[2024-01-24 13:10:03,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,929] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd75bb18-8205-4b34-b46d-1c6bde53ec6e/dqc_reference
[2024-01-24 13:10:05,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,297] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b2710ad-e883-4b3d-86ae-6a3b94a396b2/GCF_021394575.1_ASM2139457v1_genomic.fna.gz | prodigal -d GCF_021394575.1_ASM2139457v1_genomic.fna/cds.fna -a GCF_021394575.1_ASM2139457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:22,813] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:22,813] [INFO] Task started: HMMsearch
[2024-01-24 13:10:22,814] [INFO] Running command: hmmsearch --tblout GCF_021394575.1_ASM2139457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd75bb18-8205-4b34-b46d-1c6bde53ec6e/dqc_reference/reference_markers.hmm GCF_021394575.1_ASM2139457v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:23,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:23,174] [INFO] Found 6/6 markers.
[2024-01-24 13:10:23,222] [INFO] Query marker FASTA was written to GCF_021394575.1_ASM2139457v1_genomic.fna/markers.fasta
[2024-01-24 13:10:23,223] [INFO] Task started: Blastn
[2024-01-24 13:10:23,223] [INFO] Running command: blastn -query GCF_021394575.1_ASM2139457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd75bb18-8205-4b34-b46d-1c6bde53ec6e/dqc_reference/reference_markers.fasta -out GCF_021394575.1_ASM2139457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:24,558] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:24,562] [INFO] Selected 9 target genomes.
[2024-01-24 13:10:24,562] [INFO] Target genome list was writen to GCF_021394575.1_ASM2139457v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:24,564] [INFO] Task started: fastANI
[2024-01-24 13:10:24,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b2710ad-e883-4b3d-86ae-6a3b94a396b2/GCF_021394575.1_ASM2139457v1_genomic.fna.gz --refList GCF_021394575.1_ASM2139457v1_genomic.fna/target_genomes.txt --output GCF_021394575.1_ASM2139457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:40,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:40,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd75bb18-8205-4b34-b46d-1c6bde53ec6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:40,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd75bb18-8205-4b34-b46d-1c6bde53ec6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:40,404] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:10:40,405] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:10:40,405] [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
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	100.0	2017	2017	95	inconclusive
Streptomyces thermodiastaticus	strain=JCM 4840	GCA_014656135.1	44061	44061	type	True	99.9851	1986	2017	95	inconclusive
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	95.3671	1723	2017	95	inconclusive
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=JCM 4843	GCA_014650975.1	66860	1952	type	True	95.3629	1736	2017	95	inconclusive
Streptomyces thermoviolaceus subsp. apingens	strain=JCM 4312	GCA_014649255.1	66859	1952	type	True	95.2706	1772	2017	95	inconclusive
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	86.3365	1427	2017	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.736	1247	2017	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.3821	1470	2017	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.1722	1432	2017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:40,406] [INFO] DFAST Taxonomy check result was written to GCF_021394575.1_ASM2139457v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:40,407] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:40,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:40,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd75bb18-8205-4b34-b46d-1c6bde53ec6e/dqc_reference/checkm_data
[2024-01-24 13:10:40,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:40,468] [INFO] Task started: CheckM
[2024-01-24 13:10:40,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021394575.1_ASM2139457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021394575.1_ASM2139457v1_genomic.fna/checkm_input GCF_021394575.1_ASM2139457v1_genomic.fna/checkm_result
[2024-01-24 13:12:16,210] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:16,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:16,238] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:16,238] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:16,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021394575.1_ASM2139457v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:16,239] [INFO] Task started: Blastn
[2024-01-24 13:12:16,239] [INFO] Running command: blastn -query GCF_021394575.1_ASM2139457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd75bb18-8205-4b34-b46d-1c6bde53ec6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_021394575.1_ASM2139457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:18,384] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:18,387] [INFO] Selected 16 target genomes.
[2024-01-24 13:12:18,387] [INFO] Target genome list was writen to GCF_021394575.1_ASM2139457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:18,450] [INFO] Task started: fastANI
[2024-01-24 13:12:18,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b2710ad-e883-4b3d-86ae-6a3b94a396b2/GCF_021394575.1_ASM2139457v1_genomic.fna.gz --refList GCF_021394575.1_ASM2139457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021394575.1_ASM2139457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:47,851] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:47,864] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:47,865] [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_014656135.1	s__Streptomyces thermodiastaticus	99.9851	1986	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.31	95.26	0.89	0.88	5	conclusive
GCF_902506575.1	s__Streptomyces mexicanus	89.9768	1625	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014654675.1	s__Streptomyces spiralis	86.5627	1561	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_002154505.1	s__Streptomyces carpinensis	86.2677	1402	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	86.2424	1505	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_000720185.1	s__Streptomyces sp000720185	86.0809	1526	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654495.1	s__Streptomyces sp001654495	85.9809	1484	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.91	96.91	0.92	0.92	2	-
GCF_014650655.1	s__Streptomyces anandii	85.9565	1466	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	84.6535	1378	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001013905.1	s__Streptomyces leeuwenhoekii	84.6476	1369	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	99.67	99.36	0.97	0.94	3	-
GCF_014649115.1	s__Streptomyces eurythermus	84.5279	1466	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_002155905.1	s__Streptomyces tricolor	84.4651	1247	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_001636945.1	s__Streptomyces sp001636945	84.1407	1398	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	84.1063	1416	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293595.1	s__Streptomyces sp001293595	83.8574	1314	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.56	99.56	0.94	0.94	2	-
GCA_014656015.1	s__Streptomyces griseoaurantiacus	83.5258	1299	2017	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.09	98.94	0.94	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:47,866] [INFO] GTDB search result was written to GCF_021394575.1_ASM2139457v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:47,867] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:47,870] [INFO] DFAST_QC result json was written to GCF_021394575.1_ASM2139457v1_genomic.fna/dqc_result.json
[2024-01-24 13:12:47,871] [INFO] DFAST_QC completed!
[2024-01-24 13:12:47,871] [INFO] Total running time: 0h2m44s