[2024-01-24 14:31:14,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,339] [INFO] DQC Reference Directory: /var/lib/cwl/stge368d014-663e-49a2-8eed-1e3a5a3aaec9/dqc_reference
[2024-01-24 14:31:15,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:15,561] [INFO] Task started: Prodigal
[2024-01-24 14:31:15,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg576aaacd-bd31-481b-9197-4abeec73d136/GCF_014202475.1_ASM1420247v1_genomic.fna.gz | prodigal -d GCF_014202475.1_ASM1420247v1_genomic.fna/cds.fna -a GCF_014202475.1_ASM1420247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:39,973] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:39,974] [INFO] Task started: HMMsearch
[2024-01-24 14:31:39,974] [INFO] Running command: hmmsearch --tblout GCF_014202475.1_ASM1420247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge368d014-663e-49a2-8eed-1e3a5a3aaec9/dqc_reference/reference_markers.hmm GCF_014202475.1_ASM1420247v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:40,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:40,399] [INFO] Found 6/6 markers.
[2024-01-24 14:31:40,472] [INFO] Query marker FASTA was written to GCF_014202475.1_ASM1420247v1_genomic.fna/markers.fasta
[2024-01-24 14:31:40,472] [INFO] Task started: Blastn
[2024-01-24 14:31:40,472] [INFO] Running command: blastn -query GCF_014202475.1_ASM1420247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge368d014-663e-49a2-8eed-1e3a5a3aaec9/dqc_reference/reference_markers.fasta -out GCF_014202475.1_ASM1420247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:41,798] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:41,802] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:41,803] [INFO] Target genome list was writen to GCF_014202475.1_ASM1420247v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:41,815] [INFO] Task started: fastANI
[2024-01-24 14:31:41,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg576aaacd-bd31-481b-9197-4abeec73d136/GCF_014202475.1_ASM1420247v1_genomic.fna.gz --refList GCF_014202475.1_ASM1420247v1_genomic.fna/target_genomes.txt --output GCF_014202475.1_ASM1420247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:17,367] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:17,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge368d014-663e-49a2-8eed-1e3a5a3aaec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:17,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge368d014-663e-49a2-8eed-1e3a5a3aaec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:17,385] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:32:17,385] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:32:17,386] [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 violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	94.7577	2426	2837	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	94.7103	2309	2837	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	93.8052	1876	2837	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	93.2199	2279	2837	95	below_threshold
Streptomyces flavovariabilis	strain=NRRL B-16367	GCA_000725785.1	284031	284031	type	True	93.1293	2279	2837	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	92.9677	2374	2837	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	92.6428	2098	2837	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	92.5318	2286	2837	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	92.5161	2288	2837	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	91.9987	2027	2837	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.1403	2183	2837	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.8377	2213	2837	95	below_threshold
Streptomyces resistomycificus	strain=DSM 40133	GCA_001514265.1	67356	67356	type	True	85.9244	2010	2837	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	85.8737	1987	2837	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.422	1830	2837	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.4158	1491	2837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:17,388] [INFO] DFAST Taxonomy check result was written to GCF_014202475.1_ASM1420247v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:17,388] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:17,389] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:17,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge368d014-663e-49a2-8eed-1e3a5a3aaec9/dqc_reference/checkm_data
[2024-01-24 14:32:17,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:17,471] [INFO] Task started: CheckM
[2024-01-24 14:32:17,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202475.1_ASM1420247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202475.1_ASM1420247v1_genomic.fna/checkm_input GCF_014202475.1_ASM1420247v1_genomic.fna/checkm_result
[2024-01-24 14:34:19,103] [INFO] Task succeeded: CheckM
[2024-01-24 14:34:19,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:34:19,137] [INFO] ===== Completeness check finished =====
[2024-01-24 14:34:19,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:34:19,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202475.1_ASM1420247v1_genomic.fna/markers.fasta)
[2024-01-24 14:34:19,138] [INFO] Task started: Blastn
[2024-01-24 14:34:19,139] [INFO] Running command: blastn -query GCF_014202475.1_ASM1420247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge368d014-663e-49a2-8eed-1e3a5a3aaec9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202475.1_ASM1420247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:34:21,221] [INFO] Task succeeded: Blastn
[2024-01-24 14:34:21,225] [INFO] Selected 10 target genomes.
[2024-01-24 14:34:21,225] [INFO] Target genome list was writen to GCF_014202475.1_ASM1420247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:34:21,253] [INFO] Task started: fastANI
[2024-01-24 14:34:21,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg576aaacd-bd31-481b-9197-4abeec73d136/GCF_014202475.1_ASM1420247v1_genomic.fna.gz --refList GCF_014202475.1_ASM1420247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202475.1_ASM1420247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:45,960] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:45,972] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:45,972] [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_014202475.1	s__Streptomyces paradoxus	100.0	2835	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014204745.1	s__Streptomyces collinus	94.7865	2440	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_000717055.1	s__Streptomyces iakyrus	94.7011	2310	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_001611795.1	s__Streptomyces qaidamensis	94.5811	2373	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_004803895.1	s__Streptomyces hawaiiensis	93.2389	2277	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014648995.1	s__Streptomyces massasporeus	92.9531	2376	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCF_007655005.1	s__Streptomyces tibetensis	92.5239	2287	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001280065.1	s__Streptomyces sp001280065	92.1432	2168	2837	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	85.7946	1987	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656055.1	s__Streptomyces griseosporeus	85.4055	1833	2837	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:45,974] [INFO] GTDB search result was written to GCF_014202475.1_ASM1420247v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:45,974] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:45,978] [INFO] DFAST_QC result json was written to GCF_014202475.1_ASM1420247v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:45,978] [INFO] DFAST_QC completed!
[2024-01-24 14:34:45,978] [INFO] Total running time: 0h3m32s