[2024-01-24 14:15:34,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e0c993a-0ca3-42a0-9c9d-2e0df8befaac/dqc_reference
[2024-01-24 14:15:35,701] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,712] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ec0bada-1d61-4564-bdf7-864533aaa485/GCF_016461745.1_ASM1646174v1_genomic.fna.gz | prodigal -d GCF_016461745.1_ASM1646174v1_genomic.fna/cds.fna -a GCF_016461745.1_ASM1646174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:46,671] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:46,672] [INFO] Task started: HMMsearch
[2024-01-24 14:15:46,672] [INFO] Running command: hmmsearch --tblout GCF_016461745.1_ASM1646174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e0c993a-0ca3-42a0-9c9d-2e0df8befaac/dqc_reference/reference_markers.hmm GCF_016461745.1_ASM1646174v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:46,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:46,980] [INFO] Found 6/6 markers.
[2024-01-24 14:15:47,012] [INFO] Query marker FASTA was written to GCF_016461745.1_ASM1646174v1_genomic.fna/markers.fasta
[2024-01-24 14:15:47,013] [INFO] Task started: Blastn
[2024-01-24 14:15:47,013] [INFO] Running command: blastn -query GCF_016461745.1_ASM1646174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0c993a-0ca3-42a0-9c9d-2e0df8befaac/dqc_reference/reference_markers.fasta -out GCF_016461745.1_ASM1646174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:47,982] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:47,985] [INFO] Selected 19 target genomes.
[2024-01-24 14:15:47,986] [INFO] Target genome list was writen to GCF_016461745.1_ASM1646174v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:47,996] [INFO] Task started: fastANI
[2024-01-24 14:15:47,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ec0bada-1d61-4564-bdf7-864533aaa485/GCF_016461745.1_ASM1646174v1_genomic.fna.gz --refList GCF_016461745.1_ASM1646174v1_genomic.fna/target_genomes.txt --output GCF_016461745.1_ASM1646174v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:02,773] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:02,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e0c993a-0ca3-42a0-9c9d-2e0df8befaac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:02,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e0c993a-0ca3-42a0-9c9d-2e0df8befaac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:02,796] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:16:02,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:02,797] [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
Rhodomicrobium udaipurense	strain=JA643	GCA_016461795.1	1202716	1202716	type	True	96.3878	1052	1216	95	conclusive
Rhodomicrobium udaipurense	strain=JA643	GCA_000636015.1	1202716	1202716	type	True	96.3635	956	1216	95	conclusive
Rhodomicrobium lacus	strain=JA980	GCA_003992725.1	2498452	2498452	type	True	87.8607	950	1216	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	76.839	112	1216	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.7928	202	1216	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.7625	207	1216	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	76.714	107	1216	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.7032	125	1216	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.6231	159	1216	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.61	183	1216	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	76.5896	159	1216	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	76.5849	140	1216	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.5523	132	1216	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	76.415	172	1216	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	76.3703	135	1216	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	76.265	133	1216	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.224	157	1216	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	76.2144	114	1216	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.964	142	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:02,798] [INFO] DFAST Taxonomy check result was written to GCF_016461745.1_ASM1646174v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:02,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:02,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:02,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e0c993a-0ca3-42a0-9c9d-2e0df8befaac/dqc_reference/checkm_data
[2024-01-24 14:16:02,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:02,839] [INFO] Task started: CheckM
[2024-01-24 14:16:02,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016461745.1_ASM1646174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016461745.1_ASM1646174v1_genomic.fna/checkm_input GCF_016461745.1_ASM1646174v1_genomic.fna/checkm_result
[2024-01-24 14:16:38,747] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:38,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:38,770] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:38,771] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:38,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016461745.1_ASM1646174v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:38,772] [INFO] Task started: Blastn
[2024-01-24 14:16:38,772] [INFO] Running command: blastn -query GCF_016461745.1_ASM1646174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0c993a-0ca3-42a0-9c9d-2e0df8befaac/dqc_reference/reference_markers_gtdb.fasta -out GCF_016461745.1_ASM1646174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:40,537] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:40,541] [INFO] Selected 8 target genomes.
[2024-01-24 14:16:40,542] [INFO] Target genome list was writen to GCF_016461745.1_ASM1646174v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:40,549] [INFO] Task started: fastANI
[2024-01-24 14:16:40,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ec0bada-1d61-4564-bdf7-864533aaa485/GCF_016461745.1_ASM1646174v1_genomic.fna.gz --refList GCF_016461745.1_ASM1646174v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016461745.1_ASM1646174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:48,257] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:48,267] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:48,267] [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_000636015.1	s__Rhodomicrobium udaipurense	96.3635	956	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	98.25	96.51	0.94	0.88	3	conclusive
GCF_000166055.1	s__Rhodomicrobium vannielii	94.867	1028	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018619475.1	s__Rhodomicrobium sp018619475	88.6608	904	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992725.1	s__Rhodomicrobium lacus	87.879	948	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153975.1	s__Rhodomicrobium sp003153975	77.6408	315	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Rhodomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198715.1	s__R-RK-3 sp002198715	77.2093	234	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__R-RK-3	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	76.4217	194	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550175.1	s__Dichotomicrobium thermohalophilum	76.265	133	1216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__Dichotomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:48,271] [INFO] GTDB search result was written to GCF_016461745.1_ASM1646174v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:48,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:48,275] [INFO] DFAST_QC result json was written to GCF_016461745.1_ASM1646174v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:48,276] [INFO] DFAST_QC completed!
[2024-01-24 14:16:48,276] [INFO] Total running time: 0h1m14s