[2024-01-24 12:06:50,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc09eb78-11a4-4af6-9fbd-d55a6b95d421/dqc_reference
[2024-01-24 12:06:51,581] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:51,582] [INFO] Task started: Prodigal
[2024-01-24 12:06:51,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg003f6e91-7e9a-4662-a90e-dbb8bed72169/GCF_017921815.1_ASM1792181v1_genomic.fna.gz | prodigal -d GCF_017921815.1_ASM1792181v1_genomic.fna/cds.fna -a GCF_017921815.1_ASM1792181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:05,134] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:05,134] [INFO] Task started: HMMsearch
[2024-01-24 12:07:05,135] [INFO] Running command: hmmsearch --tblout GCF_017921815.1_ASM1792181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc09eb78-11a4-4af6-9fbd-d55a6b95d421/dqc_reference/reference_markers.hmm GCF_017921815.1_ASM1792181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:05,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:05,416] [INFO] Found 6/6 markers.
[2024-01-24 12:07:05,456] [INFO] Query marker FASTA was written to GCF_017921815.1_ASM1792181v1_genomic.fna/markers.fasta
[2024-01-24 12:07:05,457] [INFO] Task started: Blastn
[2024-01-24 12:07:05,457] [INFO] Running command: blastn -query GCF_017921815.1_ASM1792181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc09eb78-11a4-4af6-9fbd-d55a6b95d421/dqc_reference/reference_markers.fasta -out GCF_017921815.1_ASM1792181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:06,437] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:06,440] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:06,441] [INFO] Target genome list was writen to GCF_017921815.1_ASM1792181v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:06,464] [INFO] Task started: fastANI
[2024-01-24 12:07:06,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg003f6e91-7e9a-4662-a90e-dbb8bed72169/GCF_017921815.1_ASM1792181v1_genomic.fna.gz --refList GCF_017921815.1_ASM1792181v1_genomic.fna/target_genomes.txt --output GCF_017921815.1_ASM1792181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:23,792] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:23,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc09eb78-11a4-4af6-9fbd-d55a6b95d421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:23,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc09eb78-11a4-4af6-9fbd-d55a6b95d421/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:23,806] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:23,806] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:23,807] [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 antarctica	strain=3D7	GCA_017921815.1	2819233	2819233	type	True	100.0	1479	1480	95	conclusive
Microvirga brassicacearum	strain=CDVBN77	GCA_008757455.1	2580413	2580413	type	True	81.5018	694	1480	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	80.0717	590	1480	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	79.8917	632	1480	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	79.8668	606	1480	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	79.8039	574	1480	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	79.783	615	1480	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	79.7572	555	1480	95	below_threshold
Microvirga aerophila	strain=DSM 21344	GCA_003332305.1	670291	670291	type	True	79.6238	543	1480	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	79.6235	572	1480	95	below_threshold
Microvirga aerophila	strain=NBRC 106136	GCA_007991675.1	670291	670291	type	True	79.6006	534	1480	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	79.5317	537	1480	95	below_threshold
Microvirga pudoricolor	strain=BT291	GCA_016892705.1	2778729	2778729	type	True	79.4701	555	1480	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	79.4576	546	1480	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	79.2525	498	1480	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.0062	396	1480	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.7159	358	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:23,808] [INFO] DFAST Taxonomy check result was written to GCF_017921815.1_ASM1792181v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:23,809] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:23,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:23,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc09eb78-11a4-4af6-9fbd-d55a6b95d421/dqc_reference/checkm_data
[2024-01-24 12:07:23,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:23,859] [INFO] Task started: CheckM
[2024-01-24 12:07:23,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017921815.1_ASM1792181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017921815.1_ASM1792181v1_genomic.fna/checkm_input GCF_017921815.1_ASM1792181v1_genomic.fna/checkm_result
[2024-01-24 12:08:07,363] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:07,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:07,386] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:07,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:07,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017921815.1_ASM1792181v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:07,387] [INFO] Task started: Blastn
[2024-01-24 12:08:07,387] [INFO] Running command: blastn -query GCF_017921815.1_ASM1792181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc09eb78-11a4-4af6-9fbd-d55a6b95d421/dqc_reference/reference_markers_gtdb.fasta -out GCF_017921815.1_ASM1792181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:09,280] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:09,284] [INFO] Selected 16 target genomes.
[2024-01-24 12:08:09,284] [INFO] Target genome list was writen to GCF_017921815.1_ASM1792181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:09,292] [INFO] Task started: fastANI
[2024-01-24 12:08:09,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg003f6e91-7e9a-4662-a90e-dbb8bed72169/GCF_017921815.1_ASM1792181v1_genomic.fna.gz --refList GCF_017921815.1_ASM1792181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017921815.1_ASM1792181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:25,355] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:25,371] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:25,371] [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_017921815.1	s__Microvirga sp017921815	100.0	1479	1480	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_008757455.1	s__Microvirga brassicacearum	81.5036	693	1480	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	79.8929	631	1480	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	79.8812	610	1480	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	79.8521	607	1480	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	79.7777	603	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016735695.1	s__Microvirga zambiensis	79.7739	616	1480	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	79.7477	556	1480	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	79.6395	599	1480	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	79.6238	543	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	99.85	99.85	0.93	0.93	2	-
GCF_009363855.1	s__Microvirga thermotolerans	79.6186	573	1480	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	79.5886	575	1480	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	79.557	609	1480	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	79.5317	537	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016892705.1	s__Microvirga sp016892705	79.4435	558	1480	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	79.2525	498	1480	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 12:08:25,372] [INFO] GTDB search result was written to GCF_017921815.1_ASM1792181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:25,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:25,377] [INFO] DFAST_QC result json was written to GCF_017921815.1_ASM1792181v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:25,377] [INFO] DFAST_QC completed!
[2024-01-24 12:08:25,377] [INFO] Total running time: 0h1m35s