[2024-01-24 11:51:10,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8a340ef-fbe9-4f57-86f7-a7d1a26c29bb/dqc_reference
[2024-01-24 11:51:12,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,396] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,397] [INFO] Running command: gunzip -c /var/lib/cwl/stgd56cf313-bc46-4fae-8ab8-ce8bb99d5501/GCF_013410595.1_ASM1341059v1_genomic.fna.gz | prodigal -d GCF_013410595.1_ASM1341059v1_genomic.fna/cds.fna -a GCF_013410595.1_ASM1341059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:18,469] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:18,469] [INFO] Task started: HMMsearch
[2024-01-24 11:51:18,469] [INFO] Running command: hmmsearch --tblout GCF_013410595.1_ASM1341059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8a340ef-fbe9-4f57-86f7-a7d1a26c29bb/dqc_reference/reference_markers.hmm GCF_013410595.1_ASM1341059v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:18,756] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:18,758] [INFO] Found 6/6 markers.
[2024-01-24 11:51:18,794] [INFO] Query marker FASTA was written to GCF_013410595.1_ASM1341059v1_genomic.fna/markers.fasta
[2024-01-24 11:51:18,795] [INFO] Task started: Blastn
[2024-01-24 11:51:18,795] [INFO] Running command: blastn -query GCF_013410595.1_ASM1341059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8a340ef-fbe9-4f57-86f7-a7d1a26c29bb/dqc_reference/reference_markers.fasta -out GCF_013410595.1_ASM1341059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:20,014] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:20,021] [INFO] Selected 23 target genomes.
[2024-01-24 11:51:20,021] [INFO] Target genome list was writen to GCF_013410595.1_ASM1341059v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:20,031] [INFO] Task started: fastANI
[2024-01-24 11:51:20,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgd56cf313-bc46-4fae-8ab8-ce8bb99d5501/GCF_013410595.1_ASM1341059v1_genomic.fna.gz --refList GCF_013410595.1_ASM1341059v1_genomic.fna/target_genomes.txt --output GCF_013410595.1_ASM1341059v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:35,227] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:35,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8a340ef-fbe9-4f57-86f7-a7d1a26c29bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:35,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8a340ef-fbe9-4f57-86f7-a7d1a26c29bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:35,245] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:35,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:35,245] [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
Pseudoclavibacter caeni	strain=DSM 26484	GCA_013410595.1	908846	908846	type	True	100.0	689	690	95	conclusive
Pseudoclavibacter caeni	strain=JCM 16921	GCA_008831125.1	908846	908846	type	True	99.9918	678	690	95	conclusive
Pseudoclavibacter soli	strain=DSM 23366	GCA_000423505.1	452623	452623	type	True	78.7907	272	690	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	77.6392	201	690	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.5731	231	690	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	77.4968	189	690	95	below_threshold
Microbacterium paulum	strain=2C	GCA_015707995.1	2707006	2707006	type	True	77.4319	202	690	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	77.3977	214	690	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	77.3292	232	690	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	77.2564	212	690	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	77.2549	206	690	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	77.2476	260	690	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	77.2129	233	690	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	77.2106	186	690	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	77.15	225	690	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.0827	204	690	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	77.0667	212	690	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	77.0577	170	690	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	77.0454	221	690	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	77.0447	203	690	95	below_threshold
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	76.6759	72	690	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.2953	229	690	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.277	150	690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:35,254] [INFO] DFAST Taxonomy check result was written to GCF_013410595.1_ASM1341059v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:35,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:35,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:35,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8a340ef-fbe9-4f57-86f7-a7d1a26c29bb/dqc_reference/checkm_data
[2024-01-24 11:51:35,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:35,306] [INFO] Task started: CheckM
[2024-01-24 11:51:35,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410595.1_ASM1341059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410595.1_ASM1341059v1_genomic.fna/checkm_input GCF_013410595.1_ASM1341059v1_genomic.fna/checkm_result
[2024-01-24 11:52:06,346] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:06,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:06,368] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:06,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:06,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410595.1_ASM1341059v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:06,368] [INFO] Task started: Blastn
[2024-01-24 11:52:06,368] [INFO] Running command: blastn -query GCF_013410595.1_ASM1341059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8a340ef-fbe9-4f57-86f7-a7d1a26c29bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410595.1_ASM1341059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:08,127] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:08,132] [INFO] Selected 25 target genomes.
[2024-01-24 11:52:08,132] [INFO] Target genome list was writen to GCF_013410595.1_ASM1341059v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:08,164] [INFO] Task started: fastANI
[2024-01-24 11:52:08,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgd56cf313-bc46-4fae-8ab8-ce8bb99d5501/GCF_013410595.1_ASM1341059v1_genomic.fna.gz --refList GCF_013410595.1_ASM1341059v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410595.1_ASM1341059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:22,278] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:22,297] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:22,297] [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_008831125.1	s__Pseudoclavibacter_A caeni	99.9918	678	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008831235.1	s__Pseudoclavibacter_A sp008831235	79.6209	346	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter_A	95.0	97.03	96.49	0.85	0.83	4	-
GCF_000423505.1	s__Pseudoclavibacter_A soli	78.775	273	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634555.1	s__Frondihabitans australicus	77.8092	200	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910822395.1	s__Pseudoclavibacter sp910822395	77.7073	213	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200395.1	s__Chryseoglobus frigidaquae	77.5905	208	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016771945.1	s__Leucobacter sulfamidivorax	77.5108	203	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015707995.1	s__Microbacterium sp015707995	77.4027	204	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364555.1	s__Amnibacterium kyonggiense	77.3844	215	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355185.1	s__Rathayibacter sp017355185	77.377	201	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806325.1	s__Curtobacterium sp001806325	77.3761	209	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.12	98.02	0.92	0.92	4	-
GCF_003751785.1	s__Frigoribacterium sp003751785	77.3603	220	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044275.1	s__Rathayibacter caricis	77.3495	237	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	97.11	96.36	0.88	0.87	3	-
GCF_004959775.1	s__Agromyces sp004959775	77.3484	224	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484985.1	s__Agrococcus sp005484985	77.3451	234	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005490985.1	s__Curtobacterium oceanosedimentum	77.3241	218	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	95.58	95.49	0.91	0.91	3	-
GCF_009729855.1	s__Agromyces luteolus	77.2906	256	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645655.1	s__Agromyces bauzanensis	77.2304	208	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565705.1	s__Leucobacter ruminantium	77.2107	186	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069225.1	s__Clavibacter sepedonicus	77.1606	214	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
GCA_018268515.1	s__Microbacterium sp018268515	77.1257	193	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576185.1	s__Clavibacter phaseoli	77.1133	178	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	-
GCF_016522505.1	s__Leucobacter sp016522505	77.0204	205	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	76.6369	196	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708885.1	s__Cellulomonas sp000708885	76.4807	209	690	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:22,299] [INFO] GTDB search result was written to GCF_013410595.1_ASM1341059v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:22,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:22,304] [INFO] DFAST_QC result json was written to GCF_013410595.1_ASM1341059v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:22,304] [INFO] DFAST_QC completed!
[2024-01-24 11:52:22,304] [INFO] Total running time: 0h1m11s