[2024-01-24 13:21:55,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:55,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:55,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg77f1d2b6-faac-4116-9515-c67139e666e3/dqc_reference
[2024-01-24 13:21:57,109] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:57,110] [INFO] Task started: Prodigal
[2024-01-24 13:21:57,110] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3a829e3-ab38-4b6f-9df9-e524985e1ba3/GCF_001680875.1_ASM168087v1_genomic.fna.gz | prodigal -d GCF_001680875.1_ASM168087v1_genomic.fna/cds.fna -a GCF_001680875.1_ASM168087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,914] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,914] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,914] [INFO] Running command: hmmsearch --tblout GCF_001680875.1_ASM168087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77f1d2b6-faac-4116-9515-c67139e666e3/dqc_reference/reference_markers.hmm GCF_001680875.1_ASM168087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,243] [INFO] Found 6/6 markers.
[2024-01-24 13:22:09,290] [INFO] Query marker FASTA was written to GCF_001680875.1_ASM168087v1_genomic.fna/markers.fasta
[2024-01-24 13:22:09,290] [INFO] Task started: Blastn
[2024-01-24 13:22:09,290] [INFO] Running command: blastn -query GCF_001680875.1_ASM168087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f1d2b6-faac-4116-9515-c67139e666e3/dqc_reference/reference_markers.fasta -out GCF_001680875.1_ASM168087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:10,008] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:10,012] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:10,012] [INFO] Target genome list was writen to GCF_001680875.1_ASM168087v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:10,018] [INFO] Task started: fastANI
[2024-01-24 13:22:10,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a829e3-ab38-4b6f-9df9-e524985e1ba3/GCF_001680875.1_ASM168087v1_genomic.fna.gz --refList GCF_001680875.1_ASM168087v1_genomic.fna/target_genomes.txt --output GCF_001680875.1_ASM168087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:20,393] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:20,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77f1d2b6-faac-4116-9515-c67139e666e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:20,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77f1d2b6-faac-4116-9515-c67139e666e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:20,406] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:22:20,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:20,406] [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 reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	100.0	1348	1348	95	conclusive
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	99.9992	1347	1348	95	conclusive
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	99.9804	1344	1348	95	conclusive
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	99.9736	1322	1348	95	conclusive
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	82.2465	771	1348	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	81.6063	657	1348	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	81.5664	670	1348	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	81.2781	691	1348	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	81.1233	708	1348	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.8561	643	1348	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.8285	636	1348	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.66	490	1348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:20,408] [INFO] DFAST Taxonomy check result was written to GCF_001680875.1_ASM168087v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:20,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:20,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:20,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77f1d2b6-faac-4116-9515-c67139e666e3/dqc_reference/checkm_data
[2024-01-24 13:22:20,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:20,452] [INFO] Task started: CheckM
[2024-01-24 13:22:20,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001680875.1_ASM168087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001680875.1_ASM168087v1_genomic.fna/checkm_input GCF_001680875.1_ASM168087v1_genomic.fna/checkm_result
[2024-01-24 13:22:57,234] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:57,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:57,259] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:57,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:57,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001680875.1_ASM168087v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:57,260] [INFO] Task started: Blastn
[2024-01-24 13:22:57,260] [INFO] Running command: blastn -query GCF_001680875.1_ASM168087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f1d2b6-faac-4116-9515-c67139e666e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001680875.1_ASM168087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:58,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:58,280] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:58,280] [INFO] Target genome list was writen to GCF_001680875.1_ASM168087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:58,291] [INFO] Task started: fastANI
[2024-01-24 13:22:58,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a829e3-ab38-4b6f-9df9-e524985e1ba3/GCF_001680875.1_ASM168087v1_genomic.fna.gz --refList GCF_001680875.1_ASM168087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001680875.1_ASM168087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:08,524] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:08,536] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:08,536] [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_001975665.1	s__Polaribacter reichenbachii	99.9992	1347	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	conclusive
GCF_018861005.1	s__Polaribacter vadi_A	89.4221	964	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	82.2416	768	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105145.1	s__Polaribacter sp900105145	82.2296	789	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	81.6736	660	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000687935.1	s__Polaribacter sp000687935	81.6217	751	1348	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	81.5862	718	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	81.3375	656	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	81.1125	706	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	80.7892	707	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	80.7262	662	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	79.8452	634	1348	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 13:23:08,538] [INFO] GTDB search result was written to GCF_001680875.1_ASM168087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:08,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:08,542] [INFO] DFAST_QC result json was written to GCF_001680875.1_ASM168087v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:08,542] [INFO] DFAST_QC completed!
[2024-01-24 13:23:08,542] [INFO] Total running time: 0h1m13s