[2024-01-25 19:07:05,745] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:05,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:05,748] [INFO] DQC Reference Directory: /var/lib/cwl/stgd985bfe3-6620-4353-a6f5-fb2213223624/dqc_reference
[2024-01-25 19:07:06,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:06,940] [INFO] Task started: Prodigal
[2024-01-25 19:07:06,941] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5ee6801-46bd-423e-b9e4-91091e29f088/GCF_900119795.1_MARIT_PRJEB17743_genomic.fna.gz | prodigal -d GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/cds.fna -a GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:15,730] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:15,731] [INFO] Task started: HMMsearch
[2024-01-25 19:07:15,731] [INFO] Running command: hmmsearch --tblout GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd985bfe3-6620-4353-a6f5-fb2213223624/dqc_reference/reference_markers.hmm GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:15,948] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:15,949] [INFO] Found 6/6 markers.
[2024-01-25 19:07:15,977] [INFO] Query marker FASTA was written to GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/markers.fasta
[2024-01-25 19:07:15,977] [INFO] Task started: Blastn
[2024-01-25 19:07:15,977] [INFO] Running command: blastn -query GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/markers.fasta -db /var/lib/cwl/stgd985bfe3-6620-4353-a6f5-fb2213223624/dqc_reference/reference_markers.fasta -out GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:16,598] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:16,602] [INFO] Selected 20 target genomes.
[2024-01-25 19:07:16,602] [INFO] Target genome list was writen to GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/target_genomes.txt
[2024-01-25 19:07:16,614] [INFO] Task started: fastANI
[2024-01-25 19:07:16,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ee6801-46bd-423e-b9e4-91091e29f088/GCF_900119795.1_MARIT_PRJEB17743_genomic.fna.gz --refList GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/target_genomes.txt --output GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:32,305] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:32,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd985bfe3-6620-4353-a6f5-fb2213223624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:32,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd985bfe3-6620-4353-a6f5-fb2213223624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:32,318] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:32,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:32,318] [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
Tenacibaculum maritimum		GCA_900119795.1	107401	107401	type	True	100.0	1143	1145	95	conclusive
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	78.6165	312	1145	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	78.2722	353	1145	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	78.2158	367	1145	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	78.0125	367	1145	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	77.9784	312	1145	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	77.9606	312	1145	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	77.9343	301	1145	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.8811	294	1145	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.8613	345	1145	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.7823	279	1145	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	77.7689	339	1145	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.7327	277	1145	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.5406	235	1145	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.488	260	1145	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	77.3658	179	1145	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.2795	233	1145	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	77.171	241	1145	95	below_threshold
Tenacibaculum agarivorans	strain=HZ1	GCA_001936575.1	1908389	1908389	type	True	77.1619	263	1145	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	75.5678	70	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:32,320] [INFO] DFAST Taxonomy check result was written to GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/tc_result.tsv
[2024-01-25 19:07:32,321] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:32,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:32,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd985bfe3-6620-4353-a6f5-fb2213223624/dqc_reference/checkm_data
[2024-01-25 19:07:32,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:32,357] [INFO] Task started: CheckM
[2024-01-25 19:07:32,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/checkm_input GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/checkm_result
[2024-01-25 19:08:00,943] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:00,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:00,965] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:00,965] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:00,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/markers.fasta)
[2024-01-25 19:08:00,965] [INFO] Task started: Blastn
[2024-01-25 19:08:00,965] [INFO] Running command: blastn -query GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/markers.fasta -db /var/lib/cwl/stgd985bfe3-6620-4353-a6f5-fb2213223624/dqc_reference/reference_markers_gtdb.fasta -out GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:01,868] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:01,923] [INFO] Selected 19 target genomes.
[2024-01-25 19:08:01,923] [INFO] Target genome list was writen to GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:01,951] [INFO] Task started: fastANI
[2024-01-25 19:08:01,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5ee6801-46bd-423e-b9e4-91091e29f088/GCF_900119795.1_MARIT_PRJEB17743_genomic.fna.gz --refList GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/target_genomes_gtdb.txt --output GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:16,294] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:16,306] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:16,306] [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_900119795.1	s__Tenacibaculum maritimum	100.0	1143	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.84	97.91	0.93	0.90	25	conclusive
GCF_014062345.1	s__Tenacibaculum pelagium	78.3494	351	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836595.1	s__Tenacibaculum sp002836595	78.225	381	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	78.2135	348	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	78.205	368	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	78.0996	346	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	78.0208	366	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_003610735.1	s__Tenacibaculum lutimaris	77.9678	313	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	77.934	301	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239505.1	s__Tenacibaculum piscium	77.8546	258	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_900105145.1	s__Polaribacter sp900105145	77.8407	279	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004762155.1	s__Tenacibaculum sp004762155	77.7983	341	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	77.7788	338	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	77.7217	282	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105455.1	s__Tenacibaculum sp900105455	77.6016	271	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	77.5223	257	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813915.1	s__Tenacibaculum sp002813915	77.445	231	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936575.1	s__Tenacibaculum agarivorans	77.1761	262	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	77.1623	241	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:16,308] [INFO] GTDB search result was written to GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:16,308] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:16,312] [INFO] DFAST_QC result json was written to GCF_900119795.1_MARIT_PRJEB17743_genomic.fna/dqc_result.json
[2024-01-25 19:08:16,312] [INFO] DFAST_QC completed!
[2024-01-25 19:08:16,312] [INFO] Total running time: 0h1m11s