[2024-01-24 13:40:34,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg835562ee-bbec-4b7d-aed0-747891896e44/dqc_reference
[2024-01-24 13:40:36,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,416] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d55d00a-538a-471e-94fa-faa6b16e000d/GCF_009834025.1_ASM983402v1_genomic.fna.gz | prodigal -d GCF_009834025.1_ASM983402v1_genomic.fna/cds.fna -a GCF_009834025.1_ASM983402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,635] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,636] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,636] [INFO] Running command: hmmsearch --tblout GCF_009834025.1_ASM983402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg835562ee-bbec-4b7d-aed0-747891896e44/dqc_reference/reference_markers.hmm GCF_009834025.1_ASM983402v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:48,955] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:48,957] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,996] [INFO] Query marker FASTA was written to GCF_009834025.1_ASM983402v1_genomic.fna/markers.fasta
[2024-01-24 13:40:48,996] [INFO] Task started: Blastn
[2024-01-24 13:40:48,996] [INFO] Running command: blastn -query GCF_009834025.1_ASM983402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg835562ee-bbec-4b7d-aed0-747891896e44/dqc_reference/reference_markers.fasta -out GCF_009834025.1_ASM983402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,190] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,194] [INFO] Selected 24 target genomes.
[2024-01-24 13:40:50,194] [INFO] Target genome list was writen to GCF_009834025.1_ASM983402v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,205] [INFO] Task started: fastANI
[2024-01-24 13:40:50,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d55d00a-538a-471e-94fa-faa6b16e000d/GCF_009834025.1_ASM983402v1_genomic.fna.gz --refList GCF_009834025.1_ASM983402v1_genomic.fna/target_genomes.txt --output GCF_009834025.1_ASM983402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,200] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg835562ee-bbec-4b7d-aed0-747891896e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg835562ee-bbec-4b7d-aed0-747891896e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,218] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:14,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:14,218] [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
Cumulibacter soli	strain=G-1	GCA_004382795.1	2546344	2546344	type	True	78.1082	292	1339	95	below_threshold
Antricoccus suffuscus	strain=DSM 100065	GCA_003003235.1	1629062	1629062	type	True	77.8414	341	1339	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	77.3257	297	1339	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	77.2984	291	1339	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	77.1872	289	1339	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	77.1196	266	1339	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.9797	303	1339	95	below_threshold
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	76.9285	169	1339	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	76.9089	269	1339	95	below_threshold
Amycolatopsis australiensis	strain=DSM 44671	GCA_900119165.1	546364	546364	type	True	76.9012	312	1339	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.8862	275	1339	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.8582	285	1339	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	76.8491	250	1339	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	76.8379	310	1339	95	below_threshold
Salinispora mooreana	strain=DSM 45549	GCA_000379065.1	999545	999545	type	True	76.8264	144	1339	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	76.8213	218	1339	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	76.8196	280	1339	95	below_threshold
Tsukamurella asaccharolytica	strain=HKU71	GCA_007858435.1	2592067	2592067	type	True	76.7446	216	1339	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	76.7176	314	1339	95	below_threshold
Sporichthya polymorpha	strain=DSM 43042	GCA_000384115.1	35751	35751	type	True	76.6991	243	1339	95	below_threshold
Micromonospora noduli	strain=GUI43	GCA_003264365.1	709876	709876	type	True	76.6574	229	1339	95	below_threshold
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	76.6462	284	1339	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	76.4779	146	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,220] [INFO] DFAST Taxonomy check result was written to GCF_009834025.1_ASM983402v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg835562ee-bbec-4b7d-aed0-747891896e44/dqc_reference/checkm_data
[2024-01-24 13:41:14,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,264] [INFO] Task started: CheckM
[2024-01-24 13:41:14,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009834025.1_ASM983402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009834025.1_ASM983402v1_genomic.fna/checkm_input GCF_009834025.1_ASM983402v1_genomic.fna/checkm_result
[2024-01-24 13:41:53,400] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:53,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:53,424] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:53,425] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:53,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009834025.1_ASM983402v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:53,426] [INFO] Task started: Blastn
[2024-01-24 13:41:53,426] [INFO] Running command: blastn -query GCF_009834025.1_ASM983402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg835562ee-bbec-4b7d-aed0-747891896e44/dqc_reference/reference_markers_gtdb.fasta -out GCF_009834025.1_ASM983402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:55,218] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:55,228] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:55,228] [INFO] Target genome list was writen to GCF_009834025.1_ASM983402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:55,237] [INFO] Task started: fastANI
[2024-01-24 13:41:55,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d55d00a-538a-471e-94fa-faa6b16e000d/GCF_009834025.1_ASM983402v1_genomic.fna.gz --refList GCF_009834025.1_ASM983402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009834025.1_ASM983402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:04,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:04,485] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:04,485] [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_009834025.1	s__Epidermidibacterium keratini	100.0	1339	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Epidermidibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009602465.1	s__Cumulibacter manganitolerans	79.8897	566	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900292035.1	s__Cumulibacter sp900292035	79.5611	491	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004382795.1	s__Cumulibacter soli	78.1205	291	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Cumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003235.1	s__Antricoccus suffuscus	77.8317	342	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Antricoccaceae;g__Antricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557055.1	s__Nocardioides sp009557055	77.2102	266	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111175.1	s__Actinokineospora terrae	76.8839	272	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_010993745.1	s__Fodinicola acaciae	76.661	282	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__HKI-0501;g__Fodinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	76.6316	226	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014267345.1	s__Corynebacterium sp014267345	76.1853	52	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:04,487] [INFO] GTDB search result was written to GCF_009834025.1_ASM983402v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:04,487] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:04,491] [INFO] DFAST_QC result json was written to GCF_009834025.1_ASM983402v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:04,491] [INFO] DFAST_QC completed!
[2024-01-24 13:42:04,491] [INFO] Total running time: 0h1m30s