[2024-01-24 12:31:33,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg972acfa2-81a5-4b7f-b1ee-e5d51e0ec883/dqc_reference
[2024-01-24 12:31:34,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:34,327] [INFO] Task started: Prodigal
[2024-01-24 12:31:34,328] [INFO] Running command: gunzip -c /var/lib/cwl/stgc310a69f-374e-4848-849c-586626d7ee67/GCF_030769565.1_ASM3076956v1_genomic.fna.gz | prodigal -d GCF_030769565.1_ASM3076956v1_genomic.fna/cds.fna -a GCF_030769565.1_ASM3076956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:43,336] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:43,337] [INFO] Task started: HMMsearch
[2024-01-24 12:31:43,337] [INFO] Running command: hmmsearch --tblout GCF_030769565.1_ASM3076956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg972acfa2-81a5-4b7f-b1ee-e5d51e0ec883/dqc_reference/reference_markers.hmm GCF_030769565.1_ASM3076956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:43,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:43,552] [INFO] Found 6/6 markers.
[2024-01-24 12:31:43,579] [INFO] Query marker FASTA was written to GCF_030769565.1_ASM3076956v1_genomic.fna/markers.fasta
[2024-01-24 12:31:43,579] [INFO] Task started: Blastn
[2024-01-24 12:31:43,579] [INFO] Running command: blastn -query GCF_030769565.1_ASM3076956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg972acfa2-81a5-4b7f-b1ee-e5d51e0ec883/dqc_reference/reference_markers.fasta -out GCF_030769565.1_ASM3076956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:44,205] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:44,209] [INFO] Selected 24 target genomes.
[2024-01-24 12:31:44,210] [INFO] Target genome list was writen to GCF_030769565.1_ASM3076956v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:44,218] [INFO] Task started: fastANI
[2024-01-24 12:31:44,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgc310a69f-374e-4848-849c-586626d7ee67/GCF_030769565.1_ASM3076956v1_genomic.fna.gz --refList GCF_030769565.1_ASM3076956v1_genomic.fna/target_genomes.txt --output GCF_030769565.1_ASM3076956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:56,622] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:56,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg972acfa2-81a5-4b7f-b1ee-e5d51e0ec883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:56,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg972acfa2-81a5-4b7f-b1ee-e5d51e0ec883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:56,634] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:56,634] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:56,634] [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
Methylophilus methylotrophus	strain=ATCC 53528	GCA_000378225.1	17	17	type	True	79.3192	404	963	95	below_threshold
Methylophilus rhizosphaerae	strain=CBMB127	GCA_900100975.1	492660	492660	type	True	79.1386	369	963	95	below_threshold
Methyloradius palustris	strain=Zm11	GCA_019703875.1	2778876	2778876	type	True	76.9109	79	963	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	76.8388	123	963	95	below_threshold
Methylotenera mobilis	strain=JLW8	GCA_000023705.1	359408	359408	type	True	76.7181	98	963	95	below_threshold
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	76.7142	140	963	95	below_threshold
Methylobacillus caricis	strain=VKM B-3158	GCA_020532705.1	1971611	1971611	type	True	76.6731	88	963	95	below_threshold
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	76.6576	81	963	95	below_threshold
Methylobacillus glycogenes	strain=JCM 2850	GCA_000617925.1	406	406	type	True	76.6124	96	963	95	below_threshold
Methylotenera versatilis	strain=301	GCA_000093025.1	1055487	1055487	type	True	76.5783	66	963	95	below_threshold
Methylobacillus gramineus	strain=VKM B-2591	GCA_020532675.1	755169	755169	type	True	76.5743	77	963	95	below_threshold
Methylobacillus methanolivorans	strain=VKM B-3037	GCA_020531845.1	1848927	1848927	type	True	76.4388	84	963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:56,636] [INFO] DFAST Taxonomy check result was written to GCF_030769565.1_ASM3076956v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:56,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:56,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:56,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg972acfa2-81a5-4b7f-b1ee-e5d51e0ec883/dqc_reference/checkm_data
[2024-01-24 12:31:56,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:56,668] [INFO] Task started: CheckM
[2024-01-24 12:31:56,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030769565.1_ASM3076956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030769565.1_ASM3076956v1_genomic.fna/checkm_input GCF_030769565.1_ASM3076956v1_genomic.fna/checkm_result
[2024-01-24 12:32:26,998] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:26,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:27,018] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:27,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:27,019] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030769565.1_ASM3076956v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:27,019] [INFO] Task started: Blastn
[2024-01-24 12:32:27,019] [INFO] Running command: blastn -query GCF_030769565.1_ASM3076956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg972acfa2-81a5-4b7f-b1ee-e5d51e0ec883/dqc_reference/reference_markers_gtdb.fasta -out GCF_030769565.1_ASM3076956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:27,969] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:27,972] [INFO] Selected 13 target genomes.
[2024-01-24 12:32:27,972] [INFO] Target genome list was writen to GCF_030769565.1_ASM3076956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:28,005] [INFO] Task started: fastANI
[2024-01-24 12:32:28,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgc310a69f-374e-4848-849c-586626d7ee67/GCF_030769565.1_ASM3076956v1_genomic.fna.gz --refList GCF_030769565.1_ASM3076956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030769565.1_ASM3076956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:35,214] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:35,224] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:32:35,225] [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_015354345.1	s__Methylophilus sp015354345	79.666	447	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354445.1	s__Methylophilus sp015354445	79.6492	437	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001183865.1	s__Methylophilus sp001183865	79.5162	435	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515275.1	s__Methylophilus sp000515275	79.5125	446	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384155.1	s__Methylophilus sp000384155	79.4396	434	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	97.28	96.56	0.94	0.91	6	-
GCF_015354335.1	s__Methylophilus sp015354335	79.4094	427	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015755.1	s__Methylophilus sp008015755	79.3321	414	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100975.1	s__Methylophilus rhizosphaerae	79.1386	369	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424665.1	s__Methylophilus sp001424665	78.8737	384	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	98.77	97.54	0.97	0.93	3	-
GCF_006363955.1	s__Methylophilus medardicus	78.7547	335	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylophilus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000799165.1	s__Methylotenera_A versatilis_A	76.933	96	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281815.1	s__Methylotenera sp002281815	76.9195	92	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylotenera	95.0	99.58	99.54	0.87	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:35,227] [INFO] GTDB search result was written to GCF_030769565.1_ASM3076956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:35,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:35,231] [INFO] DFAST_QC result json was written to GCF_030769565.1_ASM3076956v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:35,232] [INFO] DFAST_QC completed!
[2024-01-24 12:32:35,232] [INFO] Total running time: 0h1m2s