[2023-06-28 14:19:10,373] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:19:10,375] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:19:10,376] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1569779-b436-42c2-b30f-2a579db45292/dqc_reference
[2023-06-28 14:19:11,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:19:11,619] [INFO] Task started: Prodigal
[2023-06-28 14:19:11,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg463990cf-6ba1-4db0-aabb-9182e21bfa54/GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:19:20,306] [INFO] Task succeeded: Prodigal
[2023-06-28 14:19:20,307] [INFO] Task started: HMMsearch
[2023-06-28 14:19:20,307] [INFO] Running command: hmmsearch --tblout GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1569779-b436-42c2-b30f-2a579db45292/dqc_reference/reference_markers.hmm GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:19:20,494] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:19:20,495] [INFO] Found 6/6 markers.
[2023-06-28 14:19:20,520] [INFO] Query marker FASTA was written to GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 14:19:20,521] [INFO] Task started: Blastn
[2023-06-28 14:19:20,521] [INFO] Running command: blastn -query GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1569779-b436-42c2-b30f-2a579db45292/dqc_reference/reference_markers.fasta -out GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:19:21,168] [INFO] Task succeeded: Blastn
[2023-06-28 14:19:21,171] [INFO] Selected 21 target genomes.
[2023-06-28 14:19:21,171] [INFO] Target genome list was writen to GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 14:19:21,172] [INFO] Task started: fastANI
[2023-06-28 14:19:21,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg463990cf-6ba1-4db0-aabb-9182e21bfa54/GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:19:33,581] [INFO] Task succeeded: fastANI
[2023-06-28 14:19:33,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1569779-b436-42c2-b30f-2a579db45292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:19:33,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1569779-b436-42c2-b30f-2a579db45292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:19:33,598] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:19:33,598] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:19:33,598] [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 aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.9046	395	883	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.8826	409	883	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.8508	405	883	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.8361	396	883	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	78.8251	404	883	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.7468	399	883	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.7275	387	883	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.6976	382	883	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.6944	398	883	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.6883	412	883	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.6553	388	883	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.5964	374	883	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.3562	375	883	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	78.3558	313	883	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.3556	356	883	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	78.3483	346	883	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.341	397	883	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	78.3342	313	883	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	78.1438	291	883	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.0025	396	883	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	77.52	244	883	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:19:33,601] [INFO] DFAST Taxonomy check result was written to GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 14:19:33,601] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:19:33,602] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:19:33,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1569779-b436-42c2-b30f-2a579db45292/dqc_reference/checkm_data
[2023-06-28 14:19:33,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:19:33,634] [INFO] Task started: CheckM
[2023-06-28 14:19:33,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 14:20:03,537] [INFO] Task succeeded: CheckM
[2023-06-28 14:20:03,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:20:03,560] [INFO] ===== Completeness check finished =====
[2023-06-28 14:20:03,560] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:20:03,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 14:20:03,561] [INFO] Task started: Blastn
[2023-06-28 14:20:03,561] [INFO] Running command: blastn -query GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1569779-b436-42c2-b30f-2a579db45292/dqc_reference/reference_markers_gtdb.fasta -out GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:20:04,465] [INFO] Task succeeded: Blastn
[2023-06-28 14:20:04,470] [INFO] Selected 22 target genomes.
[2023-06-28 14:20:04,471] [INFO] Target genome list was writen to GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:20:04,477] [INFO] Task started: fastANI
[2023-06-28 14:20:04,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg463990cf-6ba1-4db0-aabb-9182e21bfa54/GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:20:18,317] [INFO] Task succeeded: fastANI
[2023-06-28 14:20:18,335] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:20:18,335] [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_016763595.1	s__Polaribacter_A sp016763595	79.7897	291	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373385.1	s__Polaribacter_A sp013373385	79.3149	469	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	78.9366	412	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	78.8832	410	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	78.8731	402	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	78.849	391	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	78.8424	396	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643655.1	s__Polaribacter_A pacificus	78.8357	403	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	78.7465	400	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954665.1	s__Polaribacter glomeratus	78.7247	387	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_007997075.1	s__Polaribacter sp007997075	78.6874	390	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	78.6727	383	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	78.6128	382	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_002814075.1	s__Polaribacter sejongensis	78.5873	384	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_003129485.1	s__Polaribacter sp003129485	78.3556	356	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	78.3556	375	883	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	78.3462	305	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	78.215	339	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	78.1524	291	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_002836595.1	s__Tenacibaculum sp002836595	78.1437	315	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664185.1	s__Tenacibaculum discolor	77.6625	277	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_900105985.1	s__Tenacibaculum sp900105985	77.5661	268	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-28 14:20:18,338] [INFO] GTDB search result was written to GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 14:20:18,338] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:20:18,343] [INFO] DFAST_QC result json was written to GCA_913065125.1_SRR5242449_bin.12_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 14:20:18,344] [INFO] DFAST_QC completed!
[2023-06-28 14:20:18,344] [INFO] Total running time: 0h1m8s