[2024-01-24 13:22:11,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,383] [INFO] DQC Reference Directory: /var/lib/cwl/stgff9af48c-4aa9-44d2-83ca-57ee289ad174/dqc_reference
[2024-01-24 13:22:13,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,358] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,358] [INFO] Running command: gunzip -c /var/lib/cwl/stga0502f70-d1e7-4590-b517-3d4d6541c97d/GCF_003432065.1_ASM343206v1_genomic.fna.gz | prodigal -d GCF_003432065.1_ASM343206v1_genomic.fna/cds.fna -a GCF_003432065.1_ASM343206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:30,350] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:30,350] [INFO] Task started: HMMsearch
[2024-01-24 13:22:30,350] [INFO] Running command: hmmsearch --tblout GCF_003432065.1_ASM343206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff9af48c-4aa9-44d2-83ca-57ee289ad174/dqc_reference/reference_markers.hmm GCF_003432065.1_ASM343206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:30,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:30,688] [INFO] Found 6/6 markers.
[2024-01-24 13:22:30,728] [INFO] Query marker FASTA was written to GCF_003432065.1_ASM343206v1_genomic.fna/markers.fasta
[2024-01-24 13:22:30,729] [INFO] Task started: Blastn
[2024-01-24 13:22:30,729] [INFO] Running command: blastn -query GCF_003432065.1_ASM343206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff9af48c-4aa9-44d2-83ca-57ee289ad174/dqc_reference/reference_markers.fasta -out GCF_003432065.1_ASM343206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:31,311] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:31,314] [INFO] Selected 20 target genomes.
[2024-01-24 13:22:31,314] [INFO] Target genome list was writen to GCF_003432065.1_ASM343206v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:31,319] [INFO] Task started: fastANI
[2024-01-24 13:22:31,319] [INFO] Running command: fastANI --query /var/lib/cwl/stga0502f70-d1e7-4590-b517-3d4d6541c97d/GCF_003432065.1_ASM343206v1_genomic.fna.gz --refList GCF_003432065.1_ASM343206v1_genomic.fna/target_genomes.txt --output GCF_003432065.1_ASM343206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:48,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:48,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff9af48c-4aa9-44d2-83ca-57ee289ad174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:48,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff9af48c-4aa9-44d2-83ca-57ee289ad174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:48,963] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:48,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:48,963] [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
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	100.0	1532	1533	95	conclusive
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	78.7757	405	1533	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	78.7397	406	1533	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	78.7381	406	1533	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	78.3009	296	1533	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	78.2633	456	1533	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	78.1914	508	1533	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	78.1774	496	1533	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	78.0467	310	1533	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.9957	410	1533	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.9119	341	1533	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.5102	166	1533	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	77.5046	237	1533	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.4678	252	1533	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.432	223	1533	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.4102	224	1533	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.314	184	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:48,964] [INFO] DFAST Taxonomy check result was written to GCF_003432065.1_ASM343206v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:48,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:48,965] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:48,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff9af48c-4aa9-44d2-83ca-57ee289ad174/dqc_reference/checkm_data
[2024-01-24 13:22:48,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:49,009] [INFO] Task started: CheckM
[2024-01-24 13:22:49,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003432065.1_ASM343206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003432065.1_ASM343206v1_genomic.fna/checkm_input GCF_003432065.1_ASM343206v1_genomic.fna/checkm_result
[2024-01-24 13:23:35,278] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:35,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:35,292] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:35,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:35,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003432065.1_ASM343206v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:35,293] [INFO] Task started: Blastn
[2024-01-24 13:23:35,293] [INFO] Running command: blastn -query GCF_003432065.1_ASM343206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff9af48c-4aa9-44d2-83ca-57ee289ad174/dqc_reference/reference_markers_gtdb.fasta -out GCF_003432065.1_ASM343206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:36,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:36,090] [INFO] Selected 25 target genomes.
[2024-01-24 13:23:36,090] [INFO] Target genome list was writen to GCF_003432065.1_ASM343206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:36,103] [INFO] Task started: fastANI
[2024-01-24 13:23:36,103] [INFO] Running command: fastANI --query /var/lib/cwl/stga0502f70-d1e7-4590-b517-3d4d6541c97d/GCF_003432065.1_ASM343206v1_genomic.fna.gz --refList GCF_003432065.1_ASM343206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003432065.1_ASM343206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:57,648] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:57,662] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:57,662] [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_003432065.1	s__Mucilaginibacter sp003432065	100.0	1532	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	78.7381	406	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_007846085.1	s__Mucilaginibacter sp007846085	78.2962	297	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013915.1	s__Mucilaginibacter pedocola	78.2633	456	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773265.1	s__Mucilaginibacter pankratovii	78.1932	507	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004054195.1	s__Mucilaginibacter sp004054195	78.1768	496	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	78.0467	310	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	77.9954	410	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636615.1	s__Mucilaginibacter sp001636615	77.9618	384	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635105.1	s__Mucilaginibacter sp003635105	77.916	394	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938025.2	s__Mucilaginibacter sp005938025	77.8755	418	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519315.1	s__Mucilaginibacter psychrotolerans	77.8635	417	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	77.8278	345	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_002288635.1	s__Mucilaginibacter sp002288635	77.8168	325	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763755.1	s__Mucilaginibacter sp016763755	77.733	273	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	77.4678	252	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	77.4438	246	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155965.1	s__Mucilaginibacter lappiensis	77.432	223	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	-
GCF_013149275.1	s__Mucilaginibacter sp013149275	77.3772	241	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971025.1	s__Mucilaginibacter ginsenosidivorans	77.1572	161	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403905.1	s__Mucilaginibacter sp002403905	77.138	158	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCA_903891475.1	s__Mucilaginibacter sp903891475	76.7361	103	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.95	99.95	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:57,663] [INFO] GTDB search result was written to GCF_003432065.1_ASM343206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:57,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:57,667] [INFO] DFAST_QC result json was written to GCF_003432065.1_ASM343206v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:57,667] [INFO] DFAST_QC completed!
[2024-01-24 13:23:57,667] [INFO] Total running time: 0h1m46s