[2024-01-24 13:58:10,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg0eaa859f-50e7-4e3c-9de4-284d795cb3b0/dqc_reference
[2024-01-24 13:58:11,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,967] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,968] [INFO] Running command: gunzip -c /var/lib/cwl/stg583f6df0-2311-45ec-8623-790af4528c67/GCF_001418655.1_ASM141865v1_genomic.fna.gz | prodigal -d GCF_001418655.1_ASM141865v1_genomic.fna/cds.fna -a GCF_001418655.1_ASM141865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:45,192] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:45,192] [INFO] Task started: HMMsearch
[2024-01-24 13:58:45,192] [INFO] Running command: hmmsearch --tblout GCF_001418655.1_ASM141865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0eaa859f-50e7-4e3c-9de4-284d795cb3b0/dqc_reference/reference_markers.hmm GCF_001418655.1_ASM141865v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:45,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:45,593] [INFO] Found 6/6 markers.
[2024-01-24 13:58:45,676] [INFO] Query marker FASTA was written to GCF_001418655.1_ASM141865v1_genomic.fna/markers.fasta
[2024-01-24 13:58:45,676] [INFO] Task started: Blastn
[2024-01-24 13:58:45,676] [INFO] Running command: blastn -query GCF_001418655.1_ASM141865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0eaa859f-50e7-4e3c-9de4-284d795cb3b0/dqc_reference/reference_markers.fasta -out GCF_001418655.1_ASM141865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:46,951] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:46,955] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:46,955] [INFO] Target genome list was writen to GCF_001418655.1_ASM141865v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:46,970] [INFO] Task started: fastANI
[2024-01-24 13:58:46,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg583f6df0-2311-45ec-8623-790af4528c67/GCF_001418655.1_ASM141865v1_genomic.fna.gz --refList GCF_001418655.1_ASM141865v1_genomic.fna/target_genomes.txt --output GCF_001418655.1_ASM141865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:31,385] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:31,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0eaa859f-50e7-4e3c-9de4-284d795cb3b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:31,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0eaa859f-50e7-4e3c-9de4-284d795cb3b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:31,402] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:31,403] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:59:31,403] [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 phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	100.0	3268	3304	95	inconclusive
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	95.9191	2926	3304	95	inconclusive
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	87.9943	1806	3304	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.4393	1933	3304	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	85.0304	2023	3304	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	85.0103	1963	3304	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	84.9685	2031	3304	95	below_threshold
Streptomyces lacrimifluminis	strain=CGMCC 4.7272	GCA_014646095.1	1500077	1500077	type	True	84.2051	1788	3304	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.9361	1613	3304	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.9246	1880	3304	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.874	1821	3304	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.8518	1958	3304	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.5047	1747	3304	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	83.1977	1507	3304	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.9116	1447	3304	95	below_threshold
Streptomyces lasiicapitis	strain=CGMCC 4.7349	GCA_014646335.1	1923961	1923961	type	True	82.4592	1645	3304	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	81.2344	1335	3304	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	81.2203	1261	3304	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	81.2121	1303	3304	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	81.1861	1298	3304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:31,405] [INFO] DFAST Taxonomy check result was written to GCF_001418655.1_ASM141865v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:31,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:31,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:31,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0eaa859f-50e7-4e3c-9de4-284d795cb3b0/dqc_reference/checkm_data
[2024-01-24 13:59:31,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:31,523] [INFO] Task started: CheckM
[2024-01-24 13:59:31,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418655.1_ASM141865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418655.1_ASM141865v1_genomic.fna/checkm_input GCF_001418655.1_ASM141865v1_genomic.fna/checkm_result
[2024-01-24 14:01:27,473] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:27,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:01:27,507] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:27,508] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:27,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418655.1_ASM141865v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:27,509] [INFO] Task started: Blastn
[2024-01-24 14:01:27,509] [INFO] Running command: blastn -query GCF_001418655.1_ASM141865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0eaa859f-50e7-4e3c-9de4-284d795cb3b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418655.1_ASM141865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:29,566] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:29,570] [INFO] Selected 12 target genomes.
[2024-01-24 14:01:29,570] [INFO] Target genome list was writen to GCF_001418655.1_ASM141865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:29,582] [INFO] Task started: fastANI
[2024-01-24 14:01:29,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg583f6df0-2311-45ec-8623-790af4528c67/GCF_001418655.1_ASM141865v1_genomic.fna.gz --refList GCF_001418655.1_ASM141865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418655.1_ASM141865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:02:00,002] [INFO] Task succeeded: fastANI
[2024-01-24 14:02:00,016] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:02:00,016] [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_001418655.1	s__Streptomyces phaeochromogenes	100.0	3268	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	conclusive
GCF_016598615.1	s__Streptomyces sp016598615	94.5162	2770	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	94.3762	2750	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	89.4104	2340	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	88.9332	2160	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070025.1	s__Streptomyces sp018070025	87.8337	2208	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024195.1	s__Streptomyces dioscori	87.8041	2133	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369065.1	s__Streptomyces sp008369065	87.3596	1882	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651055.1	s__Streptomyces fructofermentans	86.437	1935	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612545.1	s__Streptomyces sp016612545	83.9687	1827	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610995.1	s__Streptomyces sp003116725	81.2623	1278	3304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.40	95.27	0.92	0.85	7	-
GCF_002382885.1	s__Streptomyces sp002382885	81.0879	1238	3304	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 14:02:00,018] [INFO] GTDB search result was written to GCF_001418655.1_ASM141865v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:02:00,018] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:02:00,024] [INFO] DFAST_QC result json was written to GCF_001418655.1_ASM141865v1_genomic.fna/dqc_result.json
[2024-01-24 14:02:00,024] [INFO] DFAST_QC completed!
[2024-01-24 14:02:00,024] [INFO] Total running time: 0h3m49s