[2024-01-24 13:22:55,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,236] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,237] [INFO] DQC Reference Directory: /var/lib/cwl/stgff31002e-5412-48eb-a6e2-e566e720febf/dqc_reference
[2024-01-24 13:22:56,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,598] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,598] [INFO] Running command: gunzip -c /var/lib/cwl/stgc35ca566-bc40-4692-a382-b5642560171d/GCF_017355935.1_ASM1735593v1_genomic.fna.gz | prodigal -d GCF_017355935.1_ASM1735593v1_genomic.fna/cds.fna -a GCF_017355935.1_ASM1735593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:24,290] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:24,291] [INFO] Task started: HMMsearch
[2024-01-24 13:23:24,291] [INFO] Running command: hmmsearch --tblout GCF_017355935.1_ASM1735593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff31002e-5412-48eb-a6e2-e566e720febf/dqc_reference/reference_markers.hmm GCF_017355935.1_ASM1735593v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:24,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:24,628] [INFO] Found 6/6 markers.
[2024-01-24 13:23:24,687] [INFO] Query marker FASTA was written to GCF_017355935.1_ASM1735593v1_genomic.fna/markers.fasta
[2024-01-24 13:23:24,687] [INFO] Task started: Blastn
[2024-01-24 13:23:24,687] [INFO] Running command: blastn -query GCF_017355935.1_ASM1735593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff31002e-5412-48eb-a6e2-e566e720febf/dqc_reference/reference_markers.fasta -out GCF_017355935.1_ASM1735593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:25,319] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:25,324] [INFO] Selected 23 target genomes.
[2024-01-24 13:23:25,325] [INFO] Target genome list was writen to GCF_017355935.1_ASM1735593v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:25,335] [INFO] Task started: fastANI
[2024-01-24 13:23:25,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgc35ca566-bc40-4692-a382-b5642560171d/GCF_017355935.1_ASM1735593v1_genomic.fna.gz --refList GCF_017355935.1_ASM1735593v1_genomic.fna/target_genomes.txt --output GCF_017355935.1_ASM1735593v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:49,388] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:49,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff31002e-5412-48eb-a6e2-e566e720febf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:49,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff31002e-5412-48eb-a6e2-e566e720febf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:49,406] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:49,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:49,407] [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
Telluribacter humicola	strain=KCTC 42819	GCA_017355935.1	1720261	1720261	type	True	100.0	2174	2175	95	conclusive
Rhabdobacter roseus	strain=DSM 105074	GCA_014202275.1	1655419	1655419	type	True	77.0263	417	2175	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	76.6115	76	2175	95	below_threshold
Arundinibacter roseus	strain=DMA-K-7a	GCA_004348825.1	2070510	2070510	type	True	76.5121	152	2175	95	below_threshold
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	76.3824	84	2175	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	76.3191	122	2175	95	below_threshold
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	76.2036	127	2175	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	76.1937	123	2175	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	76.1172	135	2175	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	76.0381	136	2175	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	76.0004	100	2175	95	below_threshold
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	75.9671	59	2175	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	75.8346	115	2175	95	below_threshold
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	75.8163	56	2175	95	below_threshold
Spirosoma spitsbergense	strain=DSM 19989	GCA_000374085.1	431554	431554	type	True	75.6467	64	2175	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	75.6383	77	2175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:49,409] [INFO] DFAST Taxonomy check result was written to GCF_017355935.1_ASM1735593v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:49,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:49,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:49,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff31002e-5412-48eb-a6e2-e566e720febf/dqc_reference/checkm_data
[2024-01-24 13:23:49,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:49,475] [INFO] Task started: CheckM
[2024-01-24 13:23:49,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017355935.1_ASM1735593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017355935.1_ASM1735593v1_genomic.fna/checkm_input GCF_017355935.1_ASM1735593v1_genomic.fna/checkm_result
[2024-01-24 13:25:04,183] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:04,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:04,208] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:04,209] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:04,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017355935.1_ASM1735593v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:04,210] [INFO] Task started: Blastn
[2024-01-24 13:25:04,210] [INFO] Running command: blastn -query GCF_017355935.1_ASM1735593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff31002e-5412-48eb-a6e2-e566e720febf/dqc_reference/reference_markers_gtdb.fasta -out GCF_017355935.1_ASM1735593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:04,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:04,981] [INFO] Selected 24 target genomes.
[2024-01-24 13:25:04,981] [INFO] Target genome list was writen to GCF_017355935.1_ASM1735593v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:05,043] [INFO] Task started: fastANI
[2024-01-24 13:25:05,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgc35ca566-bc40-4692-a382-b5642560171d/GCF_017355935.1_ASM1735593v1_genomic.fna.gz --refList GCF_017355935.1_ASM1735593v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017355935.1_ASM1735593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:29,828] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:29,848] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:29,848] [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_017355935.1	s__Telluribacter humicola	100.0	2174	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Telluribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014202275.1	s__Rhabdobacter roseus	77.0327	416	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rhabdobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898145.1	s__Dyadobacter sp001898145	76.622	124	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_015221875.1	s__Dyadobacter sp015221875	76.6115	76	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348825.1	s__Arundinibacter roseus	76.5121	152	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arundinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009801115.1	s__Dyadobacter sp009801115	76.469	84	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280585.1	s__Dyadobacter frigoris	76.3896	76	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009296315.1	s__Persicitalea sp009296315	76.3869	262	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Persicitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023125.1	s__Dyadobacter fermentans	76.3344	121	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014695.1	s__Dyadobacter jiangsuensis	76.2174	126	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	76.2078	122	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109045.1	s__Dyadobacter sp900109045	76.1459	133	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424405.1	s__Dyadobacter sp001424405	76.0583	108	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382205.1	s__Dyadobacter beijingensis	76.0498	135	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869225.1	s__Dyadobacter bucti	76.0323	98	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583365.1	s__Fibrisoma montanum	75.8346	115	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009668025.1	s__Larkinella terrae	75.8163	56	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374085.1	s__Spirosoma spitsbergense	75.6133	63	2175	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:29,850] [INFO] GTDB search result was written to GCF_017355935.1_ASM1735593v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:29,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:29,854] [INFO] DFAST_QC result json was written to GCF_017355935.1_ASM1735593v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:29,854] [INFO] DFAST_QC completed!
[2024-01-24 13:25:29,854] [INFO] Total running time: 0h2m35s