[2024-01-25 19:53:05,510] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:05,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:05,512] [INFO] DQC Reference Directory: /var/lib/cwl/stgb46aeaa8-fedc-4494-b43b-1142a6ac29ad/dqc_reference
[2024-01-25 19:53:06,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:06,665] [INFO] Task started: Prodigal
[2024-01-25 19:53:06,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg094415d4-b3c0-4b68-bfb3-6e2175d36a15/GCF_014837245.1_ASM1483724v1_genomic.fna.gz | prodigal -d GCF_014837245.1_ASM1483724v1_genomic.fna/cds.fna -a GCF_014837245.1_ASM1483724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:17,261] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:17,261] [INFO] Task started: HMMsearch
[2024-01-25 19:53:17,261] [INFO] Running command: hmmsearch --tblout GCF_014837245.1_ASM1483724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb46aeaa8-fedc-4494-b43b-1142a6ac29ad/dqc_reference/reference_markers.hmm GCF_014837245.1_ASM1483724v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:17,487] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:17,488] [INFO] Found 6/6 markers.
[2024-01-25 19:53:17,515] [INFO] Query marker FASTA was written to GCF_014837245.1_ASM1483724v1_genomic.fna/markers.fasta
[2024-01-25 19:53:17,515] [INFO] Task started: Blastn
[2024-01-25 19:53:17,515] [INFO] Running command: blastn -query GCF_014837245.1_ASM1483724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46aeaa8-fedc-4494-b43b-1142a6ac29ad/dqc_reference/reference_markers.fasta -out GCF_014837245.1_ASM1483724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:18,309] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:18,316] [INFO] Selected 17 target genomes.
[2024-01-25 19:53:18,317] [INFO] Target genome list was writen to GCF_014837245.1_ASM1483724v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:18,327] [INFO] Task started: fastANI
[2024-01-25 19:53:18,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg094415d4-b3c0-4b68-bfb3-6e2175d36a15/GCF_014837245.1_ASM1483724v1_genomic.fna.gz --refList GCF_014837245.1_ASM1483724v1_genomic.fna/target_genomes.txt --output GCF_014837245.1_ASM1483724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:32,250] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:32,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb46aeaa8-fedc-4494-b43b-1142a6ac29ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:32,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb46aeaa8-fedc-4494-b43b-1142a6ac29ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:32,262] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:53:32,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:53:32,262] [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 salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.8556	704	1222	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.8509	639	1222	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	80.5519	639	1222	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	80.1986	602	1222	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	80.1157	600	1222	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	80.0736	586	1222	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	80.0046	608	1222	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.9818	582	1222	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	79.9797	545	1222	95	below_threshold
Devosia aurantiaca	strain=H239	GCA_011058215.1	2714858	2714858	type	True	79.8814	567	1222	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	79.6894	551	1222	95	below_threshold
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	79.6802	595	1222	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.6598	552	1222	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.542	569	1222	95	below_threshold
Devosia crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	79.5201	505	1222	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	79.311	595	1222	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.5044	194	1222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:32,263] [INFO] DFAST Taxonomy check result was written to GCF_014837245.1_ASM1483724v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:32,264] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:32,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:32,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb46aeaa8-fedc-4494-b43b-1142a6ac29ad/dqc_reference/checkm_data
[2024-01-25 19:53:32,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:32,303] [INFO] Task started: CheckM
[2024-01-25 19:53:32,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837245.1_ASM1483724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837245.1_ASM1483724v1_genomic.fna/checkm_input GCF_014837245.1_ASM1483724v1_genomic.fna/checkm_result
[2024-01-25 19:54:05,506] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:05,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:05,588] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:05,588] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:05,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837245.1_ASM1483724v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:05,590] [INFO] Task started: Blastn
[2024-01-25 19:54:05,590] [INFO] Running command: blastn -query GCF_014837245.1_ASM1483724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46aeaa8-fedc-4494-b43b-1142a6ac29ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837245.1_ASM1483724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:06,961] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:06,963] [INFO] Selected 14 target genomes.
[2024-01-25 19:54:06,964] [INFO] Target genome list was writen to GCF_014837245.1_ASM1483724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:06,978] [INFO] Task started: fastANI
[2024-01-25 19:54:06,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg094415d4-b3c0-4b68-bfb3-6e2175d36a15/GCF_014837245.1_ASM1483724v1_genomic.fna.gz --refList GCF_014837245.1_ASM1483724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837245.1_ASM1483724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:18,382] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:18,393] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:18,393] [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_014837245.1	s__Devosia sp014837245	100.0	1222	1222	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_001650025.1	s__Devosia elaeis	80.874	637	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411825.1	s__Devosia sp016411825	80.5344	641	1222	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	80.2027	602	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056405.1	s__Devosia indica	80.1104	601	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000969445.1	s__Devosia chinhatensis	80.0642	587	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631955.1	s__Devosia sp001899045	79.9933	609	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCA_014860165.1	s__Devosia sp014860165	79.9452	569	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058215.1	s__Devosia aurantiaca	79.8681	568	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758415.1	s__Devosia marina	79.8671	560	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCA_018828145.1	s__Devosia sp018828145	79.8028	624	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_000743575.1	s__Devosia riboflavina	79.6978	593	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222805.1	s__Devosia sp005222805	79.4732	566	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234425.1	s__Devosia sp015234425	79.3751	557	1222	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 19:54:18,397] [INFO] GTDB search result was written to GCF_014837245.1_ASM1483724v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:18,398] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:18,404] [INFO] DFAST_QC result json was written to GCF_014837245.1_ASM1483724v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:18,404] [INFO] DFAST_QC completed!
[2024-01-25 19:54:18,404] [INFO] Total running time: 0h1m13s