[2024-01-24 11:58:55,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg70fd930b-2f08-4070-a2cf-2817d89f1631/dqc_reference
[2024-01-24 11:58:56,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:56,784] [INFO] Task started: Prodigal
[2024-01-24 11:58:56,784] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2e3666e-992d-4084-8f21-4875d252f5c8/GCF_014643655.1_ASM1464365v1_genomic.fna.gz | prodigal -d GCF_014643655.1_ASM1464365v1_genomic.fna/cds.fna -a GCF_014643655.1_ASM1464365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:06,653] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:06,654] [INFO] Task started: HMMsearch
[2024-01-24 11:59:06,654] [INFO] Running command: hmmsearch --tblout GCF_014643655.1_ASM1464365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70fd930b-2f08-4070-a2cf-2817d89f1631/dqc_reference/reference_markers.hmm GCF_014643655.1_ASM1464365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:06,920] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:06,921] [INFO] Found 6/6 markers.
[2024-01-24 11:59:06,946] [INFO] Query marker FASTA was written to GCF_014643655.1_ASM1464365v1_genomic.fna/markers.fasta
[2024-01-24 11:59:06,947] [INFO] Task started: Blastn
[2024-01-24 11:59:06,947] [INFO] Running command: blastn -query GCF_014643655.1_ASM1464365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70fd930b-2f08-4070-a2cf-2817d89f1631/dqc_reference/reference_markers.fasta -out GCF_014643655.1_ASM1464365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:07,620] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:07,623] [INFO] Selected 25 target genomes.
[2024-01-24 11:59:07,623] [INFO] Target genome list was writen to GCF_014643655.1_ASM1464365v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:07,648] [INFO] Task started: fastANI
[2024-01-24 11:59:07,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e3666e-992d-4084-8f21-4875d252f5c8/GCF_014643655.1_ASM1464365v1_genomic.fna.gz --refList GCF_014643655.1_ASM1464365v1_genomic.fna/target_genomes.txt --output GCF_014643655.1_ASM1464365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:22,706] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:22,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70fd930b-2f08-4070-a2cf-2817d89f1631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:22,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70fd930b-2f08-4070-a2cf-2817d89f1631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:22,727] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:22,727] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:22,728] [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 pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	100.0	897	897	95	conclusive
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.2235	228	897	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.2196	257	897	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.9695	260	897	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.8732	259	897	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.8416	246	897	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.8293	251	897	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.8009	269	897	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.7765	247	897	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.6617	219	897	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.6592	222	897	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.6224	224	897	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.622	270	897	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.6208	199	897	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	77.525	206	897	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.4943	267	897	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	77.4504	184	897	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	77.4282	225	897	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	77.4172	191	897	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	77.3449	125	897	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	77.3238	180	897	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	77.248	224	897	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.2394	228	897	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	77.0965	149	897	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5597	102	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:22,729] [INFO] DFAST Taxonomy check result was written to GCF_014643655.1_ASM1464365v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:22,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:22,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:22,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70fd930b-2f08-4070-a2cf-2817d89f1631/dqc_reference/checkm_data
[2024-01-24 11:59:22,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:22,762] [INFO] Task started: CheckM
[2024-01-24 11:59:22,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643655.1_ASM1464365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643655.1_ASM1464365v1_genomic.fna/checkm_input GCF_014643655.1_ASM1464365v1_genomic.fna/checkm_result
[2024-01-24 11:59:54,956] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:54,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:54,982] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:54,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:54,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643655.1_ASM1464365v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:54,983] [INFO] Task started: Blastn
[2024-01-24 11:59:54,983] [INFO] Running command: blastn -query GCF_014643655.1_ASM1464365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70fd930b-2f08-4070-a2cf-2817d89f1631/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643655.1_ASM1464365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:55,929] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:55,933] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:55,933] [INFO] Target genome list was writen to GCF_014643655.1_ASM1464365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:55,952] [INFO] Task started: fastANI
[2024-01-24 11:59:55,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2e3666e-992d-4084-8f21-4875d252f5c8/GCF_014643655.1_ASM1464365v1_genomic.fna.gz --refList GCF_014643655.1_ASM1464365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643655.1_ASM1464365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:08,481] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:08,498] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:08,499] [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_014643655.1	s__Polaribacter_A pacificus	100.0	897	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014352875.1	s__Polaribacter sp014352875	78.1962	258	897	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	77.9987	267	897	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	77.9661	261	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013373385.1	s__Polaribacter_A sp013373385	77.853	291	897	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_003129485.1	s__Polaribacter sp003129485	77.7765	247	897	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	77.7504	233	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	77.6976	268	897	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	77.6515	265	897	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	77.6367	198	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_001280865.1	s__Polaribacter dokdonensis	77.6224	224	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905480405.1	s__Polaribacter sp905480405	77.5773	211	897	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	77.5672	234	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_000152945.2	s__Polaribacter sp000152945	77.5604	215	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763595.1	s__Polaribacter_A sp016763595	77.5599	178	897	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_014062345.1	s__Tenacibaculum pelagium	77.5248	206	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	77.5103	285	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002814075.1	s__Polaribacter sejongensis	77.4848	268	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_900105145.1	s__Polaribacter sp900105145	77.462	275	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	77.4279	202	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	77.4125	233	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002954685.1	s__Polaribacter porphyrae	77.3327	218	897	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:08,500] [INFO] GTDB search result was written to GCF_014643655.1_ASM1464365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:08,501] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:08,507] [INFO] DFAST_QC result json was written to GCF_014643655.1_ASM1464365v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:08,507] [INFO] DFAST_QC completed!
[2024-01-24 12:00:08,507] [INFO] Total running time: 0h1m13s