[2024-01-24 13:19:12,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:12,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:12,938] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa203785-7b40-4cf2-bb6a-dc71ede67866/dqc_reference
[2024-01-24 13:19:14,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,149] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,150] [INFO] Running command: gunzip -c /var/lib/cwl/stgd59fcfd3-b2d2-4940-9276-646e667df3a6/GCF_014656255.1_ASM1465625v1_genomic.fna.gz | prodigal -d GCF_014656255.1_ASM1465625v1_genomic.fna/cds.fna -a GCF_014656255.1_ASM1465625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:40,397] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:40,398] [INFO] Task started: HMMsearch
[2024-01-24 13:19:40,398] [INFO] Running command: hmmsearch --tblout GCF_014656255.1_ASM1465625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa203785-7b40-4cf2-bb6a-dc71ede67866/dqc_reference/reference_markers.hmm GCF_014656255.1_ASM1465625v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:40,778] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:40,779] [INFO] Found 6/6 markers.
[2024-01-24 13:19:40,852] [INFO] Query marker FASTA was written to GCF_014656255.1_ASM1465625v1_genomic.fna/markers.fasta
[2024-01-24 13:19:40,852] [INFO] Task started: Blastn
[2024-01-24 13:19:40,853] [INFO] Running command: blastn -query GCF_014656255.1_ASM1465625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa203785-7b40-4cf2-bb6a-dc71ede67866/dqc_reference/reference_markers.fasta -out GCF_014656255.1_ASM1465625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:42,230] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:42,234] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:42,234] [INFO] Target genome list was writen to GCF_014656255.1_ASM1465625v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:42,237] [INFO] Task started: fastANI
[2024-01-24 13:19:42,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgd59fcfd3-b2d2-4940-9276-646e667df3a6/GCF_014656255.1_ASM1465625v1_genomic.fna.gz --refList GCF_014656255.1_ASM1465625v1_genomic.fna/target_genomes.txt --output GCF_014656255.1_ASM1465625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:06,209] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:06,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa203785-7b40-4cf2-bb6a-dc71ede67866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:06,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa203785-7b40-4cf2-bb6a-dc71ede67866/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:06,220] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:20:06,220] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:20:06,220] [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 rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	100.0	2896	2896	95	inconclusive
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	99.9983	2883	2896	95	inconclusive
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	95.2007	2289	2896	95	inconclusive
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	95.1051	2328	2896	95	inconclusive
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	94.7394	2210	2896	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	88.956	1935	2896	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	87.3566	1804	2896	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.3086	1555	2896	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.0142	1512	2896	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.6652	1753	2896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:06,222] [INFO] DFAST Taxonomy check result was written to GCF_014656255.1_ASM1465625v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:06,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:06,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:06,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa203785-7b40-4cf2-bb6a-dc71ede67866/dqc_reference/checkm_data
[2024-01-24 13:20:06,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:06,309] [INFO] Task started: CheckM
[2024-01-24 13:20:06,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656255.1_ASM1465625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656255.1_ASM1465625v1_genomic.fna/checkm_input GCF_014656255.1_ASM1465625v1_genomic.fna/checkm_result
[2024-01-24 13:22:01,401] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:01,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.90%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:01,444] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:01,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:01,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656255.1_ASM1465625v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:01,445] [INFO] Task started: Blastn
[2024-01-24 13:22:01,445] [INFO] Running command: blastn -query GCF_014656255.1_ASM1465625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa203785-7b40-4cf2-bb6a-dc71ede67866/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656255.1_ASM1465625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:03,859] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:03,863] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:03,863] [INFO] Target genome list was writen to GCF_014656255.1_ASM1465625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:03,870] [INFO] Task started: fastANI
[2024-01-24 13:22:03,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgd59fcfd3-b2d2-4940-9276-646e667df3a6/GCF_014656255.1_ASM1465625v1_genomic.fna.gz --refList GCF_014656255.1_ASM1465625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656255.1_ASM1465625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:37,704] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:37,716] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:37,717] [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_016860525.1	s__Streptomyces rubradiris	99.9903	2884	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	conclusive
GCF_014649115.1	s__Streptomyces eurythermus	95.1227	2326	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_000720835.1	s__Streptomyces achromogenes	94.7294	2211	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_000718775.1	s__Streptomyces sp000718775	89.5938	1845	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	89.4214	1928	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	89.3437	1997	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	89.3198	1875	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920615.1	s__Streptomyces sp002920615	89.2788	1923	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_000716535.1	s__Streptomyces flaveolus_A	89.269	1963	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_002155905.1	s__Streptomyces tricolor	89.2069	1704	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_016741855.1	s__Streptomyces musisoli	89.2024	1938	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	89.0779	1967	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	87.2184	1808	2896	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:37,719] [INFO] GTDB search result was written to GCF_014656255.1_ASM1465625v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:37,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:37,724] [INFO] DFAST_QC result json was written to GCF_014656255.1_ASM1465625v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:37,724] [INFO] DFAST_QC completed!
[2024-01-24 13:22:37,724] [INFO] Total running time: 0h3m25s