[2024-01-24 14:39:01,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg5440851c-72d0-42a2-b373-93dbf2096999/dqc_reference
[2024-01-24 14:39:04,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,243] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg303d192b-9f5a-46fe-9687-ec9d275aeb2e/GCF_014770185.1_ASM1477018v1_genomic.fna.gz | prodigal -d GCF_014770185.1_ASM1477018v1_genomic.fna/cds.fna -a GCF_014770185.1_ASM1477018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:11,173] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:11,174] [INFO] Task started: HMMsearch
[2024-01-24 14:39:11,174] [INFO] Running command: hmmsearch --tblout GCF_014770185.1_ASM1477018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5440851c-72d0-42a2-b373-93dbf2096999/dqc_reference/reference_markers.hmm GCF_014770185.1_ASM1477018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:11,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:11,365] [INFO] Found 6/6 markers.
[2024-01-24 14:39:11,392] [INFO] Query marker FASTA was written to GCF_014770185.1_ASM1477018v1_genomic.fna/markers.fasta
[2024-01-24 14:39:11,392] [INFO] Task started: Blastn
[2024-01-24 14:39:11,392] [INFO] Running command: blastn -query GCF_014770185.1_ASM1477018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5440851c-72d0-42a2-b373-93dbf2096999/dqc_reference/reference_markers.fasta -out GCF_014770185.1_ASM1477018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:12,106] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:12,109] [INFO] Selected 19 target genomes.
[2024-01-24 14:39:12,109] [INFO] Target genome list was writen to GCF_014770185.1_ASM1477018v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:12,123] [INFO] Task started: fastANI
[2024-01-24 14:39:12,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg303d192b-9f5a-46fe-9687-ec9d275aeb2e/GCF_014770185.1_ASM1477018v1_genomic.fna.gz --refList GCF_014770185.1_ASM1477018v1_genomic.fna/target_genomes.txt --output GCF_014770185.1_ASM1477018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:23,184] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:23,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5440851c-72d0-42a2-b373-93dbf2096999/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:23,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5440851c-72d0-42a2-b373-93dbf2096999/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:23,198] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:23,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:23,198] [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 toxicus	strain=FH79	GCA_014770185.1	145458	145458	type	True	100.0	781	781	95	conclusive
Rathayibacter toxicus	strain=DSM 7488	GCA_000425325.1	145458	145458	type	True	99.7199	736	781	95	conclusive
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.2644	321	781	95	below_threshold
Rathayibacter caricis	strain=DSM 15933	GCA_003044275.1	110936	110936	type	True	79.0635	314	781	95	below_threshold
Rathayibacter oskolensis	strain=VKM Ac-2121	GCA_900177245.1	1891671	1891671	type	True	78.8474	317	781	95	below_threshold
Rathayibacter agropyri	strain=VKM Ac-2828	GCA_013249015.1	1634927	1634927	type	True	78.761	290	781	95	below_threshold
Rathayibacter tritici	strain=DSM 7486	GCA_002932875.1	33888	33888	type	True	78.7063	302	781	95	below_threshold
Rathayibacter iranicus	strain=VKM Ac-1602	GCA_003149025.1	59737	59737	type	True	78.5855	301	781	95	below_threshold
Rathayibacter rathayi	strain=VKM Ac-1601	GCA_900215645.1	33887	33887	type	True	78.501	315	781	95	below_threshold
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	77.6235	84	781	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	77.5719	111	781	95	below_threshold
Salinibacterium xinjiangense	strain=CGMCC 1.05381	GCA_900230175.1	386302	386302	type	True	77.199	58	781	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	77.158	112	781	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	77.1243	80	781	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	77.0667	77	781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:23,200] [INFO] DFAST Taxonomy check result was written to GCF_014770185.1_ASM1477018v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:23,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:23,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:23,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5440851c-72d0-42a2-b373-93dbf2096999/dqc_reference/checkm_data
[2024-01-24 14:39:23,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:23,230] [INFO] Task started: CheckM
[2024-01-24 14:39:23,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014770185.1_ASM1477018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014770185.1_ASM1477018v1_genomic.fna/checkm_input GCF_014770185.1_ASM1477018v1_genomic.fna/checkm_result
[2024-01-24 14:39:48,895] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:48,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:48,916] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:48,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:48,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014770185.1_ASM1477018v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:48,917] [INFO] Task started: Blastn
[2024-01-24 14:39:48,917] [INFO] Running command: blastn -query GCF_014770185.1_ASM1477018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5440851c-72d0-42a2-b373-93dbf2096999/dqc_reference/reference_markers_gtdb.fasta -out GCF_014770185.1_ASM1477018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:49,969] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:49,973] [INFO] Selected 20 target genomes.
[2024-01-24 14:39:49,973] [INFO] Target genome list was writen to GCF_014770185.1_ASM1477018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:49,987] [INFO] Task started: fastANI
[2024-01-24 14:39:49,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg303d192b-9f5a-46fe-9687-ec9d275aeb2e/GCF_014770185.1_ASM1477018v1_genomic.fna.gz --refList GCF_014770185.1_ASM1477018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014770185.1_ASM1477018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:02,870] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:02,889] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:02,889] [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_000425325.1	s__Rathayibacter toxicus	99.7196	735	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.73	99.47	0.99	0.98	40	conclusive
GCF_004011135.1	s__Rathayibacter festucae	79.2162	320	781	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	79.1886	328	781	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	79.1406	313	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	97.11	96.36	0.88	0.87	3	-
GCF_013205025.1	s__Rathayibacter sp013205025	79.0777	319	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013205055.1	s__Rathayibacter sp013205055	79.0693	320	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009866655.1	s__Rathayibacter sp009866655	79.0484	325	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.89	98.89	0.92	0.92	2	-
GCF_009866585.1	s__Rathayibacter sp002930885	78.9253	330	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	98.23	95.98	0.89	0.85	55	-
GCF_015351245.1	s__Rathayibacter sp015351245	78.9003	315	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177245.1	s__Rathayibacter oskolensis	78.869	316	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423885.1	s__Rathayibacter sp001423885	78.8669	325	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001995175.1	s__Rathayibacter sp001995175	78.8055	309	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249015.1	s__Rathayibacter agropyri	78.7758	289	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002932875.1	s__Rathayibacter tritici	78.694	303	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.66	99.47	0.96	0.94	6	-
GCF_017355185.1	s__Rathayibacter sp017355185	78.689	295	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149025.1	s__Rathayibacter iranicus	78.6119	299	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	99.96	99.91	0.99	0.99	6	-
GCF_003990045.1	s__Labedella endophytica	77.6235	84	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423695.1	s__Leifsonia sp001423695	77.2875	126	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565305.1	s__Leifsonia sp017565305	77.1006	120	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	97.25	97.25	0.89	0.89	2	-
GCF_004216815.1	s__Protaetiibacter sp004216815	76.8789	96	781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:02,892] [INFO] GTDB search result was written to GCF_014770185.1_ASM1477018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:02,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:02,898] [INFO] DFAST_QC result json was written to GCF_014770185.1_ASM1477018v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:02,898] [INFO] DFAST_QC completed!
[2024-01-24 14:40:02,899] [INFO] Total running time: 0h1m1s