6	-
GCA_016871445.1	s__SXTU01 sp016871445	75.4565	74	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	98.73	98.73	0.87	0.87	2	-
GCA_016219875.1	s__JACRJZ01 sp016219875	75.4092	92	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJZ01;g__JACRJZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075445.1	s__DSVZ01 sp015075445	75.4055	76	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014193395.1	s__BJHT01 sp014193395	75.3403	145	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__BJHT01;g__BJHT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860005.1	s__WYBW01 sp014860005	75.2142	73	2256	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__WYBW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:51:51,309] [INFO] GTDB search result was written to OceanDNA-b46299/result_gtdb.tsv
[2023-03-16 10:51:51,310] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:51:51,312] [INFO] DFAST_QC result json was written to OceanDNA-b46299/dqc_result.json
[2023-03-16 10:51:51,312] [INFO] DFAST_QC completed!
[2023-03-16 10:51:51,312] [INFO] Total running time: 0h5m27s