[2023-03-16 03:23:48,507] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg40515fec-f9b9-42c7-858e-5df84724cab4/dqc_reference
[2023-03-16 03:23:50,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,649] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,649] [INFO] Running command: cat /var/lib/cwl/stg6e9275d4-c60a-47da-b459-9d77961aaf7f/OceanDNA-b6768.fa | prodigal -d OceanDNA-b6768/cds.fna -a OceanDNA-b6768/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:07,954] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:07,954] [INFO] Task started: HMMsearch
[2023-03-16 03:24:07,955] [INFO] Running command: hmmsearch --tblout OceanDNA-b6768/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40515fec-f9b9-42c7-858e-5df84724cab4/dqc_reference/reference_markers.hmm OceanDNA-b6768/protein.faa > /dev/null
[2023-03-16 03:24:08,169] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:08,169] [INFO] Found 6/6 markers.
[2023-03-16 03:24:08,186] [INFO] Query marker FASTA was written to OceanDNA-b6768/markers.fasta
[2023-03-16 03:24:08,186] [INFO] Task started: Blastn
[2023-03-16 03:24:08,186] [INFO] Running command: blastn -query OceanDNA-b6768/markers.fasta -db /var/lib/cwl/stg40515fec-f9b9-42c7-858e-5df84724cab4/dqc_reference/reference_markers.fasta -out OceanDNA-b6768/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:08,738] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:08,739] [INFO] Selected 13 target genomes.
[2023-03-16 03:24:08,739] [INFO] Target genome list was writen to OceanDNA-b6768/target_genomes.txt
[2023-03-16 03:24:08,749] [INFO] Task started: fastANI
[2023-03-16 03:24:08,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e9275d4-c60a-47da-b459-9d77961aaf7f/OceanDNA-b6768.fa --refList OceanDNA-b6768/target_genomes.txt --output OceanDNA-b6768/fastani_result.tsv --threads 1
[2023-03-16 03:24:17,573] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:17,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40515fec-f9b9-42c7-858e-5df84724cab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:17,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40515fec-f9b9-42c7-858e-5df84724cab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:17,581] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:17,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:17,581] [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
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	79.4994	441	859	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	79.0767	463	859	95	below_threshold
Flavobacterium arcticum	strain=SM1502	GCA_003344925.1	1784713	1784713	type	True	78.6166	383	859	95	below_threshold
Flavobacterium arcticum	strain=KCTC 42668	GCA_004634185.1	1784713	1784713	type	True	78.6139	381	859	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	78.2806	343	859	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	78.1372	310	859	95	below_threshold
Flavobacterium suaedae	strain=CGMCC 1.15461	GCA_014642915.1	1767027	1767027	type	True	77.9839	333	859	95	below_threshold
Flavobacterium cyanobacteriorum	strain=TH021	GCA_002251835.1	2022802	2022802	type	True	77.2515	175	859	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	77.1034	232	859	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	76.3432	55	859	95	below_threshold
Flavobacterium kingsejongi	strain=WV39	GCA_003076475.1	1678728	1678728	type	True	76.2494	90	859	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:17,582] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6768/tc_result.tsv
[2023-03-16 03:24:17,582] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:17,582] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:17,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40515fec-f9b9-42c7-858e-5df84724cab4/dqc_reference/checkm_data
[2023-03-16 03:24:17,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:17,599] [INFO] Task started: CheckM
[2023-03-16 03:24:17,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6768/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6768/checkm_input OceanDNA-b6768/checkm_result
[2023-03-16 03:25:01,712] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:01,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:01,715] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:01,715] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:01,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6768/markers.fasta)
[2023-03-16 03:25:01,715] [INFO] Task started: Blastn
[2023-03-16 03:25:01,715] [INFO] Running command: blastn -query OceanDNA-b6768/markers.fasta -db /var/lib/cwl/stg40515fec-f9b9-42c7-858e-5df84724cab4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6768/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:02,489] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:02,490] [INFO] Selected 15 target genomes.
[2023-03-16 03:25:02,490] [INFO] Target genome list was writen to OceanDNA-b6768/target_genomes_gtdb.txt
[2023-03-16 03:25:02,671] [INFO] Task started: fastANI
[2023-03-16 03:25:02,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e9275d4-c60a-47da-b459-9d77961aaf7f/OceanDNA-b6768.fa --refList OceanDNA-b6768/target_genomes_gtdb.txt --output OceanDNA-b6768/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:12,274] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:12,283] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:25:12,283] [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
GCF_004634195.1	s__Flavobacterium sp004634195	79.0767	463	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
GCF_003344925.1	s__Flavobacterium arcticum	78.6111	383	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002714575.1	s__Flavobacterium sp002714575	78.2249	350	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642915.1	s__Flavobacterium suaedae	77.9839	333	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848495.1	s__Flavobacterium sp009848495	77.7349	278	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422725.1	s__Flavobacterium subsaxonicum	77.3399	238	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	77.259	192	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002251835.1	s__Flavobacterium cyanobacteriorum	77.2387	175	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097145.1	s__Flavobacterium sp007097145	77.0863	232	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826935.1	s__Flavobacterium sp009826935	76.9878	182	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	76.958	187	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932585.1	s__Flavobacterium sp012932585	76.8296	188	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403075.1	s__Flavobacterium sp003403075	76.699	198	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096035.1	s__Flavobacterium album	76.6534	188	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	76.1296	63	859	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:12,283] [INFO] GTDB search result was written to OceanDNA-b6768/result_gtdb.tsv
[2023-03-16 03:25:12,283] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:12,285] [INFO] DFAST_QC result json was written to OceanDNA-b6768/dqc_result.json
[2023-03-16 03:25:12,285] [INFO] DFAST_QC completed!
[2023-03-16 03:25:12,285] [INFO] Total running time: 0h1m24s