[2023-03-17 13:01:51,447] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,447] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f3d729f-2af5-4db4-8104-5887394ffa5d/dqc_reference
[2023-03-17 13:01:52,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,651] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,651] [INFO] Running command: cat /var/lib/cwl/stg6c53f6c6-bf31-4f28-8317-9995e05eb09d/OceanDNA-b5977.fa | prodigal -d OceanDNA-b5977/cds.fna -a OceanDNA-b5977/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:04,263] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:04,263] [INFO] Task started: HMMsearch
[2023-03-17 13:02:04,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b5977/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f3d729f-2af5-4db4-8104-5887394ffa5d/dqc_reference/reference_markers.hmm OceanDNA-b5977/protein.faa > /dev/null
[2023-03-17 13:02:04,473] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:04,474] [INFO] Found 6/6 markers.
[2023-03-17 13:02:04,488] [INFO] Query marker FASTA was written to OceanDNA-b5977/markers.fasta
[2023-03-17 13:02:04,489] [INFO] Task started: Blastn
[2023-03-17 13:02:04,489] [INFO] Running command: blastn -query OceanDNA-b5977/markers.fasta -db /var/lib/cwl/stg7f3d729f-2af5-4db4-8104-5887394ffa5d/dqc_reference/reference_markers.fasta -out OceanDNA-b5977/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:05,050] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:05,051] [INFO] Selected 26 target genomes.
[2023-03-17 13:02:05,051] [INFO] Target genome list was writen to OceanDNA-b5977/target_genomes.txt
[2023-03-17 13:02:05,063] [INFO] Task started: fastANI
[2023-03-17 13:02:05,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c53f6c6-bf31-4f28-8317-9995e05eb09d/OceanDNA-b5977.fa --refList OceanDNA-b5977/target_genomes.txt --output OceanDNA-b5977/fastani_result.tsv --threads 1
[2023-03-17 13:02:20,457] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:20,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f3d729f-2af5-4db4-8104-5887394ffa5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:20,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f3d729f-2af5-4db4-8104-5887394ffa5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:20,457] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:20,457] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:20,457] [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
--------------------------------------------------------------------------------
[2023-03-17 13:02:20,458] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5977/tc_result.tsv
[2023-03-17 13:02:20,458] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:20,458] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:20,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f3d729f-2af5-4db4-8104-5887394ffa5d/dqc_reference/checkm_data
[2023-03-17 13:02:20,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:20,463] [INFO] Task started: CheckM
[2023-03-17 13:02:20,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5977/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5977/checkm_input OceanDNA-b5977/checkm_result
[2023-03-17 13:02:53,904] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:53,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.34%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:53,906] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:53,906] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:53,906] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5977/markers.fasta)
[2023-03-17 13:02:53,906] [INFO] Task started: Blastn
[2023-03-17 13:02:53,907] [INFO] Running command: blastn -query OceanDNA-b5977/markers.fasta -db /var/lib/cwl/stg7f3d729f-2af5-4db4-8104-5887394ffa5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5977/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:54,815] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:54,816] [INFO] Selected 18 target genomes.
[2023-03-17 13:02:54,816] [INFO] Target genome list was writen to OceanDNA-b5977/target_genomes_gtdb.txt
[2023-03-17 13:02:55,428] [INFO] Task started: fastANI
[2023-03-17 13:02:55,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c53f6c6-bf31-4f28-8317-9995e05eb09d/OceanDNA-b5977.fa --refList OceanDNA-b5977/target_genomes_gtdb.txt --output OceanDNA-b5977/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:02,337] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:02,344] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:03:02,344] [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_003023665.1	s__UBA10364 sp003023665	97.4482	382	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.70	98.70	0.79	0.79	2	conclusive
GCA_902614915.1	s__UBA10364 sp902614915	86.2133	340	492	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	84.0374	404	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525035.1	s__UBA10364 sp011525035	78.6294	144	492	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	78.5776	142	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_002430755.1	s__UBA10364 sp002430755	78.4291	101	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545085.1	s__UBA10364 sp003545085	77.9698	85	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445735.1	s__UBA10364 sp003445735	77.9355	53	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	97.99	97.76	0.85	0.77	3	-
GCA_018623275.1	s__UBA10364 sp018623275	77.7288	105	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685435.1	s__UBA10364 sp002685435	77.6898	50	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402665.1	s__UBA10364 sp018402665	76.9511	70	492	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:02,344] [INFO] GTDB search result was written to OceanDNA-b5977/result_gtdb.tsv
[2023-03-17 13:03:02,345] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:02,345] [INFO] DFAST_QC result json was written to OceanDNA-b5977/dqc_result.json
[2023-03-17 13:03:02,346] [INFO] DFAST_QC completed!
[2023-03-17 13:03:02,346] [INFO] Total running time: 0h1m11s