[2024-01-24 13:37:05,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,101] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg97627dc5-ddcb-4037-b745-6a52f4d9b92d/dqc_reference
[2024-01-24 13:37:06,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,658] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,659] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1f7e5eb-f5bc-41e3-85f4-c54629989279/GCF_014196145.1_ASM1419614v1_genomic.fna.gz | prodigal -d GCF_014196145.1_ASM1419614v1_genomic.fna/cds.fna -a GCF_014196145.1_ASM1419614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:18,058] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:18,058] [INFO] Task started: HMMsearch
[2024-01-24 13:37:18,058] [INFO] Running command: hmmsearch --tblout GCF_014196145.1_ASM1419614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97627dc5-ddcb-4037-b745-6a52f4d9b92d/dqc_reference/reference_markers.hmm GCF_014196145.1_ASM1419614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:18,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:18,393] [INFO] Found 6/6 markers.
[2024-01-24 13:37:18,426] [INFO] Query marker FASTA was written to GCF_014196145.1_ASM1419614v1_genomic.fna/markers.fasta
[2024-01-24 13:37:18,426] [INFO] Task started: Blastn
[2024-01-24 13:37:18,426] [INFO] Running command: blastn -query GCF_014196145.1_ASM1419614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97627dc5-ddcb-4037-b745-6a52f4d9b92d/dqc_reference/reference_markers.fasta -out GCF_014196145.1_ASM1419614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:19,446] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:19,449] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:19,449] [INFO] Target genome list was writen to GCF_014196145.1_ASM1419614v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:19,456] [INFO] Task started: fastANI
[2024-01-24 13:37:19,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f7e5eb-f5bc-41e3-85f4-c54629989279/GCF_014196145.1_ASM1419614v1_genomic.fna.gz --refList GCF_014196145.1_ASM1419614v1_genomic.fna/target_genomes.txt --output GCF_014196145.1_ASM1419614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:39,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:39,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97627dc5-ddcb-4037-b745-6a52f4d9b92d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:39,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97627dc5-ddcb-4037-b745-6a52f4d9b92d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:39,080] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:39,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:39,080] [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 flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	99.9971	1316	1323	95	conclusive
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	85.3758	918	1323	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	84.8859	896	1323	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	84.8609	944	1323	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.6315	958	1323	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.5653	943	1323	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	84.5577	935	1323	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	84.499	934	1323	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	84.4419	931	1323	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	83.4696	806	1323	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	83.2835	804	1323	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.8054	783	1323	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.4742	800	1323	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	79.4887	532	1323	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.2945	471	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,082] [INFO] DFAST Taxonomy check result was written to GCF_014196145.1_ASM1419614v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:39,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:39,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:39,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97627dc5-ddcb-4037-b745-6a52f4d9b92d/dqc_reference/checkm_data
[2024-01-24 13:37:39,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:39,129] [INFO] Task started: CheckM
[2024-01-24 13:37:39,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196145.1_ASM1419614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196145.1_ASM1419614v1_genomic.fna/checkm_input GCF_014196145.1_ASM1419614v1_genomic.fna/checkm_result
[2024-01-24 13:38:16,839] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:16,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:16,861] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:16,862] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:16,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196145.1_ASM1419614v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:16,863] [INFO] Task started: Blastn
[2024-01-24 13:38:16,863] [INFO] Running command: blastn -query GCF_014196145.1_ASM1419614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97627dc5-ddcb-4037-b745-6a52f4d9b92d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196145.1_ASM1419614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:18,867] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:18,875] [INFO] Selected 15 target genomes.
[2024-01-24 13:38:18,875] [INFO] Target genome list was writen to GCF_014196145.1_ASM1419614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:18,894] [INFO] Task started: fastANI
[2024-01-24 13:38:18,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f7e5eb-f5bc-41e3-85f4-c54629989279/GCF_014196145.1_ASM1419614v1_genomic.fna.gz --refList GCF_014196145.1_ASM1419614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196145.1_ASM1419614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:38,398] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:38,418] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:38,418] [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_000518665.1	s__Microvirga flocculans	99.9971	1316	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_009910705.1	s__Microvirga sp009910705	85.5829	964	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016427565.1	s__Microvirga sp016427565	85.3766	919	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739015.1	s__Microvirga sp000739015	84.9789	916	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016892765.1	s__Microvirga sp016892765	84.885	944	1323	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	84.8772	897	1323	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	84.6317	958	1323	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	84.5827	944	1323	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	84.5757	942	1323	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	84.5626	935	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347665.1	s__Microvirga calopogonii	84.4341	932	1323	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	84.3095	961	1323	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	84.1098	889	1323	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	83.2671	806	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350535.1	s__Microvirga subterranea	82.4706	801	1323	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:38,420] [INFO] GTDB search result was written to GCF_014196145.1_ASM1419614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:38,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:38,424] [INFO] DFAST_QC result json was written to GCF_014196145.1_ASM1419614v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:38,425] [INFO] DFAST_QC completed!
[2024-01-24 13:38:38,425] [INFO] Total running time: 0h1m33s