[2024-01-24 12:07:18,659] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:18,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:18,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fd46d36-79e7-4e6f-9671-336cd5ef24b9/dqc_reference
[2024-01-24 12:07:19,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:19,847] [INFO] Task started: Prodigal
[2024-01-24 12:07:19,847] [INFO] Running command: gunzip -c /var/lib/cwl/stgb93e90af-20ea-41c6-80de-9087cdec7c93/GCF_014701095.1_ASM1470109v1_genomic.fna.gz | prodigal -d GCF_014701095.1_ASM1470109v1_genomic.fna/cds.fna -a GCF_014701095.1_ASM1470109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:40,958] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:40,959] [INFO] Task started: HMMsearch
[2024-01-24 12:07:40,959] [INFO] Running command: hmmsearch --tblout GCF_014701095.1_ASM1470109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fd46d36-79e7-4e6f-9671-336cd5ef24b9/dqc_reference/reference_markers.hmm GCF_014701095.1_ASM1470109v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:41,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:41,294] [INFO] Found 6/6 markers.
[2024-01-24 12:07:41,355] [INFO] Query marker FASTA was written to GCF_014701095.1_ASM1470109v1_genomic.fna/markers.fasta
[2024-01-24 12:07:41,356] [INFO] Task started: Blastn
[2024-01-24 12:07:41,356] [INFO] Running command: blastn -query GCF_014701095.1_ASM1470109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fd46d36-79e7-4e6f-9671-336cd5ef24b9/dqc_reference/reference_markers.fasta -out GCF_014701095.1_ASM1470109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:42,635] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:42,639] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:42,640] [INFO] Target genome list was writen to GCF_014701095.1_ASM1470109v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:42,646] [INFO] Task started: fastANI
[2024-01-24 12:07:42,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgb93e90af-20ea-41c6-80de-9087cdec7c93/GCF_014701095.1_ASM1470109v1_genomic.fna.gz --refList GCF_014701095.1_ASM1470109v1_genomic.fna/target_genomes.txt --output GCF_014701095.1_ASM1470109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:08:10,398] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:10,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fd46d36-79e7-4e6f-9671-336cd5ef24b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:08:10,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fd46d36-79e7-4e6f-9671-336cd5ef24b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:08:10,416] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:08:10,416] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:08:10,417] [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 tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	100.0	2515	2520	95	inconclusive
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	95.2383	2173	2520	95	inconclusive
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	94.409	2164	2520	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	93.0094	2118	2520	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	92.8618	2072	2520	95	below_threshold
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	92.5913	2107	2520	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	92.5366	2096	2520	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	92.5047	2100	2520	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	92.2562	1939	2520	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	92.0445	1708	2520	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.9693	2012	2520	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.6496	2025	2520	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.1514	1719	2520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:08:10,418] [INFO] DFAST Taxonomy check result was written to GCF_014701095.1_ASM1470109v1_genomic.fna/tc_result.tsv
[2024-01-24 12:08:10,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:08:10,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:08:10,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fd46d36-79e7-4e6f-9671-336cd5ef24b9/dqc_reference/checkm_data
[2024-01-24 12:08:10,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:08:10,494] [INFO] Task started: CheckM
[2024-01-24 12:08:10,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014701095.1_ASM1470109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014701095.1_ASM1470109v1_genomic.fna/checkm_input GCF_014701095.1_ASM1470109v1_genomic.fna/checkm_result
[2024-01-24 12:10:12,805] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:12,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:12,835] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:12,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:12,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014701095.1_ASM1470109v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:12,837] [INFO] Task started: Blastn
[2024-01-24 12:10:12,837] [INFO] Running command: blastn -query GCF_014701095.1_ASM1470109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fd46d36-79e7-4e6f-9671-336cd5ef24b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014701095.1_ASM1470109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:14,888] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:14,893] [INFO] Selected 9 target genomes.
[2024-01-24 12:10:14,893] [INFO] Target genome list was writen to GCF_014701095.1_ASM1470109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:14,899] [INFO] Task started: fastANI
[2024-01-24 12:10:14,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgb93e90af-20ea-41c6-80de-9087cdec7c93/GCF_014701095.1_ASM1470109v1_genomic.fna.gz --refList GCF_014701095.1_ASM1470109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014701095.1_ASM1470109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:34,730] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:34,744] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:34,744] [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_014648995.1	s__Streptomyces massasporeus	95.2236	2175	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	conclusive
GCF_014205055.1	s__Streptomyces luteogriseus	94.4205	2163	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCA_014204745.1	s__Streptomyces collinus	92.9925	2149	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	-
GCF_004803895.1	s__Streptomyces hawaiiensis	92.9111	2065	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014202475.1	s__Streptomyces paradoxus	92.7239	2097	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611795.1	s__Streptomyces qaidamensis	92.6655	2107	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_000717055.1	s__Streptomyces iakyrus	92.6083	2105	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_007655005.1	s__Streptomyces tibetensis	92.522	2098	2520	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	92.1679	2000	2520	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 12:10:34,746] [INFO] GTDB search result was written to GCF_014701095.1_ASM1470109v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:34,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:34,751] [INFO] DFAST_QC result json was written to GCF_014701095.1_ASM1470109v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:34,752] [INFO] DFAST_QC completed!
[2024-01-24 12:10:34,752] [INFO] Total running time: 0h3m16s