[2024-01-24 10:47:40,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,965] [INFO] DQC Reference Directory: /var/lib/cwl/stgda116e59-227c-4c64-9870-71e52fadf7f1/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,788] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a78527a-20dd-42b2-9ec2-50eb65ae4508/GCF_002154575.1_ASM215457v1_genomic.fna.gz | prodigal -d GCF_002154575.1_ASM215457v1_genomic.fna/cds.fna -a GCF_002154575.1_ASM215457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:04,065] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:04,066] [INFO] Task started: HMMsearch
[2024-01-24 10:48:04,066] [INFO] Running command: hmmsearch --tblout GCF_002154575.1_ASM215457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda116e59-227c-4c64-9870-71e52fadf7f1/dqc_reference/reference_markers.hmm GCF_002154575.1_ASM215457v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:04,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:04,431] [INFO] Found 6/6 markers.
[2024-01-24 10:48:04,496] [INFO] Query marker FASTA was written to GCF_002154575.1_ASM215457v1_genomic.fna/markers.fasta
[2024-01-24 10:48:04,496] [INFO] Task started: Blastn
[2024-01-24 10:48:04,496] [INFO] Running command: blastn -query GCF_002154575.1_ASM215457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda116e59-227c-4c64-9870-71e52fadf7f1/dqc_reference/reference_markers.fasta -out GCF_002154575.1_ASM215457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:05,782] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:05,785] [INFO] Selected 20 target genomes.
[2024-01-24 10:48:05,785] [INFO] Target genome list was writen to GCF_002154575.1_ASM215457v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:05,793] [INFO] Task started: fastANI
[2024-01-24 10:48:05,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a78527a-20dd-42b2-9ec2-50eb65ae4508/GCF_002154575.1_ASM215457v1_genomic.fna.gz --refList GCF_002154575.1_ASM215457v1_genomic.fna/target_genomes.txt --output GCF_002154575.1_ASM215457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:45,832] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:45,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda116e59-227c-4c64-9870-71e52fadf7f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:45,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda116e59-227c-4c64-9870-71e52fadf7f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:45,851] [INFO] Found 20 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:48:45,851] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:48:45,851] [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 bobili	strain=NRRL B-1338	GCA_002154575.1	67280	67280	type	True	100.0	2212	2244	95	inconclusive
Streptomyces galilaeus	strain=JCM 4757	GCA_014650835.1	33899	33899	type	True	97.5989	2053	2244	95	inconclusive
Streptomyces galilaeus	strain=ATCC 14969	GCA_008704575.1	33899	33899	type	True	97.5716	1906	2244	95	inconclusive
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	86.8249	1685	2244	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	86.473	1597	2244	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	86.2532	1593	2244	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	86.0632	1512	2244	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.38	1520	2244	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.2975	1587	2244	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.0647	1446	2244	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	85.0598	1267	2244	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	84.9805	1630	2244	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	84.9558	1580	2244	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	84.9388	1577	2244	95	below_threshold
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	84.9284	1581	2244	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.8565	1363	2244	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.7717	1382	2244	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.4827	1402	2244	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	84.0482	1441	2244	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	84.0423	1449	2244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:45,853] [INFO] DFAST Taxonomy check result was written to GCF_002154575.1_ASM215457v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:45,853] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:45,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:45,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda116e59-227c-4c64-9870-71e52fadf7f1/dqc_reference/checkm_data
[2024-01-24 10:48:45,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:45,927] [INFO] Task started: CheckM
[2024-01-24 10:48:45,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154575.1_ASM215457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154575.1_ASM215457v1_genomic.fna/checkm_input GCF_002154575.1_ASM215457v1_genomic.fna/checkm_result
[2024-01-24 10:49:48,134] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:48,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:48,157] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:48,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:48,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154575.1_ASM215457v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:48,159] [INFO] Task started: Blastn
[2024-01-24 10:49:48,159] [INFO] Running command: blastn -query GCF_002154575.1_ASM215457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda116e59-227c-4c64-9870-71e52fadf7f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154575.1_ASM215457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:50,195] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:50,199] [INFO] Selected 20 target genomes.
[2024-01-24 10:49:50,199] [INFO] Target genome list was writen to GCF_002154575.1_ASM215457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:50,212] [INFO] Task started: fastANI
[2024-01-24 10:49:50,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a78527a-20dd-42b2-9ec2-50eb65ae4508/GCF_002154575.1_ASM215457v1_genomic.fna.gz --refList GCF_002154575.1_ASM215457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154575.1_ASM215457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:32,652] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:32,676] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:32,676] [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_002154575.1	s__Streptomyces bobili	100.0	2212	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.61	97.61	0.88	0.85	3	conclusive
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	93.3151	1788	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	88.0546	1708	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085465.1	s__Streptomyces cacaoi_A	87.1525	1693	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129855.1	s__Streptomyces sp900129855	86.9181	1598	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_900110755.1	s__Streptomyces sp900110755	86.8359	1529	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019855.1	s__Streptomyces antibioticus_B	86.4422	1538	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_001746365.1	s__Streptomyces sp001746365	86.1389	1560	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514285.1	s__Streptomyces sp001514285	86.0566	1552	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721105.1	s__Streptomyces cellulosae_A	85.4902	1549	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	85.3035	1562	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	84.9755	1350	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513955.1	s__Streptomyces pseudovenezuelae	84.9704	1572	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746295.1	s__Streptomyces sp001746295	84.9414	1577	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	84.8943	1542	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827595.1	s__Streptomyces sp007827595	84.6212	1464	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675325.1	s__Streptomyces sp003675325	84.4712	1355	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716605.1	s__Streptomyces sp000716605	84.4266	1502	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873495.1	s__Streptomyces stelliscabiei	84.0823	1511	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_000383595.1	s__Streptomyces bottropensis	84.0367	1443	2244	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:32,678] [INFO] GTDB search result was written to GCF_002154575.1_ASM215457v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:32,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:32,682] [INFO] DFAST_QC result json was written to GCF_002154575.1_ASM215457v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:32,682] [INFO] DFAST_QC completed!
[2024-01-24 10:50:32,682] [INFO] Total running time: 0h2m52s