[2024-01-25 18:58:20,693] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:20,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:20,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg729df64e-7522-4e39-88cf-d954c4e2db55/dqc_reference
[2024-01-25 18:58:21,848] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:21,848] [INFO] Task started: Prodigal
[2024-01-25 18:58:21,849] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4087436-78d9-4377-a559-37e208349c04/GCF_003347665.1_ASM334766v1_genomic.fna.gz | prodigal -d GCF_003347665.1_ASM334766v1_genomic.fna/cds.fna -a GCF_003347665.1_ASM334766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:40,139] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:40,139] [INFO] Task started: HMMsearch
[2024-01-25 18:58:40,139] [INFO] Running command: hmmsearch --tblout GCF_003347665.1_ASM334766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg729df64e-7522-4e39-88cf-d954c4e2db55/dqc_reference/reference_markers.hmm GCF_003347665.1_ASM334766v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:40,432] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:40,433] [INFO] Found 6/6 markers.
[2024-01-25 18:58:40,490] [INFO] Query marker FASTA was written to GCF_003347665.1_ASM334766v1_genomic.fna/markers.fasta
[2024-01-25 18:58:40,490] [INFO] Task started: Blastn
[2024-01-25 18:58:40,490] [INFO] Running command: blastn -query GCF_003347665.1_ASM334766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg729df64e-7522-4e39-88cf-d954c4e2db55/dqc_reference/reference_markers.fasta -out GCF_003347665.1_ASM334766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:41,675] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:41,679] [INFO] Selected 18 target genomes.
[2024-01-25 18:58:41,680] [INFO] Target genome list was writen to GCF_003347665.1_ASM334766v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:41,681] [INFO] Task started: fastANI
[2024-01-25 18:58:41,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4087436-78d9-4377-a559-37e208349c04/GCF_003347665.1_ASM334766v1_genomic.fna.gz --refList GCF_003347665.1_ASM334766v1_genomic.fna/target_genomes.txt --output GCF_003347665.1_ASM334766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:07,209] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:07,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg729df64e-7522-4e39-88cf-d954c4e2db55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:07,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg729df64e-7522-4e39-88cf-d954c4e2db55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:07,221] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:59:07,221] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:07,221] [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
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	100.0	2326	2343	95	conclusive
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	89.4385	1344	2343	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	88.7572	1534	2343	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.4428	1305	2343	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.4172	1410	2343	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	84.3941	1069	2343	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	84.2559	948	2343	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	83.8129	1130	2343	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	83.7947	1134	2343	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.5227	892	2343	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.4683	956	2343	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.1809	871	2343	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	82.061	982	2343	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	81.9536	896	2343	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	80.1867	717	2343	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	78.4808	442	2343	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	78.3343	516	2343	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.3033	531	2343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:07,222] [INFO] DFAST Taxonomy check result was written to GCF_003347665.1_ASM334766v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:07,223] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:07,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:07,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg729df64e-7522-4e39-88cf-d954c4e2db55/dqc_reference/checkm_data
[2024-01-25 18:59:07,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:07,293] [INFO] Task started: CheckM
[2024-01-25 18:59:07,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003347665.1_ASM334766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003347665.1_ASM334766v1_genomic.fna/checkm_input GCF_003347665.1_ASM334766v1_genomic.fna/checkm_result
[2024-01-25 19:00:00,837] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:00,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:00,857] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:00,857] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:00,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003347665.1_ASM334766v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:00,858] [INFO] Task started: Blastn
[2024-01-25 19:00:00,858] [INFO] Running command: blastn -query GCF_003347665.1_ASM334766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg729df64e-7522-4e39-88cf-d954c4e2db55/dqc_reference/reference_markers_gtdb.fasta -out GCF_003347665.1_ASM334766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:03,321] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:03,324] [INFO] Selected 14 target genomes.
[2024-01-25 19:00:03,324] [INFO] Target genome list was writen to GCF_003347665.1_ASM334766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:03,331] [INFO] Task started: fastANI
[2024-01-25 19:00:03,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4087436-78d9-4377-a559-37e208349c04/GCF_003347665.1_ASM334766v1_genomic.fna.gz --refList GCF_003347665.1_ASM334766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003347665.1_ASM334766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:27,800] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:27,809] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:27,809] [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_003347665.1	s__Microvirga calopogonii	100.0	2327	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013520865.1	s__Microvirga mediterraneensis	89.4248	1343	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	88.7535	1534	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069605.1	s__Microvirga sp018069605	86.4802	1349	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383585.1	s__Microvirga sp018383585	85.9944	1242	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000517005.1	s__Microvirga lupini	85.5618	1480	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864375.1	s__Microvirga sp016864375	85.4033	1499	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741015.1	s__Microvirga ossetica	84.4938	1396	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735695.1	s__Microvirga zambiensis	84.4654	1300	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	84.2232	1049	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000739015.1	s__Microvirga sp000739015	84.0867	1092	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811235.1	s__Microvirga arabica	83.7931	1132	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699075.1	s__Microvirga sp014699075	83.5463	1211	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004458765.1	s__Microvirga pakistanensis	82.4351	960	2343	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:27,811] [INFO] GTDB search result was written to GCF_003347665.1_ASM334766v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:27,812] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:27,815] [INFO] DFAST_QC result json was written to GCF_003347665.1_ASM334766v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:27,816] [INFO] DFAST_QC completed!
[2024-01-25 19:00:27,816] [INFO] Total running time: 0h2m7s