[2024-01-24 14:06:07,020] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d6248cb-a12e-44f6-85c2-7a7705ad17eb/dqc_reference
[2024-01-24 14:06:08,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,449] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,450] [INFO] Running command: gunzip -c /var/lib/cwl/stgd971a748-e0ba-4432-b322-f4bf6685aaa4/GCF_020089865.1_ASM2008986v1_genomic.fna.gz | prodigal -d GCF_020089865.1_ASM2008986v1_genomic.fna/cds.fna -a GCF_020089865.1_ASM2008986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:24,345] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:24,346] [INFO] Task started: HMMsearch
[2024-01-24 14:06:24,346] [INFO] Running command: hmmsearch --tblout GCF_020089865.1_ASM2008986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d6248cb-a12e-44f6-85c2-7a7705ad17eb/dqc_reference/reference_markers.hmm GCF_020089865.1_ASM2008986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:24,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:24,661] [INFO] Found 6/6 markers.
[2024-01-24 14:06:24,710] [INFO] Query marker FASTA was written to GCF_020089865.1_ASM2008986v1_genomic.fna/markers.fasta
[2024-01-24 14:06:24,710] [INFO] Task started: Blastn
[2024-01-24 14:06:24,711] [INFO] Running command: blastn -query GCF_020089865.1_ASM2008986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d6248cb-a12e-44f6-85c2-7a7705ad17eb/dqc_reference/reference_markers.fasta -out GCF_020089865.1_ASM2008986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:25,729] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:25,732] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:25,732] [INFO] Target genome list was writen to GCF_020089865.1_ASM2008986v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:25,744] [INFO] Task started: fastANI
[2024-01-24 14:06:25,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgd971a748-e0ba-4432-b322-f4bf6685aaa4/GCF_020089865.1_ASM2008986v1_genomic.fna.gz --refList GCF_020089865.1_ASM2008986v1_genomic.fna/target_genomes.txt --output GCF_020089865.1_ASM2008986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:49,206] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:49,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d6248cb-a12e-44f6-85c2-7a7705ad17eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:49,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d6248cb-a12e-44f6-85c2-7a7705ad17eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:49,222] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:49,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:49,223] [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 thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	81.9589	816	1697	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	81.6675	867	1697	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	80.7789	723	1697	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	80.6992	652	1697	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	80.4648	760	1697	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	80.4534	648	1697	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	80.4236	731	1697	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	80.3303	756	1697	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	80.2646	703	1697	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	80.2502	725	1697	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	80.2374	631	1697	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	80.2086	694	1697	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	80.1053	646	1697	95	below_threshold
Microvirga aerophila	strain=DSM 21344	GCA_003332305.1	670291	670291	type	True	80.0912	612	1697	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	80.0513	630	1697	95	below_threshold
Microvirga aerophila	strain=NBRC 106136	GCA_007991675.1	670291	670291	type	True	79.9712	627	1697	95	below_threshold
Microvirga flavescens	strain=c27j1	GCA_003290125.1	2249811	2249811	type	True	79.7672	529	1697	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.8479	368	1697	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.7784	361	1697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:49,224] [INFO] DFAST Taxonomy check result was written to GCF_020089865.1_ASM2008986v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:49,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:49,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:49,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d6248cb-a12e-44f6-85c2-7a7705ad17eb/dqc_reference/checkm_data
[2024-01-24 14:06:49,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:49,282] [INFO] Task started: CheckM
[2024-01-24 14:06:49,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020089865.1_ASM2008986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020089865.1_ASM2008986v1_genomic.fna/checkm_input GCF_020089865.1_ASM2008986v1_genomic.fna/checkm_result
[2024-01-24 14:07:34,911] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:34,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:34,933] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:34,934] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:34,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020089865.1_ASM2008986v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:34,934] [INFO] Task started: Blastn
[2024-01-24 14:07:34,935] [INFO] Running command: blastn -query GCF_020089865.1_ASM2008986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d6248cb-a12e-44f6-85c2-7a7705ad17eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_020089865.1_ASM2008986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:36,823] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:36,827] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:36,827] [INFO] Target genome list was writen to GCF_020089865.1_ASM2008986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:36,846] [INFO] Task started: fastANI
[2024-01-24 14:07:36,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgd971a748-e0ba-4432-b322-f4bf6685aaa4/GCF_020089865.1_ASM2008986v1_genomic.fna.gz --refList GCF_020089865.1_ASM2008986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020089865.1_ASM2008986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:52,712] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:52,727] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:52,727] [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_009363855.1	s__Microvirga thermotolerans	81.9371	819	1697	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	81.8842	866	1697	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	80.7946	721	1697	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	80.5015	661	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002741015.1	s__Microvirga ossetica	80.468	760	1697	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	80.4592	647	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016735695.1	s__Microvirga zambiensis	80.4363	729	1697	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	80.3313	756	1697	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	80.262	725	1697	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	80.2478	705	1697	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	80.1108	645	1697	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	80.0958	612	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	99.85	99.85	0.93	0.93	2	-
GCF_011777495.1	s__Microvirga sp011777495	80.0334	629	1697	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	80.0167	755	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003290125.1	s__Microvirga flavescens	79.7458	532	1697	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 14:07:52,729] [INFO] GTDB search result was written to GCF_020089865.1_ASM2008986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:52,729] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:52,733] [INFO] DFAST_QC result json was written to GCF_020089865.1_ASM2008986v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:52,733] [INFO] DFAST_QC completed!
[2024-01-24 14:07:52,733] [INFO] Total running time: 0h1m46s