[2024-01-24 13:31:56,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:56,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:56,720] [INFO] DQC Reference Directory: /var/lib/cwl/stgd87ddf80-763a-476b-81d5-b41e519df990/dqc_reference
[2024-01-24 13:31:57,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,000] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,000] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f6cb251-d031-4ac3-9106-bd22f75deb50/GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna.gz | prodigal -d GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/cds.fna -a GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:10,084] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:10,084] [INFO] Task started: HMMsearch
[2024-01-24 13:32:10,084] [INFO] Running command: hmmsearch --tblout GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd87ddf80-763a-476b-81d5-b41e519df990/dqc_reference/reference_markers.hmm GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:10,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:10,319] [INFO] Found 6/6 markers.
[2024-01-24 13:32:10,354] [INFO] Query marker FASTA was written to GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/markers.fasta
[2024-01-24 13:32:10,354] [INFO] Task started: Blastn
[2024-01-24 13:32:10,354] [INFO] Running command: blastn -query GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/markers.fasta -db /var/lib/cwl/stgd87ddf80-763a-476b-81d5-b41e519df990/dqc_reference/reference_markers.fasta -out GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:11,097] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:11,101] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:11,102] [INFO] Target genome list was writen to GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/target_genomes.txt
[2024-01-24 13:32:11,110] [INFO] Task started: fastANI
[2024-01-24 13:32:11,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6cb251-d031-4ac3-9106-bd22f75deb50/GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna.gz --refList GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/target_genomes.txt --output GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:26,007] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:26,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd87ddf80-763a-476b-81d5-b41e519df990/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:26,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd87ddf80-763a-476b-81d5-b41e519df990/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:26,023] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:26,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:26,024] [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
Herminiimonas arsenitoxidans	strain=AS8	GCA_900130075.1	1809410	1809410	type	True	100.0	1258	1261	95	conclusive
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	81.9467	662	1261	95	below_threshold
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	81.894	665	1261	95	below_threshold
Oxalicibacterium faecigallinarum	strain=CCM 2767	GCA_014635705.1	573741	573741	type	True	79.018	369	1261	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	78.5185	244	1261	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	78.3857	393	1261	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	78.0386	267	1261	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	78.0272	252	1261	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	77.9437	300	1261	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	77.8391	249	1261	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.8112	230	1261	95	below_threshold
Undibacterium flavidum	strain=LX15W	GCA_014284175.1	2762297	2762297	type	True	77.6727	116	1261	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	77.6375	183	1261	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	77.5184	173	1261	95	below_threshold
Janthinobacterium psychrotolerans	strain=S3-2	GCA_001677885.1	1747903	1747903	type	True	77.2912	176	1261	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	77.2503	153	1261	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	77.129	158	1261	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	77.0888	166	1261	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	76.8948	159	1261	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:26,025] [INFO] DFAST Taxonomy check result was written to GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/tc_result.tsv
[2024-01-24 13:32:26,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:26,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:26,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd87ddf80-763a-476b-81d5-b41e519df990/dqc_reference/checkm_data
[2024-01-24 13:32:26,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:26,066] [INFO] Task started: CheckM
[2024-01-24 13:32:26,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/checkm_input GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/checkm_result
[2024-01-24 13:33:06,136] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:06,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:06,153] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:06,153] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:06,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/markers.fasta)
[2024-01-24 13:33:06,154] [INFO] Task started: Blastn
[2024-01-24 13:33:06,154] [INFO] Running command: blastn -query GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/markers.fasta -db /var/lib/cwl/stgd87ddf80-763a-476b-81d5-b41e519df990/dqc_reference/reference_markers_gtdb.fasta -out GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:07,507] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:07,510] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:07,510] [INFO] Target genome list was writen to GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:07,518] [INFO] Task started: fastANI
[2024-01-24 13:33:07,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6cb251-d031-4ac3-9106-bd22f75deb50/GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna.gz --refList GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/target_genomes_gtdb.txt --output GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:14,406] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:14,415] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:14,415] [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_900130075.1	s__Herminiimonas arsenitoxidans	100.0	1258	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000013625.1	s__Herminiimonas sp000013625	83.5496	854	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645465.1	s__Herminiimonas contaminans	82.957	809	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	97.73	97.73	0.94	0.94	3	-
GCF_003852535.1	s__Herminiimonas sp003852535	82.9286	791	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293745.1	s__Herminiimonas fonticola	81.9052	664	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000026125.1	s__Herminiimonas arsenicoxydans	81.6758	669	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464355.1	s__Herminiimonas sp001464355	81.6165	614	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384815.1	s__Herminiimonas sp002384815	80.8111	560	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:14,418] [INFO] GTDB search result was written to GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:14,419] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:14,425] [INFO] DFAST_QC result json was written to GCF_900130075.1_Herminiimonas_arsenitoxidans_genomic.fna/dqc_result.json
[2024-01-24 13:33:14,425] [INFO] DFAST_QC completed!
[2024-01-24 13:33:14,425] [INFO] Total running time: 0h1m18s