[2024-01-24 13:45:41,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg889cc2d3-170c-4920-8bdb-f4f51a076e85/dqc_reference
[2024-01-24 13:45:42,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,479] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,479] [INFO] Running command: gunzip -c /var/lib/cwl/stg8147c024-ffc9-4233-ab83-d579c0ebc752/GCF_020866965.1_ASM2086696v1_genomic.fna.gz | prodigal -d GCF_020866965.1_ASM2086696v1_genomic.fna/cds.fna -a GCF_020866965.1_ASM2086696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:56,116] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:56,116] [INFO] Task started: HMMsearch
[2024-01-24 13:45:56,116] [INFO] Running command: hmmsearch --tblout GCF_020866965.1_ASM2086696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg889cc2d3-170c-4920-8bdb-f4f51a076e85/dqc_reference/reference_markers.hmm GCF_020866965.1_ASM2086696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:56,418] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:56,420] [INFO] Found 6/6 markers.
[2024-01-24 13:45:56,468] [INFO] Query marker FASTA was written to GCF_020866965.1_ASM2086696v1_genomic.fna/markers.fasta
[2024-01-24 13:45:56,469] [INFO] Task started: Blastn
[2024-01-24 13:45:56,469] [INFO] Running command: blastn -query GCF_020866965.1_ASM2086696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg889cc2d3-170c-4920-8bdb-f4f51a076e85/dqc_reference/reference_markers.fasta -out GCF_020866965.1_ASM2086696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:57,389] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:57,392] [INFO] Selected 16 target genomes.
[2024-01-24 13:45:57,393] [INFO] Target genome list was writen to GCF_020866965.1_ASM2086696v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:57,408] [INFO] Task started: fastANI
[2024-01-24 13:45:57,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg8147c024-ffc9-4233-ab83-d579c0ebc752/GCF_020866965.1_ASM2086696v1_genomic.fna.gz --refList GCF_020866965.1_ASM2086696v1_genomic.fna/target_genomes.txt --output GCF_020866965.1_ASM2086696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:18,624] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:18,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg889cc2d3-170c-4920-8bdb-f4f51a076e85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:18,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg889cc2d3-170c-4920-8bdb-f4f51a076e85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:18,643] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:18,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:18,643] [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 roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	100.0	1595	1597	95	conclusive
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	83.3589	804	1597	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	83.3222	937	1597	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	82.9074	923	1597	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	82.8662	865	1597	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	82.762	924	1597	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	82.7465	919	1597	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	82.6443	902	1597	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.6305	879	1597	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	82.4895	908	1597	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	82.4556	908	1597	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.2416	855	1597	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	82.2339	827	1597	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	81.783	733	1597	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	78.3276	482	1597	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.2177	467	1597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:18,645] [INFO] DFAST Taxonomy check result was written to GCF_020866965.1_ASM2086696v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:18,646] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:18,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:18,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg889cc2d3-170c-4920-8bdb-f4f51a076e85/dqc_reference/checkm_data
[2024-01-24 13:46:18,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:18,700] [INFO] Task started: CheckM
[2024-01-24 13:46:18,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020866965.1_ASM2086696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020866965.1_ASM2086696v1_genomic.fna/checkm_input GCF_020866965.1_ASM2086696v1_genomic.fna/checkm_result
[2024-01-24 13:47:03,634] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:03,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,659] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:03,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:03,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020866965.1_ASM2086696v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:03,660] [INFO] Task started: Blastn
[2024-01-24 13:47:03,661] [INFO] Running command: blastn -query GCF_020866965.1_ASM2086696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg889cc2d3-170c-4920-8bdb-f4f51a076e85/dqc_reference/reference_markers_gtdb.fasta -out GCF_020866965.1_ASM2086696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:05,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:05,375] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:05,375] [INFO] Target genome list was writen to GCF_020866965.1_ASM2086696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:05,401] [INFO] Task started: fastANI
[2024-01-24 13:47:05,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg8147c024-ffc9-4233-ab83-d579c0ebc752/GCF_020866965.1_ASM2086696v1_genomic.fna.gz --refList GCF_020866965.1_ASM2086696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020866965.1_ASM2086696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:28,079] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:28,101] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:28,102] [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_009910705.1	s__Microvirga sp009910705	83.4324	907	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000518665.1	s__Microvirga flocculans	83.37	803	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016427565.1	s__Microvirga sp016427565	83.3129	938	1597	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	82.9197	921	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	82.866	864	1597	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	82.8493	875	1597	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	82.8221	930	1597	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	82.7431	920	1597	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	82.7266	879	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191055.1	s__Microvirga lupini_A	82.6817	869	1597	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	82.678	924	1597	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	82.6773	899	1597	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	82.6177	925	1597	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	82.4957	921	1597	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	82.493	907	1597	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	82.3686	882	1597	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	82.2248	828	1597	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363855.1	s__Microvirga thermotolerans	81.7869	732	1597	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 13:47:28,103] [INFO] GTDB search result was written to GCF_020866965.1_ASM2086696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:28,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:28,108] [INFO] DFAST_QC result json was written to GCF_020866965.1_ASM2086696v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:28,108] [INFO] DFAST_QC completed!
[2024-01-24 13:47:28,108] [INFO] Total running time: 0h1m47s