[2024-01-25 18:05:05,702] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:05,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:05,703] [INFO] DQC Reference Directory: /var/lib/cwl/stga573cbdd-9735-47f9-b5e4-ae2af416e535/dqc_reference
[2024-01-25 18:05:06,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:06,861] [INFO] Task started: Prodigal
[2024-01-25 18:05:06,861] [INFO] Running command: gunzip -c /var/lib/cwl/stgf31acfec-8453-4c20-9931-1db5462de6ad/GCF_002954685.1_ASM295468v1_genomic.fna.gz | prodigal -d GCF_002954685.1_ASM295468v1_genomic.fna/cds.fna -a GCF_002954685.1_ASM295468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:16,313] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:16,314] [INFO] Task started: HMMsearch
[2024-01-25 18:05:16,314] [INFO] Running command: hmmsearch --tblout GCF_002954685.1_ASM295468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga573cbdd-9735-47f9-b5e4-ae2af416e535/dqc_reference/reference_markers.hmm GCF_002954685.1_ASM295468v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:16,535] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:16,536] [INFO] Found 6/6 markers.
[2024-01-25 18:05:16,567] [INFO] Query marker FASTA was written to GCF_002954685.1_ASM295468v1_genomic.fna/markers.fasta
[2024-01-25 18:05:16,567] [INFO] Task started: Blastn
[2024-01-25 18:05:16,567] [INFO] Running command: blastn -query GCF_002954685.1_ASM295468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga573cbdd-9735-47f9-b5e4-ae2af416e535/dqc_reference/reference_markers.fasta -out GCF_002954685.1_ASM295468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:17,185] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:17,188] [INFO] Selected 14 target genomes.
[2024-01-25 18:05:17,188] [INFO] Target genome list was writen to GCF_002954685.1_ASM295468v1_genomic.fna/target_genomes.txt
[2024-01-25 18:05:17,202] [INFO] Task started: fastANI
[2024-01-25 18:05:17,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgf31acfec-8453-4c20-9931-1db5462de6ad/GCF_002954685.1_ASM295468v1_genomic.fna.gz --refList GCF_002954685.1_ASM295468v1_genomic.fna/target_genomes.txt --output GCF_002954685.1_ASM295468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:05:27,686] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:27,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga573cbdd-9735-47f9-b5e4-ae2af416e535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:05:27,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga573cbdd-9735-47f9-b5e4-ae2af416e535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:05:27,696] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:05:27,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:05:27,696] [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=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	99.9956	1299	1300	95	conclusive
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	99.9752	1288	1300	95	conclusive
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	81.2574	689	1300	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	81.1735	694	1300	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	81.1699	700	1300	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.8795	716	1300	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.8473	711	1300	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	80.4038	624	1300	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	80.374	621	1300	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.3692	614	1300	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	80.3677	636	1300	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.2683	641	1300	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.6517	584	1300	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.284	588	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:05:27,698] [INFO] DFAST Taxonomy check result was written to GCF_002954685.1_ASM295468v1_genomic.fna/tc_result.tsv
[2024-01-25 18:05:27,700] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:05:27,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:05:27,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga573cbdd-9735-47f9-b5e4-ae2af416e535/dqc_reference/checkm_data
[2024-01-25 18:05:27,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:05:27,743] [INFO] Task started: CheckM
[2024-01-25 18:05:27,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954685.1_ASM295468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954685.1_ASM295468v1_genomic.fna/checkm_input GCF_002954685.1_ASM295468v1_genomic.fna/checkm_result
[2024-01-25 18:05:58,152] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:58,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:58,174] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:58,175] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:58,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954685.1_ASM295468v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:58,175] [INFO] Task started: Blastn
[2024-01-25 18:05:58,175] [INFO] Running command: blastn -query GCF_002954685.1_ASM295468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga573cbdd-9735-47f9-b5e4-ae2af416e535/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954685.1_ASM295468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:59,077] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:59,081] [INFO] Selected 12 target genomes.
[2024-01-25 18:05:59,081] [INFO] Target genome list was writen to GCF_002954685.1_ASM295468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:59,094] [INFO] Task started: fastANI
[2024-01-25 18:05:59,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgf31acfec-8453-4c20-9931-1db5462de6ad/GCF_002954685.1_ASM295468v1_genomic.fna.gz --refList GCF_002954685.1_ASM295468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954685.1_ASM295468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:08,770] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:08,778] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:08,778] [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	99.9956	1299	1300	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_001975665.1	s__Polaribacter reichenbachii	81.1215	710	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018861005.1	s__Polaribacter vadi_A	81.0757	709	1300	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	80.8709	717	1300	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	80.4011	625	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009832745.1	s__Polaribacter sp009832745	80.3719	613	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	80.3664	654	1300	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	80.3276	638	1300	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	80.261	609	1300	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	80.2481	595	1300	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	79.9884	632	1300	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	79.819	575	1300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:08,779] [INFO] GTDB search result was written to GCF_002954685.1_ASM295468v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:08,780] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:08,784] [INFO] DFAST_QC result json was written to GCF_002954685.1_ASM295468v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:08,785] [INFO] DFAST_QC completed!
[2024-01-25 18:06:08,785] [INFO] Total running time: 0h1m3s