[2024-01-25 18:39:20,430] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:20,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:20,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg6be1549b-07ca-4f8d-b01e-76e325603c67/dqc_reference
[2024-01-25 18:39:21,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:21,627] [INFO] Task started: Prodigal
[2024-01-25 18:39:21,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b11ad59-97a6-49d3-98e2-46e154d0cc3b/GCF_018829635.1_ASM1882963v1_genomic.fna.gz | prodigal -d GCF_018829635.1_ASM1882963v1_genomic.fna/cds.fna -a GCF_018829635.1_ASM1882963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:47,948] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:47,948] [INFO] Task started: HMMsearch
[2024-01-25 18:39:47,949] [INFO] Running command: hmmsearch --tblout GCF_018829635.1_ASM1882963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6be1549b-07ca-4f8d-b01e-76e325603c67/dqc_reference/reference_markers.hmm GCF_018829635.1_ASM1882963v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:48,387] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:48,389] [INFO] Found 6/6 markers.
[2024-01-25 18:39:48,471] [INFO] Query marker FASTA was written to GCF_018829635.1_ASM1882963v1_genomic.fna/markers.fasta
[2024-01-25 18:39:48,471] [INFO] Task started: Blastn
[2024-01-25 18:39:48,471] [INFO] Running command: blastn -query GCF_018829635.1_ASM1882963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6be1549b-07ca-4f8d-b01e-76e325603c67/dqc_reference/reference_markers.fasta -out GCF_018829635.1_ASM1882963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:49,698] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:49,700] [INFO] Selected 11 target genomes.
[2024-01-25 18:39:49,701] [INFO] Target genome list was writen to GCF_018829635.1_ASM1882963v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:49,709] [INFO] Task started: fastANI
[2024-01-25 18:39:49,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b11ad59-97a6-49d3-98e2-46e154d0cc3b/GCF_018829635.1_ASM1882963v1_genomic.fna.gz --refList GCF_018829635.1_ASM1882963v1_genomic.fna/target_genomes.txt --output GCF_018829635.1_ASM1882963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:17,534] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:17,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6be1549b-07ca-4f8d-b01e-76e325603c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:17,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6be1549b-07ca-4f8d-b01e-76e325603c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:17,544] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:17,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:17,544] [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 bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	100.0	3370	3375	95	conclusive
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	86.7631	2559	3375	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	86.4242	2525	3375	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	86.1019	2288	3375	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	85.6872	2106	3375	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	85.6331	2161	3375	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.2368	1533	3375	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.4921	952	3375	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.4572	1278	3375	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4174	969	3375	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.1664	670	3375	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:17,545] [INFO] DFAST Taxonomy check result was written to GCF_018829635.1_ASM1882963v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:17,546] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:17,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:17,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6be1549b-07ca-4f8d-b01e-76e325603c67/dqc_reference/checkm_data
[2024-01-25 18:40:17,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:17,635] [INFO] Task started: CheckM
[2024-01-25 18:40:17,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018829635.1_ASM1882963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018829635.1_ASM1882963v1_genomic.fna/checkm_input GCF_018829635.1_ASM1882963v1_genomic.fna/checkm_result
[2024-01-25 18:42:00,932] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:00,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:00,957] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:00,957] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:00,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018829635.1_ASM1882963v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:00,958] [INFO] Task started: Blastn
[2024-01-25 18:42:00,958] [INFO] Running command: blastn -query GCF_018829635.1_ASM1882963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6be1549b-07ca-4f8d-b01e-76e325603c67/dqc_reference/reference_markers_gtdb.fasta -out GCF_018829635.1_ASM1882963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:02,796] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:02,799] [INFO] Selected 9 target genomes.
[2024-01-25 18:42:02,800] [INFO] Target genome list was writen to GCF_018829635.1_ASM1882963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:02,805] [INFO] Task started: fastANI
[2024-01-25 18:42:02,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b11ad59-97a6-49d3-98e2-46e154d0cc3b/GCF_018829635.1_ASM1882963v1_genomic.fna.gz --refList GCF_018829635.1_ASM1882963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018829635.1_ASM1882963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:36,858] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:36,866] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:36,866] [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_018829635.1	s__Actinoplanes bogorensis	100.0	3370	3375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016834655.1	s__Actinoplanes sp016834655	86.7376	2566	3375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785085.1	s__Actinoplanes sp016785085	86.4683	2516	3375	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	86.1428	2280	3375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004362215.1	s__Actinoplanes brasiliensis	85.6705	2153	3375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003999975.1	s__Actinoplanes sp003999975	84.1299	2018	3375	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	82.9016	1936	3375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	81.7645	1767	3375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	80.59	1727	3375	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:36,867] [INFO] GTDB search result was written to GCF_018829635.1_ASM1882963v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:36,868] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:36,871] [INFO] DFAST_QC result json was written to GCF_018829635.1_ASM1882963v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:36,871] [INFO] DFAST_QC completed!
[2024-01-25 18:42:36,871] [INFO] Total running time: 0h3m16s