[2024-01-24 12:42:09,598] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,602] [INFO] DQC Reference Directory: /var/lib/cwl/stgc724a747-2a77-48cd-9949-a0fcc335b825/dqc_reference
[2024-01-24 12:42:10,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,917] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,917] [INFO] Running command: gunzip -c /var/lib/cwl/stge87dcfa0-fb7c-43c3-a559-54fea323cc6a/GCF_030161035.1_ASM3016103v1_genomic.fna.gz | prodigal -d GCF_030161035.1_ASM3016103v1_genomic.fna/cds.fna -a GCF_030161035.1_ASM3016103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:23,526] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:23,526] [INFO] Task started: HMMsearch
[2024-01-24 12:42:23,526] [INFO] Running command: hmmsearch --tblout GCF_030161035.1_ASM3016103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc724a747-2a77-48cd-9949-a0fcc335b825/dqc_reference/reference_markers.hmm GCF_030161035.1_ASM3016103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:23,829] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:23,830] [INFO] Found 6/6 markers.
[2024-01-24 12:42:23,872] [INFO] Query marker FASTA was written to GCF_030161035.1_ASM3016103v1_genomic.fna/markers.fasta
[2024-01-24 12:42:23,872] [INFO] Task started: Blastn
[2024-01-24 12:42:23,872] [INFO] Running command: blastn -query GCF_030161035.1_ASM3016103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc724a747-2a77-48cd-9949-a0fcc335b825/dqc_reference/reference_markers.fasta -out GCF_030161035.1_ASM3016103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:25,035] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:25,039] [INFO] Selected 13 target genomes.
[2024-01-24 12:42:25,039] [INFO] Target genome list was writen to GCF_030161035.1_ASM3016103v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:25,042] [INFO] Task started: fastANI
[2024-01-24 12:42:25,042] [INFO] Running command: fastANI --query /var/lib/cwl/stge87dcfa0-fb7c-43c3-a559-54fea323cc6a/GCF_030161035.1_ASM3016103v1_genomic.fna.gz --refList GCF_030161035.1_ASM3016103v1_genomic.fna/target_genomes.txt --output GCF_030161035.1_ASM3016103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:41,884] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:41,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc724a747-2a77-48cd-9949-a0fcc335b825/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:41,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc724a747-2a77-48cd-9949-a0fcc335b825/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:41,901] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:41,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:41,901] [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
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	99.9949	1654	1656	95	conclusive
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	99.6454	1216	1656	95	conclusive
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	81.0594	837	1656	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	80.7943	864	1656	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	80.2302	749	1656	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	80.1014	747	1656	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.2186	603	1656	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.8506	624	1656	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.7092	744	1656	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.6538	718	1656	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.4877	630	1656	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.4479	544	1656	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.3851	506	1656	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:41,903] [INFO] DFAST Taxonomy check result was written to GCF_030161035.1_ASM3016103v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:41,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:41,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:41,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc724a747-2a77-48cd-9949-a0fcc335b825/dqc_reference/checkm_data
[2024-01-24 12:42:41,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:41,953] [INFO] Task started: CheckM
[2024-01-24 12:42:41,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161035.1_ASM3016103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161035.1_ASM3016103v1_genomic.fna/checkm_input GCF_030161035.1_ASM3016103v1_genomic.fna/checkm_result
[2024-01-24 12:43:39,180] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:39,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:39,204] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:39,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:39,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161035.1_ASM3016103v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:39,205] [INFO] Task started: Blastn
[2024-01-24 12:43:39,205] [INFO] Running command: blastn -query GCF_030161035.1_ASM3016103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc724a747-2a77-48cd-9949-a0fcc335b825/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161035.1_ASM3016103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:41,565] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:41,569] [INFO] Selected 8 target genomes.
[2024-01-24 12:43:41,569] [INFO] Target genome list was writen to GCF_030161035.1_ASM3016103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:41,594] [INFO] Task started: fastANI
[2024-01-24 12:43:41,595] [INFO] Running command: fastANI --query /var/lib/cwl/stge87dcfa0-fb7c-43c3-a559-54fea323cc6a/GCF_030161035.1_ASM3016103v1_genomic.fna.gz --refList GCF_030161035.1_ASM3016103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161035.1_ASM3016103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:52,401] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:52,411] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:52,412] [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_004362745.1	s__Oharaeibacter diazotrophicus	99.9949	1654	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	conclusive
GCF_013839445.1	s__Chthonobacter albigriseus	81.0799	834	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839525.1	s__Mongoliimonas rhizosphaerae	80.8961	886	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927285.1	s__Mongoliimonas terrestris	80.8768	893	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	80.7656	868	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425185.1	s__Pleomorphomonas koreensis	80.2045	753	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	80.064	751	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_016653355.1	s__Rhodoplanes elegans	77.4972	628	1656	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:52,413] [INFO] GTDB search result was written to GCF_030161035.1_ASM3016103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:52,414] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:52,417] [INFO] DFAST_QC result json was written to GCF_030161035.1_ASM3016103v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:52,417] [INFO] DFAST_QC completed!
[2024-01-24 12:43:52,417] [INFO] Total running time: 0h1m43s