[2023-03-18 23:44:06,299] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,299] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a9e20cc-315d-4cc1-8cc7-829429d8461f/dqc_reference
[2023-03-18 23:44:07,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,424] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,424] [INFO] Running command: cat /var/lib/cwl/stg927de379-7460-4d95-998c-78ce46cc942c/OceanDNA-b9927.fa | prodigal -d OceanDNA-b9927/cds.fna -a OceanDNA-b9927/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:16,620] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:16,620] [INFO] Task started: HMMsearch
[2023-03-18 23:44:16,620] [INFO] Running command: hmmsearch --tblout OceanDNA-b9927/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a9e20cc-315d-4cc1-8cc7-829429d8461f/dqc_reference/reference_markers.hmm OceanDNA-b9927/protein.faa > /dev/null
[2023-03-18 23:44:16,799] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:16,800] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg927de379-7460-4d95-998c-78ce46cc942c/OceanDNA-b9927.fa]
[2023-03-18 23:44:16,813] [INFO] Query marker FASTA was written to OceanDNA-b9927/markers.fasta
[2023-03-18 23:44:16,815] [INFO] Task started: Blastn
[2023-03-18 23:44:16,815] [INFO] Running command: blastn -query OceanDNA-b9927/markers.fasta -db /var/lib/cwl/stg7a9e20cc-315d-4cc1-8cc7-829429d8461f/dqc_reference/reference_markers.fasta -out OceanDNA-b9927/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:17,373] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:17,374] [INFO] Selected 12 target genomes.
[2023-03-18 23:44:17,374] [INFO] Target genome list was writen to OceanDNA-b9927/target_genomes.txt
[2023-03-18 23:44:17,384] [INFO] Task started: fastANI
[2023-03-18 23:44:17,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg927de379-7460-4d95-998c-78ce46cc942c/OceanDNA-b9927.fa --refList OceanDNA-b9927/target_genomes.txt --output OceanDNA-b9927/fastani_result.tsv --threads 1
[2023-03-18 23:44:24,767] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:24,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a9e20cc-315d-4cc1-8cc7-829429d8461f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:24,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a9e20cc-315d-4cc1-8cc7-829429d8461f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:24,778] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:24,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:24,778] [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
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.2129	302	455	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	80.1012	289	455	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.0843	295	455	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	79.8377	278	455	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	79.7191	277	455	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	79.5198	266	455	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.4804	270	455	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	79.2145	274	455	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.1759	270	455	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.1282	275	455	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.9591	274	455	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.8905	239	455	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:24,778] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9927/tc_result.tsv
[2023-03-18 23:44:24,778] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:24,778] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:24,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a9e20cc-315d-4cc1-8cc7-829429d8461f/dqc_reference/checkm_data
[2023-03-18 23:44:24,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:25,011] [INFO] Task started: CheckM
[2023-03-18 23:44:25,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9927/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9927/checkm_input OceanDNA-b9927/checkm_result
[2023-03-18 23:44:52,541] [INFO] Task succeeded: CheckM
[2023-03-18 23:44:52,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:44:52,545] [INFO] ===== Completeness check finished =====
[2023-03-18 23:44:52,545] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:44:52,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9927/markers.fasta)
[2023-03-18 23:44:52,547] [INFO] Task started: Blastn
[2023-03-18 23:44:52,547] [INFO] Running command: blastn -query OceanDNA-b9927/markers.fasta -db /var/lib/cwl/stg7a9e20cc-315d-4cc1-8cc7-829429d8461f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9927/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:53,346] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:53,348] [INFO] Selected 15 target genomes.
[2023-03-18 23:44:53,348] [INFO] Target genome list was writen to OceanDNA-b9927/target_genomes_gtdb.txt
[2023-03-18 23:44:53,357] [INFO] Task started: fastANI
[2023-03-18 23:44:53,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg927de379-7460-4d95-998c-78ce46cc942c/OceanDNA-b9927.fa --refList OceanDNA-b9927/target_genomes_gtdb.txt --output OceanDNA-b9927/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:01,638] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:01,647] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:45:01,647] [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_002831685.1	s__Polaribacter sp002831685	82.1452	332	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181765.1	s__Polaribacter sp905181765	82.056	257	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
GCF_007997075.1	s__Polaribacter sp007997075	81.7377	331	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003537695.1	s__Polaribacter sp003537695	80.5172	238	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	80.2895	296	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	80.222	296	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	80.2029	282	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_014352875.1	s__Polaribacter sp014352875	80.1872	303	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	80.1068	294	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	80.0902	290	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796785.1	s__Polaribacter sp009796785	79.9559	283	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	79.7465	241	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	79.7006	273	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	79.5824	269	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	79.561	260	455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:01,648] [INFO] GTDB search result was written to OceanDNA-b9927/result_gtdb.tsv
[2023-03-18 23:45:01,649] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:01,652] [INFO] DFAST_QC result json was written to OceanDNA-b9927/dqc_result.json
[2023-03-18 23:45:01,652] [INFO] DFAST_QC completed!
[2023-03-18 23:45:01,653] [INFO] Total running time: 0h0m55s