[2024-01-24 14:55:51,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg2749ca7a-59a1-487c-81ce-fcbca98eb7ed/dqc_reference
[2024-01-24 14:55:52,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,539] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,540] [INFO] Running command: gunzip -c /var/lib/cwl/stgac0d89e3-6635-416f-b581-515d9232dab7/GCF_002933035.1_ASM293303v1_genomic.fna.gz | prodigal -d GCF_002933035.1_ASM293303v1_genomic.fna/cds.fna -a GCF_002933035.1_ASM293303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:01,877] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:01,878] [INFO] Task started: HMMsearch
[2024-01-24 14:56:01,878] [INFO] Running command: hmmsearch --tblout GCF_002933035.1_ASM293303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2749ca7a-59a1-487c-81ce-fcbca98eb7ed/dqc_reference/reference_markers.hmm GCF_002933035.1_ASM293303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:02,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:02,199] [INFO] Found 6/6 markers.
[2024-01-24 14:56:02,233] [INFO] Query marker FASTA was written to GCF_002933035.1_ASM293303v1_genomic.fna/markers.fasta
[2024-01-24 14:56:02,233] [INFO] Task started: Blastn
[2024-01-24 14:56:02,233] [INFO] Running command: blastn -query GCF_002933035.1_ASM293303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2749ca7a-59a1-487c-81ce-fcbca98eb7ed/dqc_reference/reference_markers.fasta -out GCF_002933035.1_ASM293303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:03,293] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:03,297] [INFO] Selected 13 target genomes.
[2024-01-24 14:56:03,298] [INFO] Target genome list was writen to GCF_002933035.1_ASM293303v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:03,303] [INFO] Task started: fastANI
[2024-01-24 14:56:03,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgac0d89e3-6635-416f-b581-515d9232dab7/GCF_002933035.1_ASM293303v1_genomic.fna.gz --refList GCF_002933035.1_ASM293303v1_genomic.fna/target_genomes.txt --output GCF_002933035.1_ASM293303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:13,210] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:13,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2749ca7a-59a1-487c-81ce-fcbca98eb7ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:13,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2749ca7a-59a1-487c-81ce-fcbca98eb7ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:13,223] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:56:13,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:13,224] [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
Rathayibacter iranicus	strain=DSM 7484	GCA_002933035.1	59737	59737	type	True	100.0	1094	1096	95	conclusive
Rathayibacter iranicus	strain=VKM Ac-1602	GCA_003149025.1	59737	59737	type	True	99.9966	1082	1096	95	conclusive
Rathayibacter iranicus	strain=VKM Ac-1602	GCA_009806955.1	59737	59737	type	True	99.9954	1079	1096	95	conclusive
Rathayibacter agropyri	strain=VKM Ac-2828	GCA_013249015.1	1634927	1634927	type	True	89.9557	889	1096	95	below_threshold
Rathayibacter tritici	strain=DSM 7486	GCA_002932875.1	33888	33888	type	True	84.5701	760	1096	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	84.2754	650	1096	95	below_threshold
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_900215645.1	33887	33887	type	True	84.2259	758	1096	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_004340625.1	1671680	1671680	type	True	84.1763	747	1096	95	below_threshold
Rathayibacter oskolensis	strain=VKM Ac-2121	GCA_900177245.1	1891671	1891671	type	True	82.8247	707	1096	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3801	326	1096	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.3003	280	1096	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.1115	296	1096	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.0605	289	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:13,227] [INFO] DFAST Taxonomy check result was written to GCF_002933035.1_ASM293303v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:13,228] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:13,228] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:13,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2749ca7a-59a1-487c-81ce-fcbca98eb7ed/dqc_reference/checkm_data
[2024-01-24 14:56:13,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:13,265] [INFO] Task started: CheckM
[2024-01-24 14:56:13,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002933035.1_ASM293303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002933035.1_ASM293303v1_genomic.fna/checkm_input GCF_002933035.1_ASM293303v1_genomic.fna/checkm_result
[2024-01-24 14:56:44,641] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:44,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:44,657] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:44,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:44,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002933035.1_ASM293303v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:44,658] [INFO] Task started: Blastn
[2024-01-24 14:56:44,658] [INFO] Running command: blastn -query GCF_002933035.1_ASM293303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2749ca7a-59a1-487c-81ce-fcbca98eb7ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_002933035.1_ASM293303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:46,247] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:46,251] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:46,251] [INFO] Target genome list was writen to GCF_002933035.1_ASM293303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:46,264] [INFO] Task started: fastANI
[2024-01-24 14:56:46,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgac0d89e3-6635-416f-b581-515d9232dab7/GCF_002933035.1_ASM293303v1_genomic.fna.gz --refList GCF_002933035.1_ASM293303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002933035.1_ASM293303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:56,016] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:56,033] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:56,034] [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_003149025.1	s__Rathayibacter iranicus	99.9966	1082	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.96	99.91	0.99	0.99	6	conclusive
GCF_013249015.1	s__Rathayibacter agropyri	89.9557	889	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866585.1	s__Rathayibacter sp002930885	85.0206	758	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.23	95.98	0.89	0.85	55	-
GCF_002932875.1	s__Rathayibacter tritici	84.5699	760	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.66	99.47	0.96	0.94	6	-
GCF_001634385.1	s__Rathayibacter tanaceti	84.276	650	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.97	99.97	1.00	1.00	3	-
GCF_004011095.1	s__Rathayibacter rathayi	84.2451	762	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.62	99.25	0.95	0.91	27	-
GCF_009866655.1	s__Rathayibacter sp009866655	83.3803	718	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_009834225.1	s__Rathayibacter sp009834225	83.3343	702	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205025.1	s__Rathayibacter sp013205025	83.319	724	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834185.1	s__Rathayibacter sp009834185	83.2866	730	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807095.1	s__Rathayibacter sp009807095	83.2066	689	1096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.31	99.31	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:56,035] [INFO] GTDB search result was written to GCF_002933035.1_ASM293303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:56,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:56,040] [INFO] DFAST_QC result json was written to GCF_002933035.1_ASM293303v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:56,040] [INFO] DFAST_QC completed!
[2024-01-24 14:56:56,040] [INFO] Total running time: 0h1m5s