[2024-01-25 20:15:20,678] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:20,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:20,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg7921d0fa-a948-412c-98c2-a62dba8e1318/dqc_reference
[2024-01-25 20:15:21,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:21,898] [INFO] Task started: Prodigal
[2024-01-25 20:15:21,898] [INFO] Running command: gunzip -c /var/lib/cwl/stgf53537ba-27df-4756-bcca-d886e87047d0/GCF_003254005.1_ASM325400v1_genomic.fna.gz | prodigal -d GCF_003254005.1_ASM325400v1_genomic.fna/cds.fna -a GCF_003254005.1_ASM325400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:32,932] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:32,933] [INFO] Task started: HMMsearch
[2024-01-25 20:15:32,933] [INFO] Running command: hmmsearch --tblout GCF_003254005.1_ASM325400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7921d0fa-a948-412c-98c2-a62dba8e1318/dqc_reference/reference_markers.hmm GCF_003254005.1_ASM325400v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:33,134] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:33,135] [INFO] Found 6/6 markers.
[2024-01-25 20:15:33,167] [INFO] Query marker FASTA was written to GCF_003254005.1_ASM325400v1_genomic.fna/markers.fasta
[2024-01-25 20:15:33,167] [INFO] Task started: Blastn
[2024-01-25 20:15:33,167] [INFO] Running command: blastn -query GCF_003254005.1_ASM325400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7921d0fa-a948-412c-98c2-a62dba8e1318/dqc_reference/reference_markers.fasta -out GCF_003254005.1_ASM325400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:34,012] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:34,019] [INFO] Selected 14 target genomes.
[2024-01-25 20:15:34,020] [INFO] Target genome list was writen to GCF_003254005.1_ASM325400v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:34,023] [INFO] Task started: fastANI
[2024-01-25 20:15:34,023] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53537ba-27df-4756-bcca-d886e87047d0/GCF_003254005.1_ASM325400v1_genomic.fna.gz --refList GCF_003254005.1_ASM325400v1_genomic.fna/target_genomes.txt --output GCF_003254005.1_ASM325400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:44,678] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:44,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7921d0fa-a948-412c-98c2-a62dba8e1318/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:44,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7921d0fa-a948-412c-98c2-a62dba8e1318/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:44,688] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:15:44,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:44,688] [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
Roseinatronobacter thiooxidans	strain=DSM 13087	GCA_003254005.1	121821	121821	type	True	100.0	1192	1196	95	conclusive
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	99.9633	1122	1196	95	conclusive
Roseinatronobacter monicus	strain=DSM 18423	GCA_006716865.1	393481	393481	type	True	83.4823	805	1196	95	below_threshold
Rhodobaca barguzinensis	strain=DSM 19920	GCA_004365885.1	441209	441209	suspected-type	True	82.4946	789	1196	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	82.4818	790	1196	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	82.4609	794	1196	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.2322	404	1196	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.2872	241	1196	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.2783	243	1196	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.231	280	1196	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0684	240	1196	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.9943	306	1196	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.963	278	1196	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.9462	280	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:44,689] [INFO] DFAST Taxonomy check result was written to GCF_003254005.1_ASM325400v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:44,690] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:44,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:44,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7921d0fa-a948-412c-98c2-a62dba8e1318/dqc_reference/checkm_data
[2024-01-25 20:15:44,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:44,727] [INFO] Task started: CheckM
[2024-01-25 20:15:44,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254005.1_ASM325400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254005.1_ASM325400v1_genomic.fna/checkm_input GCF_003254005.1_ASM325400v1_genomic.fna/checkm_result
[2024-01-25 20:16:19,390] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:19,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:19,438] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:19,438] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:19,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254005.1_ASM325400v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:19,440] [INFO] Task started: Blastn
[2024-01-25 20:16:19,440] [INFO] Running command: blastn -query GCF_003254005.1_ASM325400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7921d0fa-a948-412c-98c2-a62dba8e1318/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254005.1_ASM325400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:20,894] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:20,905] [INFO] Selected 12 target genomes.
[2024-01-25 20:16:20,905] [INFO] Target genome list was writen to GCF_003254005.1_ASM325400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:20,913] [INFO] Task started: fastANI
[2024-01-25 20:16:20,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53537ba-27df-4756-bcca-d886e87047d0/GCF_003254005.1_ASM325400v1_genomic.fna.gz --refList GCF_003254005.1_ASM325400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254005.1_ASM325400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:30,547] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:30,555] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:30,556] [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_001870675.1	s__Roseinatronobacter thiooxidans	99.9633	1122	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	97.65	95.32	0.95	0.92	3	conclusive
GCF_006716865.1	s__Roseinatronobacter monicus	83.4822	805	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	95.80	95.17	0.91	0.77	10	-
GCF_004366635.1	s__Roseinatronobacter bogoriensis	82.4781	790	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	99.99	0.99	0.99	4	-
GCA_007126715.1	s__Roseinatronobacter sp007126715	82.4261	658	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.26	99.26	0.87	0.87	2	-
GCF_001884735.1	s__Roseinatronobacter thiooxidans_A	80.1961	633	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118295.1	s__Roseinatronobacter sp007118295	80.0644	525	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.27	99.27	0.83	0.83	2	-
GCA_017510335.1	s__Roseinatronobacter sp017510335	80.0483	551	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131465.1	s__Roseinatronobacter sp007131465	79.9779	384	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	79.7575	468	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCA_003565055.1	s__Roseinatronobacter sp003565055	79.2993	415	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937725.1	s__Roseinatronobacter sp016937725	78.7583	376	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908405.1	s__Roseinatronobacter sp009908405	78.7545	375	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:30,557] [INFO] GTDB search result was written to GCF_003254005.1_ASM325400v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:30,558] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:30,561] [INFO] DFAST_QC result json was written to GCF_003254005.1_ASM325400v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:30,561] [INFO] DFAST_QC completed!
[2024-01-25 20:16:30,561] [INFO] Total running time: 0h1m10s