[2024-01-24 12:37:07,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:07,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:07,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg51f43016-f698-4d85-a60f-272bf1b47dfb/dqc_reference
[2024-01-24 12:37:08,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:08,514] [INFO] Task started: Prodigal
[2024-01-24 12:37:08,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f500e80-03ff-4b47-8f60-e38c0db97b4c/GCF_013408985.1_ASM1340898v1_genomic.fna.gz | prodigal -d GCF_013408985.1_ASM1340898v1_genomic.fna/cds.fna -a GCF_013408985.1_ASM1340898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:22,470] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:22,470] [INFO] Task started: HMMsearch
[2024-01-24 12:37:22,470] [INFO] Running command: hmmsearch --tblout GCF_013408985.1_ASM1340898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51f43016-f698-4d85-a60f-272bf1b47dfb/dqc_reference/reference_markers.hmm GCF_013408985.1_ASM1340898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:22,777] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:22,778] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9f500e80-03ff-4b47-8f60-e38c0db97b4c/GCF_013408985.1_ASM1340898v1_genomic.fna.gz]
[2024-01-24 12:37:22,826] [INFO] Query marker FASTA was written to GCF_013408985.1_ASM1340898v1_genomic.fna/markers.fasta
[2024-01-24 12:37:22,827] [INFO] Task started: Blastn
[2024-01-24 12:37:22,827] [INFO] Running command: blastn -query GCF_013408985.1_ASM1340898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f43016-f698-4d85-a60f-272bf1b47dfb/dqc_reference/reference_markers.fasta -out GCF_013408985.1_ASM1340898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:24,168] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:24,173] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:24,174] [INFO] Target genome list was writen to GCF_013408985.1_ASM1340898v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:24,181] [INFO] Task started: fastANI
[2024-01-24 12:37:24,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f500e80-03ff-4b47-8f60-e38c0db97b4c/GCF_013408985.1_ASM1340898v1_genomic.fna.gz --refList GCF_013408985.1_ASM1340898v1_genomic.fna/target_genomes.txt --output GCF_013408985.1_ASM1340898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:44,129] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:44,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51f43016-f698-4d85-a60f-272bf1b47dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:44,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51f43016-f698-4d85-a60f-272bf1b47dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:44,141] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:44,141] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:44,141] [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
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	100.0	1792	1792	95	conclusive
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	83.159	1008	1792	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	83.1364	913	1792	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	83.1336	1040	1792	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	83.0427	1036	1792	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	83.009	1031	1792	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	82.9439	1042	1792	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	82.9333	917	1792	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	82.902	1000	1792	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	82.7977	1056	1792	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	82.7724	1019	1792	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.7572	1056	1792	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	82.3532	897	1792	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	82.2817	967	1792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:44,143] [INFO] DFAST Taxonomy check result was written to GCF_013408985.1_ASM1340898v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:44,144] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:44,144] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:44,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51f43016-f698-4d85-a60f-272bf1b47dfb/dqc_reference/checkm_data
[2024-01-24 12:37:44,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:44,195] [INFO] Task started: CheckM
[2024-01-24 12:37:44,195] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408985.1_ASM1340898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408985.1_ASM1340898v1_genomic.fna/checkm_input GCF_013408985.1_ASM1340898v1_genomic.fna/checkm_result
[2024-01-24 12:38:58,727] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:58,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:58,753] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:58,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:58,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408985.1_ASM1340898v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:58,755] [INFO] Task started: Blastn
[2024-01-24 12:38:58,755] [INFO] Running command: blastn -query GCF_013408985.1_ASM1340898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f43016-f698-4d85-a60f-272bf1b47dfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408985.1_ASM1340898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:00,870] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:00,874] [INFO] Selected 15 target genomes.
[2024-01-24 12:39:00,874] [INFO] Target genome list was writen to GCF_013408985.1_ASM1340898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:00,895] [INFO] Task started: fastANI
[2024-01-24 12:39:00,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f500e80-03ff-4b47-8f60-e38c0db97b4c/GCF_013408985.1_ASM1340898v1_genomic.fna.gz --refList GCF_013408985.1_ASM1340898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408985.1_ASM1340898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:21,409] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:21,425] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:21,425] [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_013408985.1	s__Geodermatophilus_A daqingensis	100.0	1792	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002802985.1	s__Geodermatophilus chilensis	83.1523	911	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570425.1	s__Blastococcus sp004570425	83.0743	924	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182485.1	s__Geodermatophilus normandii	83.0332	1035	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907675.1	s__Geodermatophilus bullaregiensis	82.976	1031	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104025.1	s__Geodermatophilus sp900104025	82.9746	986	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188205.1	s__Geodermatophilus saharensis	82.9089	1047	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	82.8803	923	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075095.1	s__Blastococcus litoris	82.7775	1058	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107105.1	s__Geodermatophilus africanus	82.7522	1020	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319125.1	s__Geodermatophilus sp003319125	82.6016	956	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109665.1	s__Blastococcus sp900109665	82.5797	929	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319105.1	s__Blastococcus sp003319105	82.4546	898	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284015.1	s__Blastococcus saxobsidens_A	82.2661	901	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717095.1	s__Blastococcus colisei	82.2363	972	1792	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:21,427] [INFO] GTDB search result was written to GCF_013408985.1_ASM1340898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:21,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:21,431] [INFO] DFAST_QC result json was written to GCF_013408985.1_ASM1340898v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:21,431] [INFO] DFAST_QC completed!
[2024-01-24 12:39:21,432] [INFO] Total running time: 0h2m14s