[2024-01-24 13:49:25,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:25,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:25,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg0897c25a-ce61-49ef-b903-6d4056be2660/dqc_reference
[2024-01-24 13:49:26,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:26,589] [INFO] Task started: Prodigal
[2024-01-24 13:49:26,590] [INFO] Running command: gunzip -c /var/lib/cwl/stg76537a9f-f433-415d-b337-9dee7f5953dd/GCF_020532745.1_ASM2053274v1_genomic.fna.gz | prodigal -d GCF_020532745.1_ASM2053274v1_genomic.fna/cds.fna -a GCF_020532745.1_ASM2053274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:38,588] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:38,589] [INFO] Task started: HMMsearch
[2024-01-24 13:49:38,589] [INFO] Running command: hmmsearch --tblout GCF_020532745.1_ASM2053274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0897c25a-ce61-49ef-b903-6d4056be2660/dqc_reference/reference_markers.hmm GCF_020532745.1_ASM2053274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:38,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:38,855] [INFO] Found 6/6 markers.
[2024-01-24 13:49:38,895] [INFO] Query marker FASTA was written to GCF_020532745.1_ASM2053274v1_genomic.fna/markers.fasta
[2024-01-24 13:49:38,896] [INFO] Task started: Blastn
[2024-01-24 13:49:38,896] [INFO] Running command: blastn -query GCF_020532745.1_ASM2053274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0897c25a-ce61-49ef-b903-6d4056be2660/dqc_reference/reference_markers.fasta -out GCF_020532745.1_ASM2053274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:39,700] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:39,704] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:39,704] [INFO] Target genome list was writen to GCF_020532745.1_ASM2053274v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:39,715] [INFO] Task started: fastANI
[2024-01-24 13:49:39,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg76537a9f-f433-415d-b337-9dee7f5953dd/GCF_020532745.1_ASM2053274v1_genomic.fna.gz --refList GCF_020532745.1_ASM2053274v1_genomic.fna/target_genomes.txt --output GCF_020532745.1_ASM2053274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:50,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:50,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0897c25a-ce61-49ef-b903-6d4056be2660/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:50,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0897c25a-ce61-49ef-b903-6d4056be2660/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:50,093] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:50,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:50,093] [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 porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	100.0	1289	1289	95	conclusive
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	99.9933	1287	1289	95	conclusive
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	81.1339	700	1289	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	81.1086	707	1289	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	81.0174	716	1289	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.8926	706	1289	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.8608	716	1289	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	80.4627	619	1289	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	80.4413	625	1289	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	80.4239	631	1289	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.3427	633	1289	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.2701	608	1289	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.7552	587	1289	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.3883	582	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,095] [INFO] DFAST Taxonomy check result was written to GCF_020532745.1_ASM2053274v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:50,096] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:50,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:50,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0897c25a-ce61-49ef-b903-6d4056be2660/dqc_reference/checkm_data
[2024-01-24 13:49:50,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:50,137] [INFO] Task started: CheckM
[2024-01-24 13:49:50,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020532745.1_ASM2053274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020532745.1_ASM2053274v1_genomic.fna/checkm_input GCF_020532745.1_ASM2053274v1_genomic.fna/checkm_result
[2024-01-24 13:50:27,167] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:27,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:27,189] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:27,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:27,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020532745.1_ASM2053274v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:27,190] [INFO] Task started: Blastn
[2024-01-24 13:50:27,190] [INFO] Running command: blastn -query GCF_020532745.1_ASM2053274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0897c25a-ce61-49ef-b903-6d4056be2660/dqc_reference/reference_markers_gtdb.fasta -out GCF_020532745.1_ASM2053274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:28,111] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:28,115] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:28,115] [INFO] Target genome list was writen to GCF_020532745.1_ASM2053274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:28,123] [INFO] Task started: fastANI
[2024-01-24 13:50:28,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg76537a9f-f433-415d-b337-9dee7f5953dd/GCF_020532745.1_ASM2053274v1_genomic.fna.gz --refList GCF_020532745.1_ASM2053274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020532745.1_ASM2053274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:37,776] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:37,787] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:37,787] [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_002954685.1	s__Polaribacter porphyrae	99.9933	1287	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018861005.1	s__Polaribacter vadi_A	81.0346	720	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	80.997	721	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001761365.1	s__Polaribacter vadi	80.888	707	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001280865.1	s__Polaribacter dokdonensis	80.4438	621	1289	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	80.3593	647	1289	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	80.3253	634	1289	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	80.2709	596	1289	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	80.2527	610	1289	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	80.1396	610	1289	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	80.0358	624	1289	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	79.9444	568	1289	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 13:50:37,789] [INFO] GTDB search result was written to GCF_020532745.1_ASM2053274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:37,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:37,793] [INFO] DFAST_QC result json was written to GCF_020532745.1_ASM2053274v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:37,793] [INFO] DFAST_QC completed!
[2024-01-24 13:50:37,793] [INFO] Total running time: 0h1m12s