[2024-01-24 11:34:40,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg437c1a94-1f03-4aef-a767-48259c40b126/dqc_reference
[2024-01-24 11:34:41,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,764] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg77e678d5-1846-450b-b58d-9f8b0f2474f4/GCF_014656315.1_ASM1465631v1_genomic.fna.gz | prodigal -d GCF_014656315.1_ASM1465631v1_genomic.fna/cds.fna -a GCF_014656315.1_ASM1465631v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:09,068] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:09,068] [INFO] Task started: HMMsearch
[2024-01-24 11:35:09,068] [INFO] Running command: hmmsearch --tblout GCF_014656315.1_ASM1465631v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg437c1a94-1f03-4aef-a767-48259c40b126/dqc_reference/reference_markers.hmm GCF_014656315.1_ASM1465631v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:09,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:09,500] [INFO] Found 6/6 markers.
[2024-01-24 11:35:09,568] [INFO] Query marker FASTA was written to GCF_014656315.1_ASM1465631v1_genomic.fna/markers.fasta
[2024-01-24 11:35:09,568] [INFO] Task started: Blastn
[2024-01-24 11:35:09,569] [INFO] Running command: blastn -query GCF_014656315.1_ASM1465631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg437c1a94-1f03-4aef-a767-48259c40b126/dqc_reference/reference_markers.fasta -out GCF_014656315.1_ASM1465631v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:10,928] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:10,931] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:10,931] [INFO] Target genome list was writen to GCF_014656315.1_ASM1465631v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:10,937] [INFO] Task started: fastANI
[2024-01-24 11:35:10,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg77e678d5-1846-450b-b58d-9f8b0f2474f4/GCF_014656315.1_ASM1465631v1_genomic.fna.gz --refList GCF_014656315.1_ASM1465631v1_genomic.fna/target_genomes.txt --output GCF_014656315.1_ASM1465631v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:45,232] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:45,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg437c1a94-1f03-4aef-a767-48259c40b126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:45,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg437c1a94-1f03-4aef-a767-48259c40b126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:45,246] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:45,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:45,247] [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 capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	100.0	2765	2766	95	conclusive
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	99.9946	2756	2766	95	conclusive
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	92.8246	2172	2766	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	92.7547	2173	2766	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	91.5482	2137	2766	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	89.7411	1930	2766	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	89.7337	1935	2766	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	89.5606	1923	2766	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	89.0542	1883	2766	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.5273	1809	2766	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	86.362	1734	2766	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.3274	1804	2766	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	86.091	1631	2766	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	86.066	1801	2766	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.8191	1534	2766	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,248] [INFO] DFAST Taxonomy check result was written to GCF_014656315.1_ASM1465631v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:45,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:45,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:45,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg437c1a94-1f03-4aef-a767-48259c40b126/dqc_reference/checkm_data
[2024-01-24 11:35:45,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:45,328] [INFO] Task started: CheckM
[2024-01-24 11:35:45,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656315.1_ASM1465631v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656315.1_ASM1465631v1_genomic.fna/checkm_input GCF_014656315.1_ASM1465631v1_genomic.fna/checkm_result
[2024-01-24 11:38:00,334] [INFO] Task succeeded: CheckM
[2024-01-24 11:38:00,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:38:00,359] [INFO] ===== Completeness check finished =====
[2024-01-24 11:38:00,359] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:38:00,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656315.1_ASM1465631v1_genomic.fna/markers.fasta)
[2024-01-24 11:38:00,360] [INFO] Task started: Blastn
[2024-01-24 11:38:00,360] [INFO] Running command: blastn -query GCF_014656315.1_ASM1465631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg437c1a94-1f03-4aef-a767-48259c40b126/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656315.1_ASM1465631v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:38:02,485] [INFO] Task succeeded: Blastn
[2024-01-24 11:38:02,489] [INFO] Selected 13 target genomes.
[2024-01-24 11:38:02,489] [INFO] Target genome list was writen to GCF_014656315.1_ASM1465631v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:38:02,540] [INFO] Task started: fastANI
[2024-01-24 11:38:02,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg77e678d5-1846-450b-b58d-9f8b0f2474f4/GCF_014656315.1_ASM1465631v1_genomic.fna.gz --refList GCF_014656315.1_ASM1465631v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656315.1_ASM1465631v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:31,133] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:31,147] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:31,147] [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_007829875.1	s__Streptomyces capillispiralis	99.9902	2756	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_014650015.1	s__Streptomyces griseoloalbus	92.8355	2192	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	-
GCF_006782915.1	s__Streptomyces calvus	91.5105	2133	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_019049255.1	s__Streptomyces sp019049255	90.5146	2034	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721605.1	s__Streptomyces sp000721605	90.3691	1985	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	90.3184	2018	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312835.1	s__Streptomyces marokkonensis	89.9328	1954	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665435.1	s__Streptomyces fungicidicus_A	89.8673	1956	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.42	0.93	0.90	4	-
GCF_009852415.1	s__Streptomyces sp009852415	89.8047	2001	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	89.686	1941	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_008704515.1	s__Streptomyces viridosporus	89.4939	1752	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_000718785.1	s__Streptomyces sp000718785	89.2618	1894	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649835.1	s__Streptomyces pilosus	89.0377	1885	2766	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.43	99.43	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:38:31,149] [INFO] GTDB search result was written to GCF_014656315.1_ASM1465631v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:31,149] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:31,153] [INFO] DFAST_QC result json was written to GCF_014656315.1_ASM1465631v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:31,153] [INFO] DFAST_QC completed!
[2024-01-24 11:38:31,153] [INFO] Total running time: 0h3m51s