[2024-01-24 13:40:28,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg28841048-7157-4aae-9ee3-1575ee2b29ac/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,144] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ff8d94f-945a-4926-a519-ac1f0727ee9a/GCF_016892705.1_ASM1689270v1_genomic.fna.gz | prodigal -d GCF_016892705.1_ASM1689270v1_genomic.fna/cds.fna -a GCF_016892705.1_ASM1689270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:45,238] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:45,239] [INFO] Task started: HMMsearch
[2024-01-24 13:40:45,239] [INFO] Running command: hmmsearch --tblout GCF_016892705.1_ASM1689270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28841048-7157-4aae-9ee3-1575ee2b29ac/dqc_reference/reference_markers.hmm GCF_016892705.1_ASM1689270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,582] [INFO] Found 6/6 markers.
[2024-01-24 13:40:45,632] [INFO] Query marker FASTA was written to GCF_016892705.1_ASM1689270v1_genomic.fna/markers.fasta
[2024-01-24 13:40:45,633] [INFO] Task started: Blastn
[2024-01-24 13:40:45,633] [INFO] Running command: blastn -query GCF_016892705.1_ASM1689270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28841048-7157-4aae-9ee3-1575ee2b29ac/dqc_reference/reference_markers.fasta -out GCF_016892705.1_ASM1689270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,650] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:46,650] [INFO] Target genome list was writen to GCF_016892705.1_ASM1689270v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,657] [INFO] Task started: fastANI
[2024-01-24 13:40:46,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff8d94f-945a-4926-a519-ac1f0727ee9a/GCF_016892705.1_ASM1689270v1_genomic.fna.gz --refList GCF_016892705.1_ASM1689270v1_genomic.fna/target_genomes.txt --output GCF_016892705.1_ASM1689270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:06,038] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:06,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28841048-7157-4aae-9ee3-1575ee2b29ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:06,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28841048-7157-4aae-9ee3-1575ee2b29ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:06,054] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:06,054] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:06,055] [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 pudoricolor	strain=BT291	GCA_016892705.1	2778729	2778729	type	True	100.0	1580	1583	95	conclusive
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	81.226	700	1583	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	81.1867	740	1583	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	81.1242	766	1583	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	81.1189	748	1583	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	80.9413	722	1583	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	80.937	667	1583	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	80.9106	765	1583	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	80.9036	705	1583	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	80.8734	690	1583	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	80.8014	757	1583	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	80.75	721	1583	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	80.5985	686	1583	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	80.5468	671	1583	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	79.9226	586	1583	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.3825	517	1583	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	78.3421	497	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,056] [INFO] DFAST Taxonomy check result was written to GCF_016892705.1_ASM1689270v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:06,057] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:06,057] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:06,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28841048-7157-4aae-9ee3-1575ee2b29ac/dqc_reference/checkm_data
[2024-01-24 13:41:06,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:06,104] [INFO] Task started: CheckM
[2024-01-24 13:41:06,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016892705.1_ASM1689270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016892705.1_ASM1689270v1_genomic.fna/checkm_input GCF_016892705.1_ASM1689270v1_genomic.fna/checkm_result
[2024-01-24 13:41:49,357] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:49,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,378] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:49,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:49,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016892705.1_ASM1689270v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:49,380] [INFO] Task started: Blastn
[2024-01-24 13:41:49,380] [INFO] Running command: blastn -query GCF_016892705.1_ASM1689270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28841048-7157-4aae-9ee3-1575ee2b29ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_016892705.1_ASM1689270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,425] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,430] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:51,430] [INFO] Target genome list was writen to GCF_016892705.1_ASM1689270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:51,452] [INFO] Task started: fastANI
[2024-01-24 13:41:51,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff8d94f-945a-4926-a519-ac1f0727ee9a/GCF_016892705.1_ASM1689270v1_genomic.fna.gz --refList GCF_016892705.1_ASM1689270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016892705.1_ASM1689270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:15,169] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:15,195] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:15,195] [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_016892705.1	s__Microvirga sp016892705	100.0	1580	1583	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_016427565.1	s__Microvirga sp016427565	81.1923	739	1583	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	81.1542	755	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003350535.1	s__Microvirga subterranea	81.1243	766	1583	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	81.1149	748	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518665.1	s__Microvirga flocculans	80.9519	666	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016743775.1	s__Microvirga aerilata	80.9413	722	1583	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	80.9131	722	1583	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	80.9097	764	1583	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	80.9034	704	1583	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	80.8962	744	1583	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	80.892	691	1583	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	80.8268	744	1583	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	80.8096	779	1583	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	80.8078	757	1583	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003151255.1	s__Microvirga sp003151255	80.781	700	1583	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	80.7698	708	1583	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	80.669	747	1583	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	80.5456	702	1583	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	80.5321	673	1583	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	79.9067	589	1583	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 13:42:15,197] [INFO] GTDB search result was written to GCF_016892705.1_ASM1689270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:15,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:15,202] [INFO] DFAST_QC result json was written to GCF_016892705.1_ASM1689270v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:15,203] [INFO] DFAST_QC completed!
[2024-01-24 13:42:15,203] [INFO] Total running time: 0h1m47s