[2024-01-24 13:28:44,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg8edcdd02-fe37-4b0f-b555-4c863e3c7575/dqc_reference
[2024-01-24 13:28:45,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,720] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c5a8376-0adc-426e-be93-83804665789e/GCF_020532845.1_ASM2053284v1_genomic.fna.gz | prodigal -d GCF_020532845.1_ASM2053284v1_genomic.fna/cds.fna -a GCF_020532845.1_ASM2053284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:56,780] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:56,781] [INFO] Task started: HMMsearch
[2024-01-24 13:28:56,781] [INFO] Running command: hmmsearch --tblout GCF_020532845.1_ASM2053284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8edcdd02-fe37-4b0f-b555-4c863e3c7575/dqc_reference/reference_markers.hmm GCF_020532845.1_ASM2053284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:57,112] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:57,113] [INFO] Found 6/6 markers.
[2024-01-24 13:28:57,154] [INFO] Query marker FASTA was written to GCF_020532845.1_ASM2053284v1_genomic.fna/markers.fasta
[2024-01-24 13:28:57,155] [INFO] Task started: Blastn
[2024-01-24 13:28:57,155] [INFO] Running command: blastn -query GCF_020532845.1_ASM2053284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8edcdd02-fe37-4b0f-b555-4c863e3c7575/dqc_reference/reference_markers.fasta -out GCF_020532845.1_ASM2053284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:57,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:57,936] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:57,937] [INFO] Target genome list was writen to GCF_020532845.1_ASM2053284v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:57,970] [INFO] Task started: fastANI
[2024-01-24 13:28:57,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c5a8376-0adc-426e-be93-83804665789e/GCF_020532845.1_ASM2053284v1_genomic.fna.gz --refList GCF_020532845.1_ASM2053284v1_genomic.fna/target_genomes.txt --output GCF_020532845.1_ASM2053284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:07,918] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:07,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8edcdd02-fe37-4b0f-b555-4c863e3c7575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:07,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8edcdd02-fe37-4b0f-b555-4c863e3c7575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:07,932] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:29:07,933] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:07,933] [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=LMG 26443	GCA_020532845.1	996801	996801	type	True	100.0	1335	1336	95	conclusive
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	99.9986	1335	1336	95	conclusive
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	99.9893	1316	1336	95	conclusive
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	99.9781	1334	1336	95	conclusive
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	82.1291	765	1336	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	81.724	654	1336	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	81.6939	655	1336	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	81.2558	686	1336	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	81.0259	698	1336	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.7564	654	1336	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.7547	621	1336	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.6534	484	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:07,935] [INFO] DFAST Taxonomy check result was written to GCF_020532845.1_ASM2053284v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:07,935] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:07,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:07,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8edcdd02-fe37-4b0f-b555-4c863e3c7575/dqc_reference/checkm_data
[2024-01-24 13:29:07,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:07,988] [INFO] Task started: CheckM
[2024-01-24 13:29:07,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020532845.1_ASM2053284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020532845.1_ASM2053284v1_genomic.fna/checkm_input GCF_020532845.1_ASM2053284v1_genomic.fna/checkm_result
[2024-01-24 13:29:45,635] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:45,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:45,657] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:45,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:45,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020532845.1_ASM2053284v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:45,658] [INFO] Task started: Blastn
[2024-01-24 13:29:45,658] [INFO] Running command: blastn -query GCF_020532845.1_ASM2053284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8edcdd02-fe37-4b0f-b555-4c863e3c7575/dqc_reference/reference_markers_gtdb.fasta -out GCF_020532845.1_ASM2053284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:46,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:46,622] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:46,622] [INFO] Target genome list was writen to GCF_020532845.1_ASM2053284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:46,632] [INFO] Task started: fastANI
[2024-01-24 13:29:46,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c5a8376-0adc-426e-be93-83804665789e/GCF_020532845.1_ASM2053284v1_genomic.fna.gz --refList GCF_020532845.1_ASM2053284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020532845.1_ASM2053284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:57,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:57,050] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:57,051] [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	99.9986	1335	1336	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	89.4218	970	1336	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	82.1985	769	1336	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	82.1227	766	1336	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	81.748	649	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	81.6263	717	1336	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687935.1	s__Polaribacter sp000687935	81.4876	761	1336	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	81.2296	638	1336	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	80.9175	708	1336	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	80.8129	690	1336	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	80.7772	654	1336	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	79.771	619	1336	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 13:29:57,053] [INFO] GTDB search result was written to GCF_020532845.1_ASM2053284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:57,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:57,057] [INFO] DFAST_QC result json was written to GCF_020532845.1_ASM2053284v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:57,057] [INFO] DFAST_QC completed!
[2024-01-24 13:29:57,057] [INFO] Total running time: 0h1m13s