[2023-06-17 02:02:16,318] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:02:16,325] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:02:16,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg86068011-a9ce-443d-8035-42c4c8ba76e9/dqc_reference
[2023-06-17 02:02:18,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:02:18,549] [INFO] Task started: Prodigal
[2023-06-17 02:02:18,550] [INFO] Running command: gunzip -c /var/lib/cwl/stg62289e9f-51dd-4b62-a979-cd086e84fa8f/GCA_028291765.1_ASM2829176v1_genomic.fna.gz | prodigal -d GCA_028291765.1_ASM2829176v1_genomic.fna/cds.fna -a GCA_028291765.1_ASM2829176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:02:31,601] [INFO] Task succeeded: Prodigal
[2023-06-17 02:02:31,601] [INFO] Task started: HMMsearch
[2023-06-17 02:02:31,602] [INFO] Running command: hmmsearch --tblout GCA_028291765.1_ASM2829176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86068011-a9ce-443d-8035-42c4c8ba76e9/dqc_reference/reference_markers.hmm GCA_028291765.1_ASM2829176v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:02:31,891] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:02:31,893] [INFO] Found 6/6 markers.
[2023-06-17 02:02:31,940] [INFO] Query marker FASTA was written to GCA_028291765.1_ASM2829176v1_genomic.fna/markers.fasta
[2023-06-17 02:02:31,941] [INFO] Task started: Blastn
[2023-06-17 02:02:31,941] [INFO] Running command: blastn -query GCA_028291765.1_ASM2829176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86068011-a9ce-443d-8035-42c4c8ba76e9/dqc_reference/reference_markers.fasta -out GCA_028291765.1_ASM2829176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:02:32,726] [INFO] Task succeeded: Blastn
[2023-06-17 02:02:32,730] [INFO] Selected 19 target genomes.
[2023-06-17 02:02:32,731] [INFO] Target genome list was writen to GCA_028291765.1_ASM2829176v1_genomic.fna/target_genomes.txt
[2023-06-17 02:02:32,736] [INFO] Task started: fastANI
[2023-06-17 02:02:32,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg62289e9f-51dd-4b62-a979-cd086e84fa8f/GCA_028291765.1_ASM2829176v1_genomic.fna.gz --refList GCA_028291765.1_ASM2829176v1_genomic.fna/target_genomes.txt --output GCA_028291765.1_ASM2829176v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:02:48,453] [INFO] Task succeeded: fastANI
[2023-06-17 02:02:48,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86068011-a9ce-443d-8035-42c4c8ba76e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:02:48,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86068011-a9ce-443d-8035-42c4c8ba76e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:02:48,475] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:02:48,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 02:02:48,475] [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
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	78.4513	363	1397	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	78.336	324	1397	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	78.3268	393	1397	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	78.3255	337	1397	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	78.295	356	1397	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	78.2057	335	1397	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	78.1757	325	1397	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	78.1461	346	1397	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	78.1384	297	1397	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	78.053	295	1397	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	77.7527	236	1397	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	77.6269	204	1397	95	below_threshold
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	77.6168	204	1397	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	77.3097	285	1397	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	77.2239	230	1397	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	77.0369	268	1397	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	76.9693	262	1397	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.8255	245	1397	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.8016	210	1397	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 02:02:48,477] [INFO] DFAST Taxonomy check result was written to GCA_028291765.1_ASM2829176v1_genomic.fna/tc_result.tsv
[2023-06-17 02:02:48,478] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:02:48,478] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:02:48,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86068011-a9ce-443d-8035-42c4c8ba76e9/dqc_reference/checkm_data
[2023-06-17 02:02:48,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:02:48,530] [INFO] Task started: CheckM
[2023-06-17 02:02:48,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028291765.1_ASM2829176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028291765.1_ASM2829176v1_genomic.fna/checkm_input GCA_028291765.1_ASM2829176v1_genomic.fna/checkm_result
[2023-06-17 02:03:29,368] [INFO] Task succeeded: CheckM
[2023-06-17 02:03:29,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:03:29,392] [INFO] ===== Completeness check finished =====
[2023-06-17 02:03:29,393] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:03:29,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028291765.1_ASM2829176v1_genomic.fna/markers.fasta)
[2023-06-17 02:03:29,393] [INFO] Task started: Blastn
[2023-06-17 02:03:29,394] [INFO] Running command: blastn -query GCA_028291765.1_ASM2829176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86068011-a9ce-443d-8035-42c4c8ba76e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_028291765.1_ASM2829176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:03:30,752] [INFO] Task succeeded: Blastn
[2023-06-17 02:03:30,758] [INFO] Selected 20 target genomes.
[2023-06-17 02:03:30,758] [INFO] Target genome list was writen to GCA_028291765.1_ASM2829176v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:03:30,773] [INFO] Task started: fastANI
[2023-06-17 02:03:30,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg62289e9f-51dd-4b62-a979-cd086e84fa8f/GCA_028291765.1_ASM2829176v1_genomic.fna.gz --refList GCA_028291765.1_ASM2829176v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028291765.1_ASM2829176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:03:46,982] [INFO] Task succeeded: fastANI
[2023-06-17 02:03:47,003] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 02:03:47,003] [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
GCA_004134995.1	s__Herbaspirillum sp004134995	81.3981	782	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267925.1	s__Herbaspirillum hiltneri	78.4294	365	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.60	97.60	0.89	0.89	2	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	78.3268	393	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000256565.1	s__Herbaspirillum lusitanum	78.3255	337	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	78.3238	325	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_900112135.1	s__Collimonas sp900112135	78.2868	331	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_000282135.1	s__Herbaspirillum sp000282135	78.262	378	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107095.1	s__Collimonas sp900107095	78.2568	304	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577615.1	s__Herbaspirillum sp000577615	78.2123	378	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113705.1	s__Collimonas sp900113705	78.2026	292	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000221045.1	s__Collimonas fungivorans_A	78.2025	333	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_018305005.1	s__Collimonas sp018305005	78.1572	326	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564105.1	s__Collimonas sp002564105	78.1522	344	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018304945.1	s__Collimonas sp018304945	78.1461	346	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_001584165.1	s__Collimonas arenae	78.0528	295	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	99.97	99.97	1.00	1.00	2	-
GCA_002415335.1	s__UBA5157 sp002415335	77.5007	200	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA5157	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114795.1	s__Paucimonas sp004114795	77.3696	197	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365165.1	s__CAILRJ01 sp010365165	77.2019	188	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836575.1	s__CAILRJ01 sp903836575	76.9991	169	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:03:47,006] [INFO] GTDB search result was written to GCA_028291765.1_ASM2829176v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:03:47,007] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:03:47,014] [INFO] DFAST_QC result json was written to GCA_028291765.1_ASM2829176v1_genomic.fna/dqc_result.json
[2023-06-17 02:03:47,015] [INFO] DFAST_QC completed!
[2023-06-17 02:03:47,015] [INFO] Total running time: 0h1m31s