[2024-01-24 13:46:01,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b087b9d-b959-4ff3-9f91-464773ba2eec/dqc_reference
[2024-01-24 13:46:03,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,068] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d307be2-b183-4ff7-8a51-ad7166ccf30a/GCF_020595095.1_ASM2059509v1_genomic.fna.gz | prodigal -d GCF_020595095.1_ASM2059509v1_genomic.fna/cds.fna -a GCF_020595095.1_ASM2059509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:17,886] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:17,886] [INFO] Task started: HMMsearch
[2024-01-24 13:46:17,886] [INFO] Running command: hmmsearch --tblout GCF_020595095.1_ASM2059509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b087b9d-b959-4ff3-9f91-464773ba2eec/dqc_reference/reference_markers.hmm GCF_020595095.1_ASM2059509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:18,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:18,192] [INFO] Found 6/6 markers.
[2024-01-24 13:46:18,235] [INFO] Query marker FASTA was written to GCF_020595095.1_ASM2059509v1_genomic.fna/markers.fasta
[2024-01-24 13:46:18,235] [INFO] Task started: Blastn
[2024-01-24 13:46:18,235] [INFO] Running command: blastn -query GCF_020595095.1_ASM2059509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b087b9d-b959-4ff3-9f91-464773ba2eec/dqc_reference/reference_markers.fasta -out GCF_020595095.1_ASM2059509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:19,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:19,185] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:19,185] [INFO] Target genome list was writen to GCF_020595095.1_ASM2059509v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:19,197] [INFO] Task started: fastANI
[2024-01-24 13:46:19,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d307be2-b183-4ff7-8a51-ad7166ccf30a/GCF_020595095.1_ASM2059509v1_genomic.fna.gz --refList GCF_020595095.1_ASM2059509v1_genomic.fna/target_genomes.txt --output GCF_020595095.1_ASM2059509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:45,228] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:45,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b087b9d-b959-4ff3-9f91-464773ba2eec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:45,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b087b9d-b959-4ff3-9f91-464773ba2eec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:45,248] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:45,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:45,248] [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 rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	100.0	1651	1653	95	conclusive
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	81.4814	792	1653	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	80.5052	714	1653	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	80.3618	674	1653	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	80.3339	772	1653	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	80.2548	612	1653	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	80.15	685	1653	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	80.1414	726	1653	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	80.0642	733	1653	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	80.0378	667	1653	95	below_threshold
Microvirga aerophila	strain=DSM 21344	GCA_003332305.1	670291	670291	type	True	79.9829	635	1653	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	79.9508	713	1653	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	79.9281	616	1653	95	below_threshold
Microvirga aerophila	strain=NBRC 106136	GCA_007991675.1	670291	670291	type	True	79.8371	633	1653	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	79.7925	568	1653	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	79.7869	642	1653	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	79.7697	616	1653	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	79.7238	697	1653	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	79.6143	589	1653	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	78.0818	355	1653	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.6393	328	1653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:45,251] [INFO] DFAST Taxonomy check result was written to GCF_020595095.1_ASM2059509v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:45,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:45,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:45,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b087b9d-b959-4ff3-9f91-464773ba2eec/dqc_reference/checkm_data
[2024-01-24 13:46:45,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:45,304] [INFO] Task started: CheckM
[2024-01-24 13:46:45,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020595095.1_ASM2059509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020595095.1_ASM2059509v1_genomic.fna/checkm_input GCF_020595095.1_ASM2059509v1_genomic.fna/checkm_result
[2024-01-24 13:47:31,391] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:31,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:31,413] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:31,414] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:31,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020595095.1_ASM2059509v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:31,415] [INFO] Task started: Blastn
[2024-01-24 13:47:31,415] [INFO] Running command: blastn -query GCF_020595095.1_ASM2059509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b087b9d-b959-4ff3-9f91-464773ba2eec/dqc_reference/reference_markers_gtdb.fasta -out GCF_020595095.1_ASM2059509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:33,159] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:33,163] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:33,163] [INFO] Target genome list was writen to GCF_020595095.1_ASM2059509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:33,179] [INFO] Task started: fastANI
[2024-01-24 13:47:33,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d307be2-b183-4ff7-8a51-ad7166ccf30a/GCF_020595095.1_ASM2059509v1_genomic.fna.gz --refList GCF_020595095.1_ASM2059509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020595095.1_ASM2059509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:54,578] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:54,594] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:54,595] [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_003151255.1	s__Microvirga sp003151255	81.7759	806	1653	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	81.4991	790	1653	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	80.4777	718	1653	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	80.3416	772	1653	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	80.1385	725	1653	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	80.1365	687	1653	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	80.1337	681	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003347665.1	s__Microvirga calopogonii	80.0496	733	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427565.1	s__Microvirga sp016427565	80.0482	665	1653	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	80.0223	726	1653	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	80.0121	665	1653	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	79.9886	661	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332305.1	s__Microvirga aerophila	79.9776	636	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	99.85	99.85	0.93	0.93	2	-
GCF_016735695.1	s__Microvirga zambiensis	79.9592	710	1653	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	79.9519	663	1653	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	79.9348	616	1653	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	79.8254	681	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694465.1	s__Microvirga sp015694465	79.809	568	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017175.1	s__Microvirga vignae	79.7697	616	1653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075415.1	s__Microvirga sp003075415	79.657	615	1653	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 13:47:54,596] [INFO] GTDB search result was written to GCF_020595095.1_ASM2059509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:54,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:54,600] [INFO] DFAST_QC result json was written to GCF_020595095.1_ASM2059509v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:54,601] [INFO] DFAST_QC completed!
[2024-01-24 13:47:54,601] [INFO] Total running time: 0h1m53s