[2024-01-24 12:06:34,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:34,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:34,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg676d8d1a-c6b4-4f01-8c3a-d9cc330e6496/dqc_reference
[2024-01-24 12:06:35,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,916] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg63fe6d12-b3be-4280-bf0c-fcf94a759cbe/GCF_016599145.1_ASM1659914v1_genomic.fna.gz | prodigal -d GCF_016599145.1_ASM1659914v1_genomic.fna/cds.fna -a GCF_016599145.1_ASM1659914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:50,552] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:50,553] [INFO] Task started: HMMsearch
[2024-01-24 12:06:50,553] [INFO] Running command: hmmsearch --tblout GCF_016599145.1_ASM1659914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg676d8d1a-c6b4-4f01-8c3a-d9cc330e6496/dqc_reference/reference_markers.hmm GCF_016599145.1_ASM1659914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:50,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:50,806] [INFO] Found 6/6 markers.
[2024-01-24 12:06:50,855] [INFO] Query marker FASTA was written to GCF_016599145.1_ASM1659914v1_genomic.fna/markers.fasta
[2024-01-24 12:06:50,855] [INFO] Task started: Blastn
[2024-01-24 12:06:50,856] [INFO] Running command: blastn -query GCF_016599145.1_ASM1659914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg676d8d1a-c6b4-4f01-8c3a-d9cc330e6496/dqc_reference/reference_markers.fasta -out GCF_016599145.1_ASM1659914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:52,003] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:52,007] [INFO] Selected 9 target genomes.
[2024-01-24 12:06:52,008] [INFO] Target genome list was writen to GCF_016599145.1_ASM1659914v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:52,014] [INFO] Task started: fastANI
[2024-01-24 12:06:52,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg63fe6d12-b3be-4280-bf0c-fcf94a759cbe/GCF_016599145.1_ASM1659914v1_genomic.fna.gz --refList GCF_016599145.1_ASM1659914v1_genomic.fna/target_genomes.txt --output GCF_016599145.1_ASM1659914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:00,110] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:00,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg676d8d1a-c6b4-4f01-8c3a-d9cc330e6496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:00,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg676d8d1a-c6b4-4f01-8c3a-d9cc330e6496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:00,120] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:00,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:00,120] [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
Tomitella cavernea	strain=JCM 18542	GCA_016599145.1	1387982	1387982	type	True	100.0	1277	1287	95	conclusive
Tomitella gaofuii	strain=HY172	GCA_014126825.1	2760083	2760083	type	True	92.5963	1145	1287	95	below_threshold
Tomitella gaofuii	strain=HY172	GCA_023162085.1	2760083	2760083	type	True	92.5387	1140	1287	95	below_threshold
Tomitella fengzijianii	strain=HY188	GCA_007559025.1	2597660	2597660	type	True	88.413	1071	1287	95	below_threshold
Tomitella fengzijianii	strain=HY188	GCA_023162105.1	2597660	2597660	type	True	88.3619	1006	1287	95	below_threshold
Tomitella biformata	strain=DSM 45403	GCA_016599245.1	630403	630403	type	True	78.9207	575	1287	95	below_threshold
Tomitella biformata	strain=AHU 1821	GCA_000524475.1	630403	630403	type	True	78.8556	567	1287	95	below_threshold
Rhodococcus triatomae	strain=DSM 44892	GCA_900099725.1	300028	300028	type	True	77.7474	380	1287	95	below_threshold
Rhodococcus triatomae	strain=DSM 44892	GCA_014217785.1	300028	300028	type	True	77.7364	383	1287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:00,122] [INFO] DFAST Taxonomy check result was written to GCF_016599145.1_ASM1659914v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:00,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:00,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:00,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg676d8d1a-c6b4-4f01-8c3a-d9cc330e6496/dqc_reference/checkm_data
[2024-01-24 12:07:00,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:00,172] [INFO] Task started: CheckM
[2024-01-24 12:07:00,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016599145.1_ASM1659914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016599145.1_ASM1659914v1_genomic.fna/checkm_input GCF_016599145.1_ASM1659914v1_genomic.fna/checkm_result
[2024-01-24 12:07:45,575] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:45,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:45,597] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:45,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:45,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016599145.1_ASM1659914v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:45,598] [INFO] Task started: Blastn
[2024-01-24 12:07:45,598] [INFO] Running command: blastn -query GCF_016599145.1_ASM1659914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg676d8d1a-c6b4-4f01-8c3a-d9cc330e6496/dqc_reference/reference_markers_gtdb.fasta -out GCF_016599145.1_ASM1659914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:47,330] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:47,344] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:47,345] [INFO] Target genome list was writen to GCF_016599145.1_ASM1659914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:47,383] [INFO] Task started: fastANI
[2024-01-24 12:07:47,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg63fe6d12-b3be-4280-bf0c-fcf94a759cbe/GCF_016599145.1_ASM1659914v1_genomic.fna.gz --refList GCF_016599145.1_ASM1659914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016599145.1_ASM1659914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:01,802] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:01,814] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:01,815] [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_016599145.1	s__Tomitella cavernea	100.0	1277	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014126825.1	s__Tomitella sp014126825	92.5964	1145	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	97.57	97.57	0.88	0.88	2	-
GCF_007559025.1	s__Tomitella sp007559025	88.413	1071	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	99.43	99.43	0.96	0.96	2	-
GCF_000524475.1	s__Tomitella biformata	78.859	567	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	78.1564	487	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.1248	468	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	78.0362	455	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_001646645.1	s__Rhodococcus hoagii	77.9506	423	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_005049235.1	s__Rhodococcus oryzae	77.8339	443	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_014217785.1	s__Rhodococcus triatomae	77.7805	377	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	4	-
GCF_000308555.1	s__Nocardia cyriacigeorgica	77.603	383	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.94	96.19	0.91	0.88	19	-
GCF_001485495.1	s__Gordonia desulfuricans	77.5739	344	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_000308695.1	s__Nocardia takedensis	77.5248	402	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362555.1	s__JABFVX01 sp013362555	77.2586	230	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__JABFVX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552855.1	s__Skermania piniformis	77.048	254	1287	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Skermania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:01,817] [INFO] GTDB search result was written to GCF_016599145.1_ASM1659914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:01,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:01,824] [INFO] DFAST_QC result json was written to GCF_016599145.1_ASM1659914v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:01,825] [INFO] DFAST_QC completed!
[2024-01-24 12:08:01,825] [INFO] Total running time: 0h1m27s