[2024-01-24 11:26:27,013] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,015] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,015] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd3fc026-681a-4418-b3cc-081c92a4641c/dqc_reference
[2024-01-24 11:26:28,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:28,368] [INFO] Task started: Prodigal
[2024-01-24 11:26:28,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg0100c86c-e4ee-4765-8e83-68bbc87c015d/GCF_016907715.1_ASM1690771v1_genomic.fna.gz | prodigal -d GCF_016907715.1_ASM1690771v1_genomic.fna/cds.fna -a GCF_016907715.1_ASM1690771v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:57,811] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:57,812] [INFO] Task started: HMMsearch
[2024-01-24 11:26:57,812] [INFO] Running command: hmmsearch --tblout GCF_016907715.1_ASM1690771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd3fc026-681a-4418-b3cc-081c92a4641c/dqc_reference/reference_markers.hmm GCF_016907715.1_ASM1690771v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:58,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:58,288] [INFO] Found 6/6 markers.
[2024-01-24 11:26:58,355] [INFO] Query marker FASTA was written to GCF_016907715.1_ASM1690771v1_genomic.fna/markers.fasta
[2024-01-24 11:26:58,356] [INFO] Task started: Blastn
[2024-01-24 11:26:58,356] [INFO] Running command: blastn -query GCF_016907715.1_ASM1690771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd3fc026-681a-4418-b3cc-081c92a4641c/dqc_reference/reference_markers.fasta -out GCF_016907715.1_ASM1690771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:59,609] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:59,613] [INFO] Selected 20 target genomes.
[2024-01-24 11:26:59,614] [INFO] Target genome list was writen to GCF_016907715.1_ASM1690771v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:59,621] [INFO] Task started: fastANI
[2024-01-24 11:26:59,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg0100c86c-e4ee-4765-8e83-68bbc87c015d/GCF_016907715.1_ASM1690771v1_genomic.fna.gz --refList GCF_016907715.1_ASM1690771v1_genomic.fna/target_genomes.txt --output GCF_016907715.1_ASM1690771v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:30,896] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:30,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd3fc026-681a-4418-b3cc-081c92a4641c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:30,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd3fc026-681a-4418-b3cc-081c92a4641c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:30,923] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:30,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:30,923] [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
Tenggerimyces flavus	strain=DSM 28944	GCA_016907715.1	1708749	1708749	type	True	100.0	2838	2839	95	conclusive
Actinopolymorpha rutila	strain=DSM 18448	GCA_013407855.1	446787	446787	type	True	78.4756	803	2839	95	below_threshold
Actinopolymorpha cephalotaxi	strain=DSM 45117	GCA_013408535.1	504797	504797	type	True	78.4695	810	2839	95	below_threshold
Actinopolymorpha singaporensis	strain=DSM 22024	GCA_900104745.1	117157	117157	type	True	78.3416	789	2839	95	below_threshold
Actinopolymorpha alba	strain=DSM 45243	GCA_000373925.1	533267	533267	type	True	77.9888	760	2839	95	below_threshold
Actinopolymorpha pittospori	strain=DSM 45354	GCA_014873875.1	648752	648752	type	True	77.904	846	2839	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	77.8332	552	2839	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	77.2002	677	2839	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	77.1243	528	2839	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	77.0768	664	2839	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.0608	520	2839	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	76.9876	712	2839	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	76.9851	671	2839	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	76.8939	363	2839	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.6641	478	2839	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	76.6108	487	2839	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	76.5843	581	2839	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	76.4594	684	2839	95	below_threshold
Actinomadura harenae	strain=NEAU-Ht49	GCA_003696215.1	2483351	2483351	type	True	76.2959	574	2839	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	76.1428	271	2839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,925] [INFO] DFAST Taxonomy check result was written to GCF_016907715.1_ASM1690771v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:30,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:30,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:30,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd3fc026-681a-4418-b3cc-081c92a4641c/dqc_reference/checkm_data
[2024-01-24 11:27:30,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:31,005] [INFO] Task started: CheckM
[2024-01-24 11:27:31,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907715.1_ASM1690771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907715.1_ASM1690771v1_genomic.fna/checkm_input GCF_016907715.1_ASM1690771v1_genomic.fna/checkm_result
[2024-01-24 11:28:58,275] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:58,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:58,310] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:58,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:58,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907715.1_ASM1690771v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:58,312] [INFO] Task started: Blastn
[2024-01-24 11:28:58,312] [INFO] Running command: blastn -query GCF_016907715.1_ASM1690771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd3fc026-681a-4418-b3cc-081c92a4641c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907715.1_ASM1690771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:00,109] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:00,113] [INFO] Selected 16 target genomes.
[2024-01-24 11:29:00,114] [INFO] Target genome list was writen to GCF_016907715.1_ASM1690771v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:00,127] [INFO] Task started: fastANI
[2024-01-24 11:29:00,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg0100c86c-e4ee-4765-8e83-68bbc87c015d/GCF_016907715.1_ASM1690771v1_genomic.fna.gz --refList GCF_016907715.1_ASM1690771v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907715.1_ASM1690771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:23,770] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:23,788] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:23,788] [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_016907715.1	s__Tenggerimyces flavus	100.0	2839	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Tenggerimyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013407855.1	s__Actinopolymorpha rutila	78.4793	801	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408535.1	s__Actinopolymorpha cephalotaxi	78.4708	813	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900104745.1	s__Actinopolymorpha singaporensis	78.3324	791	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373925.1	s__Actinopolymorpha alba	77.9745	763	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873875.1	s__Actinopolymorpha pittospori	77.8901	850	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386795.1	s__Thermasporomyces composti	77.819	555	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Thermasporomyces	95.0	99.77	99.77	0.94	0.94	2	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	77.1304	527	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217565.1	s__Kribbella qitaiheensis	77.0784	558	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331435.1	s__Kribbella sindirgiensis	76.9885	670	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.59	95.53	0.88	0.88	3	-
GCF_000515395.1	s__Jiangella gansuensis	76.6252	484	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428125.1	s__Nocardioides sp001428125	76.624	388	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349065.1	s__Jiangella asiatica	76.5647	585	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003427025.1	s__Jiangella endophytica	76.4335	691	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011393335.1	s__Brevilactibacter coleopterorum	76.1305	273	2839	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128305.1	s__Streptomyces sp002128305	76.1133	446	2839	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 11:29:23,790] [INFO] GTDB search result was written to GCF_016907715.1_ASM1690771v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:23,791] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:23,795] [INFO] DFAST_QC result json was written to GCF_016907715.1_ASM1690771v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:23,795] [INFO] DFAST_QC completed!
[2024-01-24 11:29:23,795] [INFO] Total running time: 0h2m57s