[2024-01-24 11:50:49,136] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,138] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e913479-87d5-4f96-9978-457184476d5d/dqc_reference
[2024-01-24 11:50:50,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,368] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,369] [INFO] Running command: gunzip -c /var/lib/cwl/stgeddcf7e2-9577-45b8-b563-0f7b319b5dc7/GCF_027922345.1_ASM2792234v1_genomic.fna.gz | prodigal -d GCF_027922345.1_ASM2792234v1_genomic.fna/cds.fna -a GCF_027922345.1_ASM2792234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:06,104] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:06,104] [INFO] Task started: HMMsearch
[2024-01-24 11:51:06,105] [INFO] Running command: hmmsearch --tblout GCF_027922345.1_ASM2792234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e913479-87d5-4f96-9978-457184476d5d/dqc_reference/reference_markers.hmm GCF_027922345.1_ASM2792234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:06,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:06,408] [INFO] Found 6/6 markers.
[2024-01-24 11:51:06,455] [INFO] Query marker FASTA was written to GCF_027922345.1_ASM2792234v1_genomic.fna/markers.fasta
[2024-01-24 11:51:06,455] [INFO] Task started: Blastn
[2024-01-24 11:51:06,456] [INFO] Running command: blastn -query GCF_027922345.1_ASM2792234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e913479-87d5-4f96-9978-457184476d5d/dqc_reference/reference_markers.fasta -out GCF_027922345.1_ASM2792234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:07,505] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:07,510] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:07,510] [INFO] Target genome list was writen to GCF_027922345.1_ASM2792234v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:07,526] [INFO] Task started: fastANI
[2024-01-24 11:51:07,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgeddcf7e2-9577-45b8-b563-0f7b319b5dc7/GCF_027922345.1_ASM2792234v1_genomic.fna.gz --refList GCF_027922345.1_ASM2792234v1_genomic.fna/target_genomes.txt --output GCF_027922345.1_ASM2792234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:19,469] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:19,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e913479-87d5-4f96-9978-457184476d5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:19,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e913479-87d5-4f96-9978-457184476d5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:19,483] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:19,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:19,484] [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
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	100.0	1746	1747	95	conclusive
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	89.2088	1398	1747	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	88.9117	1349	1747	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	84.0142	1035	1747	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	83.5012	928	1747	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	83.4845	986	1747	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	83.1906	948	1747	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	78.6576	618	1747	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	78.6357	615	1747	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	77.437	419	1747	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:19,486] [INFO] DFAST Taxonomy check result was written to GCF_027922345.1_ASM2792234v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:19,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:19,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:19,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e913479-87d5-4f96-9978-457184476d5d/dqc_reference/checkm_data
[2024-01-24 11:51:19,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:19,537] [INFO] Task started: CheckM
[2024-01-24 11:51:19,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027922345.1_ASM2792234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027922345.1_ASM2792234v1_genomic.fna/checkm_input GCF_027922345.1_ASM2792234v1_genomic.fna/checkm_result
[2024-01-24 11:52:09,031] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:09,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:09,059] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:09,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:09,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027922345.1_ASM2792234v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:09,060] [INFO] Task started: Blastn
[2024-01-24 11:52:09,061] [INFO] Running command: blastn -query GCF_027922345.1_ASM2792234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e913479-87d5-4f96-9978-457184476d5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_027922345.1_ASM2792234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:11,176] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:11,180] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:11,180] [INFO] Target genome list was writen to GCF_027922345.1_ASM2792234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:11,203] [INFO] Task started: fastANI
[2024-01-24 11:52:11,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgeddcf7e2-9577-45b8-b563-0f7b319b5dc7/GCF_027922345.1_ASM2792234v1_genomic.fna.gz --refList GCF_027922345.1_ASM2792234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027922345.1_ASM2792234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:25,801] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:25,814] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:25,814] [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_018390605.1	s__Ancylobacter_B defluvii	100.0	1746	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018390695.1	s__Ancylobacter_B sonchi	89.2058	1398	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390555.1	s__Ancylobacter_B oerskovii	88.9439	1346	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	84.025	1034	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	83.9242	999	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009223885.1	s__Ancylobacter sp009223885	83.659	927	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	83.6302	914	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	83.4868	986	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	83.3384	952	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195655.1	s__Angulomicrobium tetraedrale	83.1421	1006	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012971745.1	s__ORNL1 sp012971745	82.4844	1013	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__ORNL1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390635.1	s__Ancylobacter_C lacus	82.3969	919	1747	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:25,817] [INFO] GTDB search result was written to GCF_027922345.1_ASM2792234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:25,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:25,823] [INFO] DFAST_QC result json was written to GCF_027922345.1_ASM2792234v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:25,823] [INFO] DFAST_QC completed!
[2024-01-24 11:52:25,824] [INFO] Total running time: 0h1m37s