[2024-01-24 15:06:36,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,732] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7f37cbc-5413-4ddc-aea3-9884273d7ba4/dqc_reference
[2024-01-24 15:06:38,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,057] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,057] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8f9c03a-4030-4f44-bc4b-3d48c90a1b0b/GCF_008632455.1_ASM863245v1_genomic.fna.gz | prodigal -d GCF_008632455.1_ASM863245v1_genomic.fna/cds.fna -a GCF_008632455.1_ASM863245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:07:00,403] [INFO] Task succeeded: Prodigal
[2024-01-24 15:07:00,403] [INFO] Task started: HMMsearch
[2024-01-24 15:07:00,404] [INFO] Running command: hmmsearch --tblout GCF_008632455.1_ASM863245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7f37cbc-5413-4ddc-aea3-9884273d7ba4/dqc_reference/reference_markers.hmm GCF_008632455.1_ASM863245v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:07:00,704] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:07:00,706] [INFO] Found 6/6 markers.
[2024-01-24 15:07:00,763] [INFO] Query marker FASTA was written to GCF_008632455.1_ASM863245v1_genomic.fna/markers.fasta
[2024-01-24 15:07:00,764] [INFO] Task started: Blastn
[2024-01-24 15:07:00,764] [INFO] Running command: blastn -query GCF_008632455.1_ASM863245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7f37cbc-5413-4ddc-aea3-9884273d7ba4/dqc_reference/reference_markers.fasta -out GCF_008632455.1_ASM863245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:01,529] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:01,532] [INFO] Selected 22 target genomes.
[2024-01-24 15:07:01,533] [INFO] Target genome list was writen to GCF_008632455.1_ASM863245v1_genomic.fna/target_genomes.txt
[2024-01-24 15:07:01,558] [INFO] Task started: fastANI
[2024-01-24 15:07:01,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8f9c03a-4030-4f44-bc4b-3d48c90a1b0b/GCF_008632455.1_ASM863245v1_genomic.fna.gz --refList GCF_008632455.1_ASM863245v1_genomic.fna/target_genomes.txt --output GCF_008632455.1_ASM863245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:19,134] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:19,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7f37cbc-5413-4ddc-aea3-9884273d7ba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:19,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7f37cbc-5413-4ddc-aea3-9884273d7ba4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:19,144] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:19,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:19,144] [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
Methylomonas rhizoryzae	strain=GJ1	GCA_008632455.1	2608981	2608981	type	True	100.0	1518	1518	95	conclusive
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	79.062	415	1518	95	below_threshold
Methylomonas koyamae	strain=JCM 16701	GCA_001312005.1	702114	702114	suspected-type	True	78.8552	384	1518	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	78.233	286	1518	95	below_threshold
Methylomonas denitrificans	strain=FJG1	GCA_000785705.2	1538553	1538553	type	True	78.1969	349	1518	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	77.514	142	1518	95	below_threshold
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	77.2774	107	1518	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	76.9049	129	1518	95	below_threshold
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	76.5741	128	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:19,147] [INFO] DFAST Taxonomy check result was written to GCF_008632455.1_ASM863245v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:19,148] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:19,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:19,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7f37cbc-5413-4ddc-aea3-9884273d7ba4/dqc_reference/checkm_data
[2024-01-24 15:07:19,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:19,198] [INFO] Task started: CheckM
[2024-01-24 15:07:19,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008632455.1_ASM863245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008632455.1_ASM863245v1_genomic.fna/checkm_input GCF_008632455.1_ASM863245v1_genomic.fna/checkm_result
[2024-01-24 15:08:17,362] [INFO] Task succeeded: CheckM
[2024-01-24 15:08:17,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:08:17,410] [INFO] ===== Completeness check finished =====
[2024-01-24 15:08:17,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:08:17,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008632455.1_ASM863245v1_genomic.fna/markers.fasta)
[2024-01-24 15:08:17,411] [INFO] Task started: Blastn
[2024-01-24 15:08:17,411] [INFO] Running command: blastn -query GCF_008632455.1_ASM863245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7f37cbc-5413-4ddc-aea3-9884273d7ba4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008632455.1_ASM863245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:08:18,635] [INFO] Task succeeded: Blastn
[2024-01-24 15:08:18,643] [INFO] Selected 17 target genomes.
[2024-01-24 15:08:18,643] [INFO] Target genome list was writen to GCF_008632455.1_ASM863245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:08:18,689] [INFO] Task started: fastANI
[2024-01-24 15:08:18,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8f9c03a-4030-4f44-bc4b-3d48c90a1b0b/GCF_008632455.1_ASM863245v1_genomic.fna.gz --refList GCF_008632455.1_ASM863245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008632455.1_ASM863245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:32,341] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:32,367] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:32,367] [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_008632455.1	s__Methylomonas rhizoryzae	100.0	1516	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006483455.1	s__Methylomonas koyamae_B	79.4813	363	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001312005.1	s__Methylomonas koyamae	78.8554	384	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	96.46	95.49	0.87	0.86	5	-
GCF_016865255.1	s__Methylomonas sp000702925	78.5037	361	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	97.47	95.82	0.92	0.86	5	-
GCF_001644025.1	s__Methylomonas koyamae_A	78.468	392	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	97.40	97.36	0.85	0.85	3	-
GCA_018335995.1	s__Methylomonas sp018335995	78.3321	322	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711015.1	s__Methylomonas sp015711015	78.3259	394	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214665.1	s__Methylomonas methanica_B	78.2796	367	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903064685.1	s__Methylomonas sp903064685	78.2597	341	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_903064715.1	s__Methylomonas sp903064715	78.2447	284	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001644035.1	s__Methylomonas methanica_A	78.2426	331	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.96	95.96	0.85	0.85	2	-
GCA_002929135.1	s__Methylomonas sp002929135	78.0243	211	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.96	99.88	0.95	0.87	5	-
GCA_002928965.1	s__Methylomonas sp002928965	77.4422	234	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002928495.1	s__WM-3-3 sp002928495	76.618	66	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__WM-3-3	95.0	99.37	99.07	0.68	0.63	4	-
GCA_903858105.1	s__Methylomonas sp903858105	76.6107	165	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902945.1	s__Methylomonas sp903902945	76.5498	121	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:08:32,369] [INFO] GTDB search result was written to GCF_008632455.1_ASM863245v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:32,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:32,373] [INFO] DFAST_QC result json was written to GCF_008632455.1_ASM863245v1_genomic.fna/dqc_result.json
[2024-01-24 15:08:32,373] [INFO] DFAST_QC completed!
[2024-01-24 15:08:32,374] [INFO] Total running time: 0h1m56s