[2024-01-24 10:57:07,066] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg750bb1ed-635c-42e4-b79d-474d1d64d86a/dqc_reference
[2024-01-24 10:57:08,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,307] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,307] [INFO] Running command: gunzip -c /var/lib/cwl/stgad7b0255-2770-4763-8603-1805073b8ebb/GCF_004362215.1_ASM436221v1_genomic.fna.gz | prodigal -d GCF_004362215.1_ASM436221v1_genomic.fna/cds.fna -a GCF_004362215.1_ASM436221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:04,101] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:04,102] [INFO] Task started: HMMsearch
[2024-01-24 10:58:04,102] [INFO] Running command: hmmsearch --tblout GCF_004362215.1_ASM436221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg750bb1ed-635c-42e4-b79d-474d1d64d86a/dqc_reference/reference_markers.hmm GCF_004362215.1_ASM436221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:04,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:04,486] [INFO] Found 6/6 markers.
[2024-01-24 10:58:04,562] [INFO] Query marker FASTA was written to GCF_004362215.1_ASM436221v1_genomic.fna/markers.fasta
[2024-01-24 10:58:04,563] [INFO] Task started: Blastn
[2024-01-24 10:58:04,563] [INFO] Running command: blastn -query GCF_004362215.1_ASM436221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg750bb1ed-635c-42e4-b79d-474d1d64d86a/dqc_reference/reference_markers.fasta -out GCF_004362215.1_ASM436221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:05,802] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:05,821] [INFO] Selected 11 target genomes.
[2024-01-24 10:58:05,821] [INFO] Target genome list was writen to GCF_004362215.1_ASM436221v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:05,829] [INFO] Task started: fastANI
[2024-01-24 10:58:05,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgad7b0255-2770-4763-8603-1805073b8ebb/GCF_004362215.1_ASM436221v1_genomic.fna.gz --refList GCF_004362215.1_ASM436221v1_genomic.fna/target_genomes.txt --output GCF_004362215.1_ASM436221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:32,002] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:32,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg750bb1ed-635c-42e4-b79d-474d1d64d86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:32,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg750bb1ed-635c-42e4-b79d-474d1d64d86a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:32,015] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:32,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:32,016] [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
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	100.0	3249	3249	95	conclusive
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	99.9479	3119	3249	95	conclusive
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	88.0223	2373	3249	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	87.7635	2290	3249	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	86.4301	2301	3249	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	85.673	2148	3249	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.6393	1516	3249	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.7513	1124	3249	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.626	1091	3249	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.5389	927	3249	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.2377	667	3249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:32,017] [INFO] DFAST Taxonomy check result was written to GCF_004362215.1_ASM436221v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:32,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:32,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:32,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg750bb1ed-635c-42e4-b79d-474d1d64d86a/dqc_reference/checkm_data
[2024-01-24 10:58:32,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:32,105] [INFO] Task started: CheckM
[2024-01-24 10:58:32,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362215.1_ASM436221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362215.1_ASM436221v1_genomic.fna/checkm_input GCF_004362215.1_ASM436221v1_genomic.fna/checkm_result
[2024-01-24 11:01:24,600] [INFO] Task succeeded: CheckM
[2024-01-24 11:01:24,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:01:24,629] [INFO] ===== Completeness check finished =====
[2024-01-24 11:01:24,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:01:24,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362215.1_ASM436221v1_genomic.fna/markers.fasta)
[2024-01-24 11:01:24,630] [INFO] Task started: Blastn
[2024-01-24 11:01:24,630] [INFO] Running command: blastn -query GCF_004362215.1_ASM436221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg750bb1ed-635c-42e4-b79d-474d1d64d86a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362215.1_ASM436221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:01:26,526] [INFO] Task succeeded: Blastn
[2024-01-24 11:01:26,529] [INFO] Selected 7 target genomes.
[2024-01-24 11:01:26,529] [INFO] Target genome list was writen to GCF_004362215.1_ASM436221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:01:27,062] [INFO] Task started: fastANI
[2024-01-24 11:01:27,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgad7b0255-2770-4763-8603-1805073b8ebb/GCF_004362215.1_ASM436221v1_genomic.fna.gz --refList GCF_004362215.1_ASM436221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362215.1_ASM436221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:01:47,145] [INFO] Task succeeded: fastANI
[2024-01-24 11:01:47,156] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:01:47,156] [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_004362215.1	s__Actinoplanes brasiliensis	100.0	3249	3249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016785085.1	s__Actinoplanes sp016785085	88.0459	2370	3249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	87.752	2292	3249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016834655.1	s__Actinoplanes sp016834655	86.4168	2304	3249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018829635.1	s__Actinoplanes bogorensis	85.6877	2145	3249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	84.2006	1990	3249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	83.0578	1940	3249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:01:47,158] [INFO] GTDB search result was written to GCF_004362215.1_ASM436221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:01:47,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:01:47,163] [INFO] DFAST_QC result json was written to GCF_004362215.1_ASM436221v1_genomic.fna/dqc_result.json
[2024-01-24 11:01:47,163] [INFO] DFAST_QC completed!
[2024-01-24 11:01:47,163] [INFO] Total running time: 0h4m40s