[2024-01-24 12:21:43,979] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:43,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:43,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d2556ac-5745-4712-93de-e09cf3fee5ab/dqc_reference
[2024-01-24 12:21:45,469] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,470] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,471] [INFO] Running command: gunzip -c /var/lib/cwl/stgb86bb633-ae5b-49f1-9b4c-0b2d99fa6462/GCF_003290125.1_ASM329012v1_genomic.fna.gz | prodigal -d GCF_003290125.1_ASM329012v1_genomic.fna/cds.fna -a GCF_003290125.1_ASM329012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:56,291] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:56,291] [INFO] Task started: HMMsearch
[2024-01-24 12:21:56,292] [INFO] Running command: hmmsearch --tblout GCF_003290125.1_ASM329012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d2556ac-5745-4712-93de-e09cf3fee5ab/dqc_reference/reference_markers.hmm GCF_003290125.1_ASM329012v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:56,598] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:56,599] [INFO] Found 6/6 markers.
[2024-01-24 12:21:56,632] [INFO] Query marker FASTA was written to GCF_003290125.1_ASM329012v1_genomic.fna/markers.fasta
[2024-01-24 12:21:56,633] [INFO] Task started: Blastn
[2024-01-24 12:21:56,633] [INFO] Running command: blastn -query GCF_003290125.1_ASM329012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d2556ac-5745-4712-93de-e09cf3fee5ab/dqc_reference/reference_markers.fasta -out GCF_003290125.1_ASM329012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:57,656] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:57,659] [INFO] Selected 18 target genomes.
[2024-01-24 12:21:57,659] [INFO] Target genome list was writen to GCF_003290125.1_ASM329012v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:57,667] [INFO] Task started: fastANI
[2024-01-24 12:21:57,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86bb633-ae5b-49f1-9b4c-0b2d99fa6462/GCF_003290125.1_ASM329012v1_genomic.fna.gz --refList GCF_003290125.1_ASM329012v1_genomic.fna/target_genomes.txt --output GCF_003290125.1_ASM329012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:17,031] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:17,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d2556ac-5745-4712-93de-e09cf3fee5ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:17,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d2556ac-5745-4712-93de-e09cf3fee5ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:17,046] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:17,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:17,047] [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 flavescens	strain=c27j1	GCA_003290125.1	2249811	2249811	type	True	100.0	1162	1163	95	conclusive
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	81.1522	641	1163	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	81.0402	542	1163	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	80.7647	634	1163	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	80.7624	578	1163	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	80.7046	601	1163	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	80.6745	590	1163	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	80.6509	617	1163	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	80.6098	627	1163	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	80.605	642	1163	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	80.5983	575	1163	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	80.5707	621	1163	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	80.5623	614	1163	95	below_threshold
Microvirga aerophila	strain=DSM 21344	GCA_003332305.1	670291	670291	type	True	80.2523	533	1163	95	below_threshold
Microvirga aerophila	strain=NBRC 106136	GCA_007991675.1	670291	670291	type	True	80.1729	525	1163	95	below_threshold
Microvirga brassicacearum	strain=CDVBN77	GCA_008757455.1	2580413	2580413	type	True	79.4995	492	1163	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	78.5794	405	1163	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	78.1068	250	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:17,049] [INFO] DFAST Taxonomy check result was written to GCF_003290125.1_ASM329012v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:17,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:17,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:17,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d2556ac-5745-4712-93de-e09cf3fee5ab/dqc_reference/checkm_data
[2024-01-24 12:22:17,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:17,093] [INFO] Task started: CheckM
[2024-01-24 12:22:17,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003290125.1_ASM329012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003290125.1_ASM329012v1_genomic.fna/checkm_input GCF_003290125.1_ASM329012v1_genomic.fna/checkm_result
[2024-01-24 12:22:52,741] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:52,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:52,776] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:52,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:52,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003290125.1_ASM329012v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:52,778] [INFO] Task started: Blastn
[2024-01-24 12:22:52,778] [INFO] Running command: blastn -query GCF_003290125.1_ASM329012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d2556ac-5745-4712-93de-e09cf3fee5ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_003290125.1_ASM329012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:54,795] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:54,798] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:54,799] [INFO] Target genome list was writen to GCF_003290125.1_ASM329012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:54,822] [INFO] Task started: fastANI
[2024-01-24 12:22:54,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86bb633-ae5b-49f1-9b4c-0b2d99fa6462/GCF_003290125.1_ASM329012v1_genomic.fna.gz --refList GCF_003290125.1_ASM329012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003290125.1_ASM329012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:12,217] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:12,230] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:12,231] [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_003290125.1	s__Microvirga flavescens	100.0	1162	1163	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_011777495.1	s__Microvirga sp011777495	81.4118	653	1163	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	81.1522	641	1163	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	81.0597	540	1163	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	80.7611	571	1163	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	80.7546	635	1163	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	80.6713	601	1163	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	80.6647	615	1163	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	80.6102	627	1163	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	80.5795	621	1163	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	80.5769	577	1163	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	80.5215	619	1163	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	80.337	615	1163	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	80.2914	606	1163	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	80.2687	559	1163	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	80.242	534	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	99.85	99.85	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:12,234] [INFO] GTDB search result was written to GCF_003290125.1_ASM329012v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:12,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:12,240] [INFO] DFAST_QC result json was written to GCF_003290125.1_ASM329012v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:12,241] [INFO] DFAST_QC completed!
[2024-01-24 12:23:12,241] [INFO] Total running time: 0h1m28s