[2024-01-24 14:15:34,507] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg86358028-34ef-4c54-815b-05bd0355af43/dqc_reference
[2024-01-24 14:15:35,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,835] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg503d17e1-2701-41f7-bce6-4b0ee2b6b0a0/GCF_000424985.1_ASM42498v1_genomic.fna.gz | prodigal -d GCF_000424985.1_ASM42498v1_genomic.fna/cds.fna -a GCF_000424985.1_ASM42498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:51,212] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:51,213] [INFO] Task started: HMMsearch
[2024-01-24 14:15:51,213] [INFO] Running command: hmmsearch --tblout GCF_000424985.1_ASM42498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86358028-34ef-4c54-815b-05bd0355af43/dqc_reference/reference_markers.hmm GCF_000424985.1_ASM42498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:51,585] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:51,586] [INFO] Found 6/6 markers.
[2024-01-24 14:15:51,626] [INFO] Query marker FASTA was written to GCF_000424985.1_ASM42498v1_genomic.fna/markers.fasta
[2024-01-24 14:15:51,627] [INFO] Task started: Blastn
[2024-01-24 14:15:51,627] [INFO] Running command: blastn -query GCF_000424985.1_ASM42498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86358028-34ef-4c54-815b-05bd0355af43/dqc_reference/reference_markers.fasta -out GCF_000424985.1_ASM42498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:52,333] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:52,336] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:52,336] [INFO] Target genome list was writen to GCF_000424985.1_ASM42498v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:52,344] [INFO] Task started: fastANI
[2024-01-24 14:15:52,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg503d17e1-2701-41f7-bce6-4b0ee2b6b0a0/GCF_000424985.1_ASM42498v1_genomic.fna.gz --refList GCF_000424985.1_ASM42498v1_genomic.fna/target_genomes.txt --output GCF_000424985.1_ASM42498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:07,424] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:07,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86358028-34ef-4c54-815b-05bd0355af43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:07,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86358028-34ef-4c54-815b-05bd0355af43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:07,443] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:16:07,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:07,443] [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
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	100.0	1433	1440	95	conclusive
Arenibacter certesii	strain=KCTC 12113	GCA_014651295.1	228955	228955	type	True	85.6744	1157	1440	95	below_threshold
Arenibacter certesii	strain=DSM 19833	GCA_000429545.1	228955	228955	type	True	85.6396	1174	1440	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	77.4704	303	1440	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	77.4558	301	1440	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	77.367	279	1440	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	77.3438	274	1440	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	77.2671	276	1440	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	77.0021	149	1440	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	76.7832	138	1440	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.5471	99	1440	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.351	153	1440	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.3243	140	1440	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	75.8145	51	1440	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	75.5859	53	1440	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.5291	65	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:07,445] [INFO] DFAST Taxonomy check result was written to GCF_000424985.1_ASM42498v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:07,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:07,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:07,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86358028-34ef-4c54-815b-05bd0355af43/dqc_reference/checkm_data
[2024-01-24 14:16:07,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:07,496] [INFO] Task started: CheckM
[2024-01-24 14:16:07,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000424985.1_ASM42498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000424985.1_ASM42498v1_genomic.fna/checkm_input GCF_000424985.1_ASM42498v1_genomic.fna/checkm_result
[2024-01-24 14:16:54,656] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:54,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:54,684] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:54,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:54,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000424985.1_ASM42498v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:54,686] [INFO] Task started: Blastn
[2024-01-24 14:16:54,686] [INFO] Running command: blastn -query GCF_000424985.1_ASM42498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86358028-34ef-4c54-815b-05bd0355af43/dqc_reference/reference_markers_gtdb.fasta -out GCF_000424985.1_ASM42498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:55,633] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:55,637] [INFO] Selected 16 target genomes.
[2024-01-24 14:16:55,637] [INFO] Target genome list was writen to GCF_000424985.1_ASM42498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:55,669] [INFO] Task started: fastANI
[2024-01-24 14:16:55,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg503d17e1-2701-41f7-bce6-4b0ee2b6b0a0/GCF_000424985.1_ASM42498v1_genomic.fna.gz --refList GCF_000424985.1_ASM42498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000424985.1_ASM42498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:09,164] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:09,185] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:09,186] [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_000424985.1	s__Arenibacter latericius	100.0	1433	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000429545.1	s__Arenibacter certesii	85.6356	1175	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002150785.1	s__Arenibacter amylolyticus	79.8333	675	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	99.19	99.19	0.91	0.91	2	-
GCF_014397245.1	s__Arenibacter arenosicollis	77.4611	304	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	77.3677	278	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	77.2782	297	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	77.2646	277	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_003201775.1	s__Arenibacter sp003201775	77.2	285	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	77.001	150	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_005885635.1	s__RZ26 sp005885635	76.5471	99	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813425.1	s__Cellulophaga sp002813425	76.5196	147	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153165.2	s__Maribacter_A sp000153165	76.401	111	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	76.397	144	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	76.351	153	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.3435	173	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCA_018883545.1	s__Confluentibacter sp018883545	76.0411	55	1440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:09,188] [INFO] GTDB search result was written to GCF_000424985.1_ASM42498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:09,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:09,193] [INFO] DFAST_QC result json was written to GCF_000424985.1_ASM42498v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:09,194] [INFO] DFAST_QC completed!
[2024-01-24 14:17:09,194] [INFO] Total running time: 0h1m35s