[2024-01-24 15:14:51,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:51,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:51,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg0836bdca-b9b7-44ed-8a1f-5873b44c17e7/dqc_reference
[2024-01-24 15:14:53,198] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,199] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,200] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd2b33f9-6709-4fc0-b319-bf6c9a17e6ab/GCF_013520865.1_ASM1352086v1_genomic.fna.gz | prodigal -d GCF_013520865.1_ASM1352086v1_genomic.fna/cds.fna -a GCF_013520865.1_ASM1352086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:08,905] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:08,906] [INFO] Task started: HMMsearch
[2024-01-24 15:15:08,906] [INFO] Running command: hmmsearch --tblout GCF_013520865.1_ASM1352086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0836bdca-b9b7-44ed-8a1f-5873b44c17e7/dqc_reference/reference_markers.hmm GCF_013520865.1_ASM1352086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:09,239] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:09,240] [INFO] Found 6/6 markers.
[2024-01-24 15:15:09,294] [INFO] Query marker FASTA was written to GCF_013520865.1_ASM1352086v1_genomic.fna/markers.fasta
[2024-01-24 15:15:09,295] [INFO] Task started: Blastn
[2024-01-24 15:15:09,295] [INFO] Running command: blastn -query GCF_013520865.1_ASM1352086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0836bdca-b9b7-44ed-8a1f-5873b44c17e7/dqc_reference/reference_markers.fasta -out GCF_013520865.1_ASM1352086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:10,349] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:10,353] [INFO] Selected 15 target genomes.
[2024-01-24 15:15:10,353] [INFO] Target genome list was writen to GCF_013520865.1_ASM1352086v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:10,365] [INFO] Task started: fastANI
[2024-01-24 15:15:10,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd2b33f9-6709-4fc0-b319-bf6c9a17e6ab/GCF_013520865.1_ASM1352086v1_genomic.fna.gz --refList GCF_013520865.1_ASM1352086v1_genomic.fna/target_genomes.txt --output GCF_013520865.1_ASM1352086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:31,059] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:31,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0836bdca-b9b7-44ed-8a1f-5873b44c17e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:31,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0836bdca-b9b7-44ed-8a1f-5873b44c17e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:31,072] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:31,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:31,073] [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 mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	100.0	1776	1779	95	conclusive
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	90.1712	1378	1779	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	89.496	1319	1779	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	85.0432	1206	1779	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.9315	1149	1779	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	84.9036	1039	1779	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	84.6676	954	1779	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	84.3924	1003	1779	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.8135	866	1779	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.7748	894	1779	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.5969	845	1779	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	82.2976	868	1779	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	82.1996	907	1779	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	79.1805	559	1779	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.5505	534	1779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:31,074] [INFO] DFAST Taxonomy check result was written to GCF_013520865.1_ASM1352086v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:31,074] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:31,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:31,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0836bdca-b9b7-44ed-8a1f-5873b44c17e7/dqc_reference/checkm_data
[2024-01-24 15:15:31,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:31,125] [INFO] Task started: CheckM
[2024-01-24 15:15:31,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013520865.1_ASM1352086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013520865.1_ASM1352086v1_genomic.fna/checkm_input GCF_013520865.1_ASM1352086v1_genomic.fna/checkm_result
[2024-01-24 15:16:18,293] [INFO] Task succeeded: CheckM
[2024-01-24 15:16:18,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:16:18,313] [INFO] ===== Completeness check finished =====
[2024-01-24 15:16:18,314] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:16:18,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013520865.1_ASM1352086v1_genomic.fna/markers.fasta)
[2024-01-24 15:16:18,314] [INFO] Task started: Blastn
[2024-01-24 15:16:18,315] [INFO] Running command: blastn -query GCF_013520865.1_ASM1352086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0836bdca-b9b7-44ed-8a1f-5873b44c17e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013520865.1_ASM1352086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:16:20,214] [INFO] Task succeeded: Blastn
[2024-01-24 15:16:20,218] [INFO] Selected 15 target genomes.
[2024-01-24 15:16:20,219] [INFO] Target genome list was writen to GCF_013520865.1_ASM1352086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:16:20,236] [INFO] Task started: fastANI
[2024-01-24 15:16:20,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd2b33f9-6709-4fc0-b319-bf6c9a17e6ab/GCF_013520865.1_ASM1352086v1_genomic.fna.gz --refList GCF_013520865.1_ASM1352086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013520865.1_ASM1352086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:42,968] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:42,986] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:42,986] [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_013520865.1	s__Microvirga mediterraneensis	100.0	1777	1779	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_000262405.1	s__Microvirga lotononidis	90.16	1381	1779	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	89.4615	1322	1779	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	86.4935	1148	1779	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	86.261	1229	1779	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	85.8842	1170	1779	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	85.8144	1237	1779	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	85.0394	1207	1779	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	84.9568	1146	1779	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	84.6153	1039	1779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014191055.1	s__Microvirga lupini_A	84.5371	1052	1779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743775.1	s__Microvirga aerilata	84.3763	1005	1779	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	84.37	1046	1779	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694425.1	s__Microvirga sp015694425	84.0999	1005	1779	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	82.7683	897	1779	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 15:16:42,989] [INFO] GTDB search result was written to GCF_013520865.1_ASM1352086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:42,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:42,996] [INFO] DFAST_QC result json was written to GCF_013520865.1_ASM1352086v1_genomic.fna/dqc_result.json
[2024-01-24 15:16:42,996] [INFO] DFAST_QC completed!
[2024-01-24 15:16:42,997] [INFO] Total running time: 0h1m51s