[2024-01-24 11:12:39,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,727] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa40a4ce-1561-4dba-bf2b-072fb064866c/dqc_reference
[2024-01-24 11:12:41,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,063] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,064] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8ad8528-55b5-49ef-9902-57f9fd895fe1/GCF_000970455.1_ASM97045v1_genomic.fna.gz | prodigal -d GCF_000970455.1_ASM97045v1_genomic.fna/cds.fna -a GCF_000970455.1_ASM97045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:53,633] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:53,633] [INFO] Task started: HMMsearch
[2024-01-24 11:12:53,633] [INFO] Running command: hmmsearch --tblout GCF_000970455.1_ASM97045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa40a4ce-1561-4dba-bf2b-072fb064866c/dqc_reference/reference_markers.hmm GCF_000970455.1_ASM97045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:53,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:53,952] [INFO] Found 6/6 markers.
[2024-01-24 11:12:53,996] [INFO] Query marker FASTA was written to GCF_000970455.1_ASM97045v1_genomic.fna/markers.fasta
[2024-01-24 11:12:53,997] [INFO] Task started: Blastn
[2024-01-24 11:12:53,997] [INFO] Running command: blastn -query GCF_000970455.1_ASM97045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa40a4ce-1561-4dba-bf2b-072fb064866c/dqc_reference/reference_markers.fasta -out GCF_000970455.1_ASM97045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:54,860] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:54,864] [INFO] Selected 14 target genomes.
[2024-01-24 11:12:54,865] [INFO] Target genome list was writen to GCF_000970455.1_ASM97045v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:54,872] [INFO] Task started: fastANI
[2024-01-24 11:12:54,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ad8528-55b5-49ef-9902-57f9fd895fe1/GCF_000970455.1_ASM97045v1_genomic.fna.gz --refList GCF_000970455.1_ASM97045v1_genomic.fna/target_genomes.txt --output GCF_000970455.1_ASM97045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:06,556] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:06,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa40a4ce-1561-4dba-bf2b-072fb064866c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:06,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa40a4ce-1561-4dba-bf2b-072fb064866c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:06,568] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:06,569] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:06,569] [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 soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	100.0	1360	1362	95	conclusive
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	83.0005	909	1362	95	below_threshold
Devosia crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	81.0448	721	1362	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	80.4641	673	1362	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.2543	625	1362	95	below_threshold
Devosia aurantiaca	strain=H239	GCA_011058215.1	2714858	2714858	type	True	80.2308	630	1362	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	80.2161	631	1362	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.1079	674	1362	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	80.0845	615	1362	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	80.079	615	1362	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	79.64	564	1362	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.4531	568	1362	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.2419	561	1362	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.8929	624	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:06,573] [INFO] DFAST Taxonomy check result was written to GCF_000970455.1_ASM97045v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:06,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:06,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:06,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa40a4ce-1561-4dba-bf2b-072fb064866c/dqc_reference/checkm_data
[2024-01-24 11:13:06,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:06,620] [INFO] Task started: CheckM
[2024-01-24 11:13:06,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000970455.1_ASM97045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000970455.1_ASM97045v1_genomic.fna/checkm_input GCF_000970455.1_ASM97045v1_genomic.fna/checkm_result
[2024-01-24 11:13:46,088] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:46,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:46,116] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:46,117] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:46,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000970455.1_ASM97045v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:46,118] [INFO] Task started: Blastn
[2024-01-24 11:13:46,118] [INFO] Running command: blastn -query GCF_000970455.1_ASM97045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa40a4ce-1561-4dba-bf2b-072fb064866c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000970455.1_ASM97045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:47,456] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:47,460] [INFO] Selected 10 target genomes.
[2024-01-24 11:13:47,460] [INFO] Target genome list was writen to GCF_000970455.1_ASM97045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:47,467] [INFO] Task started: fastANI
[2024-01-24 11:13:47,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ad8528-55b5-49ef-9902-57f9fd895fe1/GCF_000970455.1_ASM97045v1_genomic.fna.gz --refList GCF_000970455.1_ASM97045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000970455.1_ASM97045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:57,340] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:57,353] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:57,354] [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_000970455.1	s__Devosia soli	100.0	1360	1362	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_001425445.1	s__Devosia sp001425445	84.7665	950	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	96.74	96.74	0.91	0.91	2	-
GCF_001427875.1	s__Devosia sp001427875	83.0904	889	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743575.1	s__Devosia riboflavina	83.0004	909	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744655.1	s__Devosia sp017744655	82.7872	916	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307565.1	s__Devosia sp017307565	82.5442	665	1362	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	80.4726	672	1362	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	80.252	626	1362	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	80.0871	615	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799265.1	s__Devosia sp012799265	79.3955	411	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:57,355] [INFO] GTDB search result was written to GCF_000970455.1_ASM97045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:57,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:57,359] [INFO] DFAST_QC result json was written to GCF_000970455.1_ASM97045v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:57,360] [INFO] DFAST_QC completed!
[2024-01-24 11:13:57,360] [INFO] Total running time: 0h1m18s