[2024-01-25 20:17:20,722] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:20,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:20,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e917d9d-6131-4da3-81d3-aa76ae246da8/dqc_reference
[2024-01-25 20:17:21,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:21,861] [INFO] Task started: Prodigal
[2024-01-25 20:17:21,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg55312f02-e03a-4c4c-8984-dc64fdb2a092/GCF_014197055.1_ASM1419705v1_genomic.fna.gz | prodigal -d GCF_014197055.1_ASM1419705v1_genomic.fna/cds.fna -a GCF_014197055.1_ASM1419705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:32,802] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:32,802] [INFO] Task started: HMMsearch
[2024-01-25 20:17:32,803] [INFO] Running command: hmmsearch --tblout GCF_014197055.1_ASM1419705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e917d9d-6131-4da3-81d3-aa76ae246da8/dqc_reference/reference_markers.hmm GCF_014197055.1_ASM1419705v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:33,034] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:33,036] [INFO] Found 6/6 markers.
[2024-01-25 20:17:33,065] [INFO] Query marker FASTA was written to GCF_014197055.1_ASM1419705v1_genomic.fna/markers.fasta
[2024-01-25 20:17:33,066] [INFO] Task started: Blastn
[2024-01-25 20:17:33,066] [INFO] Running command: blastn -query GCF_014197055.1_ASM1419705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e917d9d-6131-4da3-81d3-aa76ae246da8/dqc_reference/reference_markers.fasta -out GCF_014197055.1_ASM1419705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:33,848] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:33,850] [INFO] Selected 9 target genomes.
[2024-01-25 20:17:33,850] [INFO] Target genome list was writen to GCF_014197055.1_ASM1419705v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:33,861] [INFO] Task started: fastANI
[2024-01-25 20:17:33,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg55312f02-e03a-4c4c-8984-dc64fdb2a092/GCF_014197055.1_ASM1419705v1_genomic.fna.gz --refList GCF_014197055.1_ASM1419705v1_genomic.fna/target_genomes.txt --output GCF_014197055.1_ASM1419705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:41,630] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:41,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e917d9d-6131-4da3-81d3-aa76ae246da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:41,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e917d9d-6131-4da3-81d3-aa76ae246da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:41,638] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:17:41,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:41,638] [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
Devosia subaequoris	strain=DSM 23447	GCA_014197055.1	395930	395930	type	True	100.0	1243	1245	95	conclusive
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	99.9852	1223	1245	95	conclusive
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	89.1432	1013	1245	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	88.0441	963	1245	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	82.7097	867	1245	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	81.2702	729	1245	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.6183	603	1245	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	79.5095	617	1245	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.2831	560	1245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:41,639] [INFO] DFAST Taxonomy check result was written to GCF_014197055.1_ASM1419705v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:41,640] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:41,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:41,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e917d9d-6131-4da3-81d3-aa76ae246da8/dqc_reference/checkm_data
[2024-01-25 20:17:41,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:41,679] [INFO] Task started: CheckM
[2024-01-25 20:17:41,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197055.1_ASM1419705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197055.1_ASM1419705v1_genomic.fna/checkm_input GCF_014197055.1_ASM1419705v1_genomic.fna/checkm_result
[2024-01-25 20:18:14,786] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:14,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:14,807] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:14,808] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:14,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197055.1_ASM1419705v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:14,809] [INFO] Task started: Blastn
[2024-01-25 20:18:14,809] [INFO] Running command: blastn -query GCF_014197055.1_ASM1419705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e917d9d-6131-4da3-81d3-aa76ae246da8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197055.1_ASM1419705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:16,202] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:16,205] [INFO] Selected 10 target genomes.
[2024-01-25 20:18:16,205] [INFO] Target genome list was writen to GCF_014197055.1_ASM1419705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:16,217] [INFO] Task started: fastANI
[2024-01-25 20:18:16,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg55312f02-e03a-4c4c-8984-dc64fdb2a092/GCF_014197055.1_ASM1419705v1_genomic.fna.gz --refList GCF_014197055.1_ASM1419705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197055.1_ASM1419705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:25,140] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:25,148] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:25,148] [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_014197055.1	s__Devosia subaequoris	100.0	1243	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009758415.1	s__Devosia marina	89.1432	1013	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_003056405.1	s__Devosia indica	88.0301	964	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016411825.1	s__Devosia sp016411825	81.5891	769	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	81.2829	728	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015158295.1	s__Devosia sp015158295	80.5354	646	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177655.1	s__Devosia lucknowensis	80.3493	685	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	79.8697	644	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_001427875.1	s__Devosia sp001427875	79.7442	635	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698665.1	s__Devosia sp016698665	79.6269	602	1245	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:25,150] [INFO] GTDB search result was written to GCF_014197055.1_ASM1419705v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:25,151] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:25,153] [INFO] DFAST_QC result json was written to GCF_014197055.1_ASM1419705v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:25,154] [INFO] DFAST_QC completed!
[2024-01-25 20:18:25,154] [INFO] Total running time: 0h1m4s