[2024-01-24 12:09:05,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfeebfc2-0dad-47c7-8d0d-2f022b33a3d4/dqc_reference
[2024-01-24 12:09:06,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,863] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg44176de7-a41e-4ff6-aa71-9d2d79c77518/GCF_016811235.1_ASM1681123v1_genomic.fna.gz | prodigal -d GCF_016811235.1_ASM1681123v1_genomic.fna/cds.fna -a GCF_016811235.1_ASM1681123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:25,564] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:25,565] [INFO] Task started: HMMsearch
[2024-01-24 12:09:25,565] [INFO] Running command: hmmsearch --tblout GCF_016811235.1_ASM1681123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfeebfc2-0dad-47c7-8d0d-2f022b33a3d4/dqc_reference/reference_markers.hmm GCF_016811235.1_ASM1681123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:25,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:25,892] [INFO] Found 6/6 markers.
[2024-01-24 12:09:25,946] [INFO] Query marker FASTA was written to GCF_016811235.1_ASM1681123v1_genomic.fna/markers.fasta
[2024-01-24 12:09:25,946] [INFO] Task started: Blastn
[2024-01-24 12:09:25,947] [INFO] Running command: blastn -query GCF_016811235.1_ASM1681123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfeebfc2-0dad-47c7-8d0d-2f022b33a3d4/dqc_reference/reference_markers.fasta -out GCF_016811235.1_ASM1681123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:26,959] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:26,963] [INFO] Selected 18 target genomes.
[2024-01-24 12:09:26,964] [INFO] Target genome list was writen to GCF_016811235.1_ASM1681123v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:26,971] [INFO] Task started: fastANI
[2024-01-24 12:09:26,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg44176de7-a41e-4ff6-aa71-9d2d79c77518/GCF_016811235.1_ASM1681123v1_genomic.fna.gz --refList GCF_016811235.1_ASM1681123v1_genomic.fna/target_genomes.txt --output GCF_016811235.1_ASM1681123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:51,006] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:51,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfeebfc2-0dad-47c7-8d0d-2f022b33a3d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:51,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfeebfc2-0dad-47c7-8d0d-2f022b33a3d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:51,025] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:51,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:51,026] [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 arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	100.0	2103	2111	95	conclusive
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	88.6287	1243	2111	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	88.014	1358	2111	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	84.6866	936	2111	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	84.6107	1159	2111	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	84.2686	1069	2111	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.1409	1193	2111	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.1188	1097	2111	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	84.045	1117	2111	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	83.9871	1106	2111	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	82.8617	989	2111	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.7166	940	2111	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.4704	850	2111	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	82.3265	1001	2111	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	82.062	920	2111	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	79.9813	648	2111	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.3709	546	2111	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	78.35	492	2111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:51,029] [INFO] DFAST Taxonomy check result was written to GCF_016811235.1_ASM1681123v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:51,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:51,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:51,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfeebfc2-0dad-47c7-8d0d-2f022b33a3d4/dqc_reference/checkm_data
[2024-01-24 12:09:51,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:51,096] [INFO] Task started: CheckM
[2024-01-24 12:09:51,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016811235.1_ASM1681123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016811235.1_ASM1681123v1_genomic.fna/checkm_input GCF_016811235.1_ASM1681123v1_genomic.fna/checkm_result
[2024-01-24 12:10:45,695] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:45,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:45,718] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:45,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:45,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016811235.1_ASM1681123v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:45,720] [INFO] Task started: Blastn
[2024-01-24 12:10:45,720] [INFO] Running command: blastn -query GCF_016811235.1_ASM1681123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfeebfc2-0dad-47c7-8d0d-2f022b33a3d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016811235.1_ASM1681123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:47,601] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:47,605] [INFO] Selected 14 target genomes.
[2024-01-24 12:10:47,605] [INFO] Target genome list was writen to GCF_016811235.1_ASM1681123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:47,617] [INFO] Task started: fastANI
[2024-01-24 12:10:47,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg44176de7-a41e-4ff6-aa71-9d2d79c77518/GCF_016811235.1_ASM1681123v1_genomic.fna.gz --refList GCF_016811235.1_ASM1681123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016811235.1_ASM1681123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:11:08,436] [INFO] Task succeeded: fastANI
[2024-01-24 12:11:08,457] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:11:08,458] [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_016811235.1	s__Microvirga arabica	100.0	2103	2111	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_000739015.1	s__Microvirga sp000739015	89.3997	1358	2111	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	89.0555	1408	2111	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	88.6176	1244	2111	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	88.401	1146	2111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734765.1	s__Microvirga soli	87.9933	1359	2111	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	86.0594	1096	2111	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016743775.1	s__Microvirga aerilata	84.588	1161	2111	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	84.2863	1067	2111	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	84.154	1190	2111	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	84.0496	1118	2111	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	83.9974	1105	2111	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	83.7454	1200	2111	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	82.2238	900	2111	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 12:11:08,488] [INFO] GTDB search result was written to GCF_016811235.1_ASM1681123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:11:08,489] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:11:08,496] [INFO] DFAST_QC result json was written to GCF_016811235.1_ASM1681123v1_genomic.fna/dqc_result.json
[2024-01-24 12:11:08,496] [INFO] DFAST_QC completed!
[2024-01-24 12:11:08,496] [INFO] Total running time: 0h2m3s