[2023-03-16 08:10:35,193] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,194] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a61250a-7201-44e7-a18b-21d1eb33224b/dqc_reference
[2023-03-16 08:10:36,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,312] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,312] [INFO] Running command: cat /var/lib/cwl/stg15b48e78-c42f-42b6-a188-4890a9a943a3/OceanDNA-b5824.fa | prodigal -d OceanDNA-b5824/cds.fna -a OceanDNA-b5824/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:49,283] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:49,283] [INFO] Task started: HMMsearch
[2023-03-16 08:10:49,283] [INFO] Running command: hmmsearch --tblout OceanDNA-b5824/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a61250a-7201-44e7-a18b-21d1eb33224b/dqc_reference/reference_markers.hmm OceanDNA-b5824/protein.faa > /dev/null
[2023-03-16 08:10:49,456] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:49,457] [INFO] Found 6/6 markers.
[2023-03-16 08:10:49,525] [INFO] Query marker FASTA was written to OceanDNA-b5824/markers.fasta
[2023-03-16 08:10:49,526] [INFO] Task started: Blastn
[2023-03-16 08:10:49,526] [INFO] Running command: blastn -query OceanDNA-b5824/markers.fasta -db /var/lib/cwl/stg3a61250a-7201-44e7-a18b-21d1eb33224b/dqc_reference/reference_markers.fasta -out OceanDNA-b5824/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:50,064] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:50,082] [INFO] Selected 21 target genomes.
[2023-03-16 08:10:50,083] [INFO] Target genome list was writen to OceanDNA-b5824/target_genomes.txt
[2023-03-16 08:10:50,096] [INFO] Task started: fastANI
[2023-03-16 08:10:50,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg15b48e78-c42f-42b6-a188-4890a9a943a3/OceanDNA-b5824.fa --refList OceanDNA-b5824/target_genomes.txt --output OceanDNA-b5824/fastani_result.tsv --threads 1
[2023-03-16 08:11:01,765] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:01,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a61250a-7201-44e7-a18b-21d1eb33224b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:11:01,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a61250a-7201-44e7-a18b-21d1eb33224b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:11:01,766] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:11:01,766] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:11:01,766] [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
--------------------------------------------------------------------------------
[2023-03-16 08:11:01,772] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5824/tc_result.tsv
[2023-03-16 08:11:01,785] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:11:01,785] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:11:01,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a61250a-7201-44e7-a18b-21d1eb33224b/dqc_reference/checkm_data
[2023-03-16 08:11:01,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:11:01,893] [INFO] Task started: CheckM
[2023-03-16 08:11:01,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5824/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5824/checkm_input OceanDNA-b5824/checkm_result
[2023-03-16 08:11:38,372] [INFO] Task succeeded: CheckM
[2023-03-16 08:11:38,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:11:38,425] [INFO] ===== Completeness check finished =====
[2023-03-16 08:11:38,426] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:11:38,426] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5824/markers.fasta)
[2023-03-16 08:11:38,427] [INFO] Task started: Blastn
[2023-03-16 08:11:38,427] [INFO] Running command: blastn -query OceanDNA-b5824/markers.fasta -db /var/lib/cwl/stg3a61250a-7201-44e7-a18b-21d1eb33224b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5824/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:11:39,136] [INFO] Task succeeded: Blastn
[2023-03-16 08:11:39,148] [INFO] Selected 18 target genomes.
[2023-03-16 08:11:39,148] [INFO] Target genome list was writen to OceanDNA-b5824/target_genomes_gtdb.txt
[2023-03-16 08:11:39,204] [INFO] Task started: fastANI
[2023-03-16 08:11:39,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg15b48e78-c42f-42b6-a188-4890a9a943a3/OceanDNA-b5824.fa --refList OceanDNA-b5824/target_genomes_gtdb.txt --output OceanDNA-b5824/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:11:46,540] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:46,546] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:11:46,546] [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_905182675.1	s__UBA10364 sp905182675	97.2188	393	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003487785.1	s__UBA10364 sp003487785	86.849	343	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.22	99.20	0.81	0.80	3	-
GCA_003045825.1	s__UBA10364 sp003045825	77.5426	78	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	-
GCA_002430755.1	s__UBA10364 sp002430755	77.4742	53	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269745.1	s__UBA10364 sp012269745	77.2948	82	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	77.1893	92	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_011525035.1	s__UBA10364 sp011525035	77.1781	83	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478295.1	s__UBA10364 sp002387615	77.1565	91	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_018623275.1	s__UBA10364 sp018623275	76.8528	56	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707525.1	s__UBA10364 sp002707525	76.7539	69	612	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:11:46,550] [INFO] GTDB search result was written to OceanDNA-b5824/result_gtdb.tsv
[2023-03-16 08:11:46,555] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:11:46,561] [INFO] DFAST_QC result json was written to OceanDNA-b5824/dqc_result.json
[2023-03-16 08:11:46,561] [INFO] DFAST_QC completed!
[2023-03-16 08:11:46,562] [INFO] Total running time: 0h1m11s