[2024-01-25 20:20:05,632] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg91c4c9f5-2a2a-4762-a54f-87180787fabf/dqc_reference
[2024-01-25 20:20:06,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:06,868] [INFO] Task started: Prodigal
[2024-01-25 20:20:06,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg16aae631-86d9-4f09-bee7-d2a8ca9909d1/GCF_013249015.1_ASM1324901v1_genomic.fna.gz | prodigal -d GCF_013249015.1_ASM1324901v1_genomic.fna/cds.fna -a GCF_013249015.1_ASM1324901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:14,368] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:14,368] [INFO] Task started: HMMsearch
[2024-01-25 20:20:14,368] [INFO] Running command: hmmsearch --tblout GCF_013249015.1_ASM1324901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91c4c9f5-2a2a-4762-a54f-87180787fabf/dqc_reference/reference_markers.hmm GCF_013249015.1_ASM1324901v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:14,568] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:14,569] [INFO] Found 6/6 markers.
[2024-01-25 20:20:14,593] [INFO] Query marker FASTA was written to GCF_013249015.1_ASM1324901v1_genomic.fna/markers.fasta
[2024-01-25 20:20:14,593] [INFO] Task started: Blastn
[2024-01-25 20:20:14,593] [INFO] Running command: blastn -query GCF_013249015.1_ASM1324901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91c4c9f5-2a2a-4762-a54f-87180787fabf/dqc_reference/reference_markers.fasta -out GCF_013249015.1_ASM1324901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:15,642] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:15,645] [INFO] Selected 13 target genomes.
[2024-01-25 20:20:15,645] [INFO] Target genome list was writen to GCF_013249015.1_ASM1324901v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:15,660] [INFO] Task started: fastANI
[2024-01-25 20:20:15,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg16aae631-86d9-4f09-bee7-d2a8ca9909d1/GCF_013249015.1_ASM1324901v1_genomic.fna.gz --refList GCF_013249015.1_ASM1324901v1_genomic.fna/target_genomes.txt --output GCF_013249015.1_ASM1324901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:25,559] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:25,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91c4c9f5-2a2a-4762-a54f-87180787fabf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:25,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91c4c9f5-2a2a-4762-a54f-87180787fabf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:25,568] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:25,568] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:25,568] [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 agropyri	strain=VKM Ac-2828	GCA_013249015.1	1634927	1634927	type	True	100.0	1003	1003	95	conclusive
Rathayibacter iranicus	strain=VKM Ac-1602	GCA_009806955.1	59737	59737	type	True	90.1164	874	1003	95	below_threshold
Rathayibacter iranicus	strain=VKM Ac-1602	GCA_003149025.1	59737	59737	type	True	90.1092	877	1003	95	below_threshold
Rathayibacter iranicus	strain=DSM 7484	GCA_002933035.1	59737	59737	type	True	89.9909	875	1003	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	85.0755	662	1003	95	below_threshold
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_900215645.1	33887	33887	type	True	84.633	769	1003	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	84.1143	754	1003	95	below_threshold
Rathayibacter oskolensis	strain=VKM Ac-2121	GCA_900177245.1	1891671	1891671	type	True	83.5836	722	1003	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	83.5689	716	1003	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.5507	374	1003	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.5219	278	1003	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.4932	351	1003	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.1953	315	1003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:25,570] [INFO] DFAST Taxonomy check result was written to GCF_013249015.1_ASM1324901v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:25,570] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:25,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:25,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91c4c9f5-2a2a-4762-a54f-87180787fabf/dqc_reference/checkm_data
[2024-01-25 20:20:25,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:25,603] [INFO] Task started: CheckM
[2024-01-25 20:20:25,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013249015.1_ASM1324901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013249015.1_ASM1324901v1_genomic.fna/checkm_input GCF_013249015.1_ASM1324901v1_genomic.fna/checkm_result
[2024-01-25 20:20:51,189] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:51,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:51,208] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:51,208] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:51,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013249015.1_ASM1324901v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:51,208] [INFO] Task started: Blastn
[2024-01-25 20:20:51,209] [INFO] Running command: blastn -query GCF_013249015.1_ASM1324901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91c4c9f5-2a2a-4762-a54f-87180787fabf/dqc_reference/reference_markers_gtdb.fasta -out GCF_013249015.1_ASM1324901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:52,989] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:52,992] [INFO] Selected 14 target genomes.
[2024-01-25 20:20:52,992] [INFO] Target genome list was writen to GCF_013249015.1_ASM1324901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:53,017] [INFO] Task started: fastANI
[2024-01-25 20:20:53,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg16aae631-86d9-4f09-bee7-d2a8ca9909d1/GCF_013249015.1_ASM1324901v1_genomic.fna.gz --refList GCF_013249015.1_ASM1324901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013249015.1_ASM1324901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:04,456] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:04,470] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:04,470] [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_013249015.1	s__Rathayibacter agropyri	100.0	1003	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003149025.1	s__Rathayibacter iranicus	90.1092	877	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.96	99.91	0.99	0.99	6	-
GCF_009866585.1	s__Rathayibacter sp002930885	85.9626	779	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.23	95.98	0.89	0.85	55	-
GCF_001634385.1	s__Rathayibacter tanaceti	85.0915	661	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.97	99.97	1.00	1.00	3	-
GCF_002932875.1	s__Rathayibacter tritici	84.9407	774	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.66	99.47	0.96	0.94	6	-
GCF_004011095.1	s__Rathayibacter rathayi	84.6702	775	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.62	99.25	0.95	0.91	27	-
GCF_009834185.1	s__Rathayibacter sp009834185	84.2912	726	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866655.1	s__Rathayibacter sp009866655	84.1819	728	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_004011135.1	s__Rathayibacter festucae	84.1177	754	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	96.98	96.51	0.89	0.87	11	-
GCF_009834225.1	s__Rathayibacter sp009834225	84.0429	720	1003	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	83.7535	718	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.31	99.31	0.97	0.97	2	-
GCF_001995175.1	s__Rathayibacter sp001995175	83.691	683	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044275.1	s__Rathayibacter caricis	83.5626	718	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	97.11	96.36	0.88	0.87	3	-
GCF_017355185.1	s__Rathayibacter sp017355185	83.546	656	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:04,473] [INFO] GTDB search result was written to GCF_013249015.1_ASM1324901v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:04,473] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:04,477] [INFO] DFAST_QC result json was written to GCF_013249015.1_ASM1324901v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:04,478] [INFO] DFAST_QC completed!
[2024-01-25 20:21:04,478] [INFO] Total running time: 0h0m59s