[2024-01-24 13:49:27,665] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fa26e03-7585-4774-a42a-d08043fdc721/dqc_reference
[2024-01-24 13:49:29,158] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:29,159] [INFO] Task started: Prodigal
[2024-01-24 13:49:29,160] [INFO] Running command: gunzip -c /var/lib/cwl/stga1411b10-7433-434f-82ac-f6b929488f10/GCF_001017175.1_ASM101717v1_genomic.fna.gz | prodigal -d GCF_001017175.1_ASM101717v1_genomic.fna/cds.fna -a GCF_001017175.1_ASM101717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,079] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,080] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,080] [INFO] Running command: hmmsearch --tblout GCF_001017175.1_ASM101717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fa26e03-7585-4774-a42a-d08043fdc721/dqc_reference/reference_markers.hmm GCF_001017175.1_ASM101717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:49,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:49,409] [INFO] Found 6/6 markers.
[2024-01-24 13:49:49,467] [INFO] Query marker FASTA was written to GCF_001017175.1_ASM101717v1_genomic.fna/markers.fasta
[2024-01-24 13:49:49,468] [INFO] Task started: Blastn
[2024-01-24 13:49:49,468] [INFO] Running command: blastn -query GCF_001017175.1_ASM101717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa26e03-7585-4774-a42a-d08043fdc721/dqc_reference/reference_markers.fasta -out GCF_001017175.1_ASM101717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,519] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:50,519] [INFO] Target genome list was writen to GCF_001017175.1_ASM101717v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,522] [INFO] Task started: fastANI
[2024-01-24 13:49:50,522] [INFO] Running command: fastANI --query /var/lib/cwl/stga1411b10-7433-434f-82ac-f6b929488f10/GCF_001017175.1_ASM101717v1_genomic.fna.gz --refList GCF_001017175.1_ASM101717v1_genomic.fna/target_genomes.txt --output GCF_001017175.1_ASM101717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:08,593] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fa26e03-7585-4774-a42a-d08043fdc721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:08,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fa26e03-7585-4774-a42a-d08043fdc721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:08,610] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:08,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:08,611] [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 vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	100.0	2066	2076	95	conclusive
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	84.0841	1047	2076	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	84.0054	958	2076	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	83.6457	1013	2076	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	82.8869	797	2076	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	82.4428	864	2076	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	82.3343	987	2076	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	82.066	910	2076	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	82.0019	931	2076	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	81.7748	823	2076	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	81.4852	741	2076	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	81.134	799	2076	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.1297	392	2076	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.9451	416	2076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,612] [INFO] DFAST Taxonomy check result was written to GCF_001017175.1_ASM101717v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:08,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:08,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:08,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fa26e03-7585-4774-a42a-d08043fdc721/dqc_reference/checkm_data
[2024-01-24 13:50:08,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:08,680] [INFO] Task started: CheckM
[2024-01-24 13:50:08,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001017175.1_ASM101717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001017175.1_ASM101717v1_genomic.fna/checkm_input GCF_001017175.1_ASM101717v1_genomic.fna/checkm_result
[2024-01-24 13:51:04,029] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:04,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:04,056] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:04,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:04,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001017175.1_ASM101717v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:04,057] [INFO] Task started: Blastn
[2024-01-24 13:51:04,057] [INFO] Running command: blastn -query GCF_001017175.1_ASM101717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa26e03-7585-4774-a42a-d08043fdc721/dqc_reference/reference_markers_gtdb.fasta -out GCF_001017175.1_ASM101717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:05,873] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:05,877] [INFO] Selected 9 target genomes.
[2024-01-24 13:51:05,877] [INFO] Target genome list was writen to GCF_001017175.1_ASM101717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:05,888] [INFO] Task started: fastANI
[2024-01-24 13:51:05,888] [INFO] Running command: fastANI --query /var/lib/cwl/stga1411b10-7433-434f-82ac-f6b929488f10/GCF_001017175.1_ASM101717v1_genomic.fna.gz --refList GCF_001017175.1_ASM101717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001017175.1_ASM101717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:18,801] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:18,815] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:18,815] [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_001017175.1	s__Microvirga vignae	100.0	2066	2076	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_003075415.1	s__Microvirga sp003075415	90.9706	1496	2076	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	84.0815	1047	2076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102135.1	s__Microvirga guangxiensis	84.0143	957	2076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830105.1	s__Microvirga makkahensis	83.6507	1012	2076	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	82.6931	1188	2076	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	82.181	972	2076	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	82.0608	911	2076	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	81.8698	941	2076	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 13:51:18,817] [INFO] GTDB search result was written to GCF_001017175.1_ASM101717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:18,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:18,820] [INFO] DFAST_QC result json was written to GCF_001017175.1_ASM101717v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:18,820] [INFO] DFAST_QC completed!
[2024-01-24 13:51:18,821] [INFO] Total running time: 0h1m51s