[2024-01-25 20:27:20,561] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e727d95-7a18-4477-b005-a7b721aaa3b6/dqc_reference
[2024-01-25 20:27:21,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:21,741] [INFO] Task started: Prodigal
[2024-01-25 20:27:21,741] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf880fdd-0e82-44f1-84a3-fadc3510d6f4/GCF_024273205.1_ASM2427320v1_genomic.fna.gz | prodigal -d GCF_024273205.1_ASM2427320v1_genomic.fna/cds.fna -a GCF_024273205.1_ASM2427320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:32,670] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:32,671] [INFO] Task started: HMMsearch
[2024-01-25 20:27:32,671] [INFO] Running command: hmmsearch --tblout GCF_024273205.1_ASM2427320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e727d95-7a18-4477-b005-a7b721aaa3b6/dqc_reference/reference_markers.hmm GCF_024273205.1_ASM2427320v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:32,878] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:32,879] [INFO] Found 6/6 markers.
[2024-01-25 20:27:32,909] [INFO] Query marker FASTA was written to GCF_024273205.1_ASM2427320v1_genomic.fna/markers.fasta
[2024-01-25 20:27:32,909] [INFO] Task started: Blastn
[2024-01-25 20:27:32,909] [INFO] Running command: blastn -query GCF_024273205.1_ASM2427320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e727d95-7a18-4477-b005-a7b721aaa3b6/dqc_reference/reference_markers.fasta -out GCF_024273205.1_ASM2427320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:33,696] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:33,699] [INFO] Selected 13 target genomes.
[2024-01-25 20:27:33,700] [INFO] Target genome list was writen to GCF_024273205.1_ASM2427320v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:33,775] [INFO] Task started: fastANI
[2024-01-25 20:27:33,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf880fdd-0e82-44f1-84a3-fadc3510d6f4/GCF_024273205.1_ASM2427320v1_genomic.fna.gz --refList GCF_024273205.1_ASM2427320v1_genomic.fna/target_genomes.txt --output GCF_024273205.1_ASM2427320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:44,531] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:44,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e727d95-7a18-4477-b005-a7b721aaa3b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:44,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e727d95-7a18-4477-b005-a7b721aaa3b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:44,540] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:27:44,540] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:27:44,540] [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	84.0105	923	1249	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	82.8471	816	1249	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	82.8351	862	1249	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	82.4099	837	1249	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	82.0897	739	1249	95	below_threshold
Devosia subaequoris	strain=DSM 23447	GCA_014197055.1	395930	395930	type	True	81.9913	803	1249	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	81.9757	804	1249	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	81.1944	701	1249	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	81.0344	676	1249	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	80.5471	633	1249	95	below_threshold
Devosia aurantiaca	strain=H239	GCA_011058215.1	2714858	2714858	type	True	80.4959	641	1249	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	80.3765	705	1249	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.9852	666	1249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:44,543] [INFO] DFAST Taxonomy check result was written to GCF_024273205.1_ASM2427320v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:44,543] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:44,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:44,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e727d95-7a18-4477-b005-a7b721aaa3b6/dqc_reference/checkm_data
[2024-01-25 20:27:44,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:44,584] [INFO] Task started: CheckM
[2024-01-25 20:27:44,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024273205.1_ASM2427320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024273205.1_ASM2427320v1_genomic.fna/checkm_input GCF_024273205.1_ASM2427320v1_genomic.fna/checkm_result
[2024-01-25 20:28:19,473] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:19,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:19,487] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:19,487] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:19,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024273205.1_ASM2427320v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:19,488] [INFO] Task started: Blastn
[2024-01-25 20:28:19,488] [INFO] Running command: blastn -query GCF_024273205.1_ASM2427320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e727d95-7a18-4477-b005-a7b721aaa3b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_024273205.1_ASM2427320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:20,948] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:20,951] [INFO] Selected 12 target genomes.
[2024-01-25 20:28:20,951] [INFO] Target genome list was writen to GCF_024273205.1_ASM2427320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:20,975] [INFO] Task started: fastANI
[2024-01-25 20:28:20,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf880fdd-0e82-44f1-84a3-fadc3510d6f4/GCF_024273205.1_ASM2427320v1_genomic.fna.gz --refList GCF_024273205.1_ASM2427320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024273205.1_ASM2427320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:32,279] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:32,287] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:28:32,287] [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_003056405.1	s__Devosia indica	82.8374	862	1249	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	82.8268	818	1249	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	82.4	839	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_001650025.1	s__Devosia elaeis	82.0795	740	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197055.1	s__Devosia subaequoris	81.9823	804	1249	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	81.2019	701	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCF_015158295.1	s__Devosia sp015158295	81.1808	675	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969445.1	s__Devosia chinhatensis	81.0193	678	1249	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	80.5377	634	1249	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	80.5105	639	1249	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	80.4819	748	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_015234425.1	s__Devosia sp015234425	80.2214	643	1249	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 20:28:32,289] [INFO] GTDB search result was written to GCF_024273205.1_ASM2427320v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:32,290] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:32,293] [INFO] DFAST_QC result json was written to GCF_024273205.1_ASM2427320v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:32,293] [INFO] DFAST_QC completed!
[2024-01-25 20:28:32,293] [INFO] Total running time: 0h1m12s