[2024-01-24 13:24:47,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:47,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:47,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg973df217-f770-49c1-97f5-b09afc162388/dqc_reference
[2024-01-24 13:24:49,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,166] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,166] [INFO] Running command: gunzip -c /var/lib/cwl/stg08d67aa8-6c13-4ffa-a715-e1598aa24149/GCF_021654135.1_ASM2165413v1_genomic.fna.gz | prodigal -d GCF_021654135.1_ASM2165413v1_genomic.fna/cds.fna -a GCF_021654135.1_ASM2165413v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:15,622] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:15,622] [INFO] Task started: HMMsearch
[2024-01-24 13:25:15,622] [INFO] Running command: hmmsearch --tblout GCF_021654135.1_ASM2165413v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg973df217-f770-49c1-97f5-b09afc162388/dqc_reference/reference_markers.hmm GCF_021654135.1_ASM2165413v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:16,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:16,024] [INFO] Found 6/6 markers.
[2024-01-24 13:25:16,113] [INFO] Query marker FASTA was written to GCF_021654135.1_ASM2165413v1_genomic.fna/markers.fasta
[2024-01-24 13:25:16,114] [INFO] Task started: Blastn
[2024-01-24 13:25:16,114] [INFO] Running command: blastn -query GCF_021654135.1_ASM2165413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg973df217-f770-49c1-97f5-b09afc162388/dqc_reference/reference_markers.fasta -out GCF_021654135.1_ASM2165413v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:17,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:17,521] [INFO] Selected 11 target genomes.
[2024-01-24 13:25:17,522] [INFO] Target genome list was writen to GCF_021654135.1_ASM2165413v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:17,527] [INFO] Task started: fastANI
[2024-01-24 13:25:17,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d67aa8-6c13-4ffa-a715-e1598aa24149/GCF_021654135.1_ASM2165413v1_genomic.fna.gz --refList GCF_021654135.1_ASM2165413v1_genomic.fna/target_genomes.txt --output GCF_021654135.1_ASM2165413v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:39,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:39,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg973df217-f770-49c1-97f5-b09afc162388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:39,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg973df217-f770-49c1-97f5-b09afc162388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:39,598] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:39,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:39,599] [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
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	95.6614	2400	2933	95	conclusive
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	94.9447	2045	2933	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	94.888	2053	2933	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	91.8902	1886	2933	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	87.9833	1569	2933	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	87.8315	1580	2933	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	87.5801	1798	2933	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	82.0595	1487	2933	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.9729	1465	2933	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.8247	1170	2933	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.1901	1126	2933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:39,601] [INFO] DFAST Taxonomy check result was written to GCF_021654135.1_ASM2165413v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:39,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:39,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:39,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg973df217-f770-49c1-97f5-b09afc162388/dqc_reference/checkm_data
[2024-01-24 13:25:39,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:39,682] [INFO] Task started: CheckM
[2024-01-24 13:25:39,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021654135.1_ASM2165413v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021654135.1_ASM2165413v1_genomic.fna/checkm_input GCF_021654135.1_ASM2165413v1_genomic.fna/checkm_result
[2024-01-24 13:27:13,739] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:13,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:13,768] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:13,768] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:13,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021654135.1_ASM2165413v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:13,769] [INFO] Task started: Blastn
[2024-01-24 13:27:13,769] [INFO] Running command: blastn -query GCF_021654135.1_ASM2165413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg973df217-f770-49c1-97f5-b09afc162388/dqc_reference/reference_markers_gtdb.fasta -out GCF_021654135.1_ASM2165413v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:15,919] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:15,923] [INFO] Selected 5 target genomes.
[2024-01-24 13:27:15,924] [INFO] Target genome list was writen to GCF_021654135.1_ASM2165413v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:15,944] [INFO] Task started: fastANI
[2024-01-24 13:27:15,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg08d67aa8-6c13-4ffa-a715-e1598aa24149/GCF_021654135.1_ASM2165413v1_genomic.fna.gz --refList GCF_021654135.1_ASM2165413v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021654135.1_ASM2165413v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:29,178] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:29,185] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:29,185] [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_000231075.2	s__Amycolatopsis sp000231075	98.572	2495	2933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	conclusive
GCF_000473265.1	s__Amycolatopsis thermoflava	95.6507	2401	2933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	98.72	98.72	0.92	0.92	2	-
GCF_000739085.1	s__Amycolatopsis methanolica	94.9548	2044	2933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_003385215.1	s__Amycolatopsis thermalba	91.8618	1889	2933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_014653945.1	s__Amycolatopsis deserti	91.7891	2123	2933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:29,187] [INFO] GTDB search result was written to GCF_021654135.1_ASM2165413v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:29,188] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:29,191] [INFO] DFAST_QC result json was written to GCF_021654135.1_ASM2165413v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:29,191] [INFO] DFAST_QC completed!
[2024-01-24 13:27:29,191] [INFO] Total running time: 0h2m41s