[2024-01-24 12:14:09,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgc87a51f8-674f-4f85-92dd-160289701fba/dqc_reference
[2024-01-24 12:14:10,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:10,724] [INFO] Task started: Prodigal
[2024-01-24 12:14:10,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg00babec3-e343-4cc4-b5a7-a6cdc98ae439/GCF_004137085.1_ASM413708v1_genomic.fna.gz | prodigal -d GCF_004137085.1_ASM413708v1_genomic.fna/cds.fna -a GCF_004137085.1_ASM413708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:26,856] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:26,856] [INFO] Task started: HMMsearch
[2024-01-24 12:14:26,856] [INFO] Running command: hmmsearch --tblout GCF_004137085.1_ASM413708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc87a51f8-674f-4f85-92dd-160289701fba/dqc_reference/reference_markers.hmm GCF_004137085.1_ASM413708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:27,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:27,250] [INFO] Found 6/6 markers.
[2024-01-24 12:14:27,313] [INFO] Query marker FASTA was written to GCF_004137085.1_ASM413708v1_genomic.fna/markers.fasta
[2024-01-24 12:14:27,314] [INFO] Task started: Blastn
[2024-01-24 12:14:27,314] [INFO] Running command: blastn -query GCF_004137085.1_ASM413708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc87a51f8-674f-4f85-92dd-160289701fba/dqc_reference/reference_markers.fasta -out GCF_004137085.1_ASM413708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:28,439] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:28,444] [INFO] Selected 25 target genomes.
[2024-01-24 12:14:28,444] [INFO] Target genome list was writen to GCF_004137085.1_ASM413708v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:28,457] [INFO] Task started: fastANI
[2024-01-24 12:14:28,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg00babec3-e343-4cc4-b5a7-a6cdc98ae439/GCF_004137085.1_ASM413708v1_genomic.fna.gz --refList GCF_004137085.1_ASM413708v1_genomic.fna/target_genomes.txt --output GCF_004137085.1_ASM413708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:55,063] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:55,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc87a51f8-674f-4f85-92dd-160289701fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:55,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc87a51f8-674f-4f85-92dd-160289701fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:55,082] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:55,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:55,083] [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
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	100.0	1897	1900	95	conclusive
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	84.4909	1163	1900	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.6935	490	1900	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.466	363	1900	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.4277	380	1900	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	77.3886	627	1900	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	77.364	643	1900	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.3612	459	1900	95	below_threshold
Lichenihabitans psoromatis	strain=PAMC 29148	GCA_004323635.1	2528642	2528642	type	True	77.3448	393	1900	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.3382	496	1900	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	77.3061	498	1900	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.3024	538	1900	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	77.2908	477	1900	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.2884	603	1900	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.2627	644	1900	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	77.261	522	1900	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	77.2436	520	1900	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.141	473	1900	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	77.1141	510	1900	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	77.0903	494	1900	95	below_threshold
Methylocystis heyeri	strain=H2	GCA_004802635.2	391905	391905	type	True	76.9659	233	1900	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	76.8901	332	1900	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	76.879	240	1900	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.7666	344	1900	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	76.7133	359	1900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:55,085] [INFO] DFAST Taxonomy check result was written to GCF_004137085.1_ASM413708v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:55,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:55,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:55,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc87a51f8-674f-4f85-92dd-160289701fba/dqc_reference/checkm_data
[2024-01-24 12:14:55,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:55,144] [INFO] Task started: CheckM
[2024-01-24 12:14:55,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004137085.1_ASM413708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004137085.1_ASM413708v1_genomic.fna/checkm_input GCF_004137085.1_ASM413708v1_genomic.fna/checkm_result
[2024-01-24 12:16:14,935] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:14,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:14,958] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:14,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:14,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004137085.1_ASM413708v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:14,960] [INFO] Task started: Blastn
[2024-01-24 12:16:14,960] [INFO] Running command: blastn -query GCF_004137085.1_ASM413708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc87a51f8-674f-4f85-92dd-160289701fba/dqc_reference/reference_markers_gtdb.fasta -out GCF_004137085.1_ASM413708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:17,130] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:17,135] [INFO] Selected 20 target genomes.
[2024-01-24 12:16:17,135] [INFO] Target genome list was writen to GCF_004137085.1_ASM413708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:17,154] [INFO] Task started: fastANI
[2024-01-24 12:16:17,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg00babec3-e343-4cc4-b5a7-a6cdc98ae439/GCF_004137085.1_ASM413708v1_genomic.fna.gz --refList GCF_004137085.1_ASM413708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004137085.1_ASM413708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:37,415] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:37,431] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:37,432] [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_004137085.1	s__Lichenihabitans ramalinae	100.0	1897	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004137685.1	s__Lichenihabitans minor	84.5094	1160	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901457705.2	s__RH-AL1 sp901457705	77.9672	470	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
GCA_016716745.1	s__GCA-013693735 sp016716745	77.764	441	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793505.1	s__GCA-013693735 sp016793505	77.4762	449	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.4504	365	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966715.1	s__Blastochloris tepida	77.4427	378	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	77.4005	507	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_004323635.1	s__Lichenihabitans psoromatis	77.3444	393	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	97.95	97.95	0.93	0.93	2	-
GCF_001422885.1	s__Methylobacterium sp001422885	77.2407	491	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	77.221	531	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188155.2	s__Methylocystis sp000188155	77.2164	273	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040085.1	s__Methylobacterium sp008040085	77.1945	475	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470775.1	s__Bosea sp900470775	77.1926	404	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008515.1	s__Phreatobacter cathodiphilus	77.1693	473	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295925.1	s__Bosea sp001295925	77.1544	329	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141845.1	s__Methylobacterium symbioticum	77.0901	514	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745395.1	s__Methylocystis sp016745395	77.0051	259	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283235.1	s__Methylocystis parvus	76.8781	239	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003164915.1	s__Roseiarcus sp003164915	76.7374	363	1900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	99.60	99.60	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:37,434] [INFO] GTDB search result was written to GCF_004137085.1_ASM413708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:37,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:37,439] [INFO] DFAST_QC result json was written to GCF_004137085.1_ASM413708v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:37,439] [INFO] DFAST_QC completed!
[2024-01-24 12:16:37,439] [INFO] Total running time: 0h2m28s