[2023-03-19 04:29:39,808] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:39,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:39,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg49e3bcac-a3f6-403a-8062-c50e19650288/dqc_reference
[2023-03-19 04:29:40,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:40,887] [INFO] Task started: Prodigal
[2023-03-19 04:29:40,887] [INFO] Running command: cat /var/lib/cwl/stg4ee5a9f5-ee11-4f4d-8389-c831c421b74a/OceanDNA-b22650.fa | prodigal -d OceanDNA-b22650/cds.fna -a OceanDNA-b22650/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:54,706] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:54,706] [INFO] Task started: HMMsearch
[2023-03-19 04:29:54,706] [INFO] Running command: hmmsearch --tblout OceanDNA-b22650/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49e3bcac-a3f6-403a-8062-c50e19650288/dqc_reference/reference_markers.hmm OceanDNA-b22650/protein.faa > /dev/null
[2023-03-19 04:29:54,895] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:54,896] [INFO] Found 6/6 markers.
[2023-03-19 04:29:54,915] [INFO] Query marker FASTA was written to OceanDNA-b22650/markers.fasta
[2023-03-19 04:29:54,916] [INFO] Task started: Blastn
[2023-03-19 04:29:54,916] [INFO] Running command: blastn -query OceanDNA-b22650/markers.fasta -db /var/lib/cwl/stg49e3bcac-a3f6-403a-8062-c50e19650288/dqc_reference/reference_markers.fasta -out OceanDNA-b22650/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:55,452] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:55,453] [INFO] Selected 23 target genomes.
[2023-03-19 04:29:55,453] [INFO] Target genome list was writen to OceanDNA-b22650/target_genomes.txt
[2023-03-19 04:29:55,464] [INFO] Task started: fastANI
[2023-03-19 04:29:55,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee5a9f5-ee11-4f4d-8389-c831c421b74a/OceanDNA-b22650.fa --refList OceanDNA-b22650/target_genomes.txt --output OceanDNA-b22650/fastani_result.tsv --threads 1
[2023-03-19 04:30:14,136] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:14,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49e3bcac-a3f6-403a-8062-c50e19650288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:14,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49e3bcac-a3f6-403a-8062-c50e19650288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:14,137] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:14,137] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:30:14,137] [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
--------------------------------------------------------------------------------
[2023-03-19 04:30:14,137] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22650/tc_result.tsv
[2023-03-19 04:30:14,137] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:14,137] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:14,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49e3bcac-a3f6-403a-8062-c50e19650288/dqc_reference/checkm_data
[2023-03-19 04:30:14,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:14,144] [INFO] Task started: CheckM
[2023-03-19 04:30:14,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22650/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22650/checkm_input OceanDNA-b22650/checkm_result
[2023-03-19 04:30:52,031] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:52,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:52,034] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:52,034] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:52,034] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22650/markers.fasta)
[2023-03-19 04:30:52,035] [INFO] Task started: Blastn
[2023-03-19 04:30:52,035] [INFO] Running command: blastn -query OceanDNA-b22650/markers.fasta -db /var/lib/cwl/stg49e3bcac-a3f6-403a-8062-c50e19650288/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22650/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:52,751] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:52,751] [INFO] Selected 15 target genomes.
[2023-03-19 04:30:52,752] [INFO] Target genome list was writen to OceanDNA-b22650/target_genomes_gtdb.txt
[2023-03-19 04:30:52,786] [INFO] Task started: fastANI
[2023-03-19 04:30:52,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee5a9f5-ee11-4f4d-8389-c831c421b74a/OceanDNA-b22650.fa --refList OceanDNA-b22650/target_genomes_gtdb.txt --output OceanDNA-b22650/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:01,031] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:01,040] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:31:01,040] [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_009922585.1	s__UBA1268 sp009922585	84.4964	451	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523305.1	s__UBA1268 sp011523305	78.7239	204	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	76.6619	84	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	76.6239	97	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	76.3609	106	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853835.1	s__QWPN01 sp017853835	76.3461	85	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	76.2842	115	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779265.1	s__M30B53 sp016779265	76.2754	73	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	99.26	99.20	0.88	0.86	5	-
GCA_005789975.1	s__QWPN01 sp005789975	76.2445	70	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_903919035.1	s__QWPN01 sp903919035	76.2012	85	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	76.1966	87	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872955.1	s__QWPN01 sp016872955	76.195	74	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970785.1	s__F1-20-MAGs016 sp018970785	75.9688	69	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885855.1	s__QWOP01 sp903885855	75.9683	80	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	75.951	89	651	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:01,040] [INFO] GTDB search result was written to OceanDNA-b22650/result_gtdb.tsv
[2023-03-19 04:31:01,040] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:01,041] [INFO] DFAST_QC result json was written to OceanDNA-b22650/dqc_result.json
[2023-03-19 04:31:01,042] [INFO] DFAST_QC completed!
[2023-03-19 04:31:01,042] [INFO] Total running time: 0h1m21s