[2023-03-18 03:27:00,423] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,423] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg2aec4c43-740d-4b79-a428-ef304d197637/dqc_reference
[2023-03-18 03:27:01,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:01,576] [INFO] Task started: Prodigal
[2023-03-18 03:27:01,576] [INFO] Running command: cat /var/lib/cwl/stg056ea36f-7c78-433b-bbf4-0d73414a5c14/OceanDNA-b272.fa | prodigal -d OceanDNA-b272/cds.fna -a OceanDNA-b272/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:12,850] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:12,851] [INFO] Task started: HMMsearch
[2023-03-18 03:27:12,851] [INFO] Running command: hmmsearch --tblout OceanDNA-b272/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2aec4c43-740d-4b79-a428-ef304d197637/dqc_reference/reference_markers.hmm OceanDNA-b272/protein.faa > /dev/null
[2023-03-18 03:27:13,041] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:13,041] [INFO] Found 6/6 markers.
[2023-03-18 03:27:13,061] [INFO] Query marker FASTA was written to OceanDNA-b272/markers.fasta
[2023-03-18 03:27:13,062] [INFO] Task started: Blastn
[2023-03-18 03:27:13,062] [INFO] Running command: blastn -query OceanDNA-b272/markers.fasta -db /var/lib/cwl/stg2aec4c43-740d-4b79-a428-ef304d197637/dqc_reference/reference_markers.fasta -out OceanDNA-b272/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:13,693] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:13,694] [INFO] Selected 30 target genomes.
[2023-03-18 03:27:13,694] [INFO] Target genome list was writen to OceanDNA-b272/target_genomes.txt
[2023-03-18 03:27:13,709] [INFO] Task started: fastANI
[2023-03-18 03:27:13,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg056ea36f-7c78-433b-bbf4-0d73414a5c14/OceanDNA-b272.fa --refList OceanDNA-b272/target_genomes.txt --output OceanDNA-b272/fastani_result.tsv --threads 1
[2023-03-18 03:27:35,816] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:35,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2aec4c43-740d-4b79-a428-ef304d197637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:35,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2aec4c43-740d-4b79-a428-ef304d197637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:35,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:35,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:27:35,817] [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
--------------------------------------------------------------------------------
[2023-03-18 03:27:35,817] [INFO] DFAST Taxonomy check result was written to OceanDNA-b272/tc_result.tsv
[2023-03-18 03:27:35,817] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:35,817] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:35,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2aec4c43-740d-4b79-a428-ef304d197637/dqc_reference/checkm_data
[2023-03-18 03:27:35,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:35,825] [INFO] Task started: CheckM
[2023-03-18 03:27:35,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b272/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b272/checkm_input OceanDNA-b272/checkm_result
[2023-03-18 03:28:07,333] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:07,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:07,336] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:07,336] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:07,336] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b272/markers.fasta)
[2023-03-18 03:28:07,337] [INFO] Task started: Blastn
[2023-03-18 03:28:07,337] [INFO] Running command: blastn -query OceanDNA-b272/markers.fasta -db /var/lib/cwl/stg2aec4c43-740d-4b79-a428-ef304d197637/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b272/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:08,223] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:08,224] [INFO] Selected 27 target genomes.
[2023-03-18 03:28:08,224] [INFO] Target genome list was writen to OceanDNA-b272/target_genomes_gtdb.txt
[2023-03-18 03:28:08,244] [INFO] Task started: fastANI
[2023-03-18 03:28:08,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg056ea36f-7c78-433b-bbf4-0d73414a5c14/OceanDNA-b272.fa --refList OceanDNA-b272/target_genomes_gtdb.txt --output OceanDNA-b272/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:28:26,702] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:26,710] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:28:26,710] [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_002346545.1	s__UBA2994 sp002346545	82.0561	432	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_015659035.1	s__NP936 sp015659035	77.1438	147	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	76.9122	170	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	76.7057	142	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_002712885.1	s__UBA8438 sp002712885	76.6332	143	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	76.5668	158	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523485.1	s__WTFV01 sp011523485	76.5069	76	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871375.1	s__Gp6-AA40 sp016871375	76.4156	58	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.2905	61	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_016871255.1	s__VFZH01 sp016871255	76.2368	60	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464065.1	s__Luteitalea sp001464065	76.2253	66	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222675.1	s__QHWT01 sp003222675	76.1885	57	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	76.1724	53	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	-
GCA_005778315.1	s__UBA8438 sp005778315	75.8134	84	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	75.7371	54	532	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-18 03:28:26,711] [INFO] GTDB search result was written to OceanDNA-b272/result_gtdb.tsv
[2023-03-18 03:28:26,711] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:28:26,712] [INFO] DFAST_QC result json was written to OceanDNA-b272/dqc_result.json
[2023-03-18 03:28:26,712] [INFO] DFAST_QC completed!
[2023-03-18 03:28:26,712] [INFO] Total running time: 0h1m26s