[2024-01-24 13:31:33,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg71e091a3-add3-4e1d-bd2e-d8346f75357d/dqc_reference
[2024-01-24 13:31:34,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,870] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,871] [INFO] Running command: gunzip -c /var/lib/cwl/stge6ce5ecb-fce9-4325-a5ac-916a9357ecc4/GCF_009708075.1_ASM970807v1_genomic.fna.gz | prodigal -d GCF_009708075.1_ASM970807v1_genomic.fna/cds.fna -a GCF_009708075.1_ASM970807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:46,189] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:46,189] [INFO] Task started: HMMsearch
[2024-01-24 13:31:46,189] [INFO] Running command: hmmsearch --tblout GCF_009708075.1_ASM970807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71e091a3-add3-4e1d-bd2e-d8346f75357d/dqc_reference/reference_markers.hmm GCF_009708075.1_ASM970807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:46,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:46,453] [INFO] Found 6/6 markers.
[2024-01-24 13:31:46,486] [INFO] Query marker FASTA was written to GCF_009708075.1_ASM970807v1_genomic.fna/markers.fasta
[2024-01-24 13:31:46,486] [INFO] Task started: Blastn
[2024-01-24 13:31:46,487] [INFO] Running command: blastn -query GCF_009708075.1_ASM970807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71e091a3-add3-4e1d-bd2e-d8346f75357d/dqc_reference/reference_markers.fasta -out GCF_009708075.1_ASM970807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:47,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:47,548] [INFO] Selected 13 target genomes.
[2024-01-24 13:31:47,549] [INFO] Target genome list was writen to GCF_009708075.1_ASM970807v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:47,554] [INFO] Task started: fastANI
[2024-01-24 13:31:47,554] [INFO] Running command: fastANI --query /var/lib/cwl/stge6ce5ecb-fce9-4325-a5ac-916a9357ecc4/GCF_009708075.1_ASM970807v1_genomic.fna.gz --refList GCF_009708075.1_ASM970807v1_genomic.fna/target_genomes.txt --output GCF_009708075.1_ASM970807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:58,762] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71e091a3-add3-4e1d-bd2e-d8346f75357d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:58,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71e091a3-add3-4e1d-bd2e-d8346f75357d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:58,775] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:58,775] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:58,775] [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
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	100.0	1203	1207	95	conclusive
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	91.3935	929	1207	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	88.3006	878	1207	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	87.6673	863	1207	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	87.3598	781	1207	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	87.0886	845	1207	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	86.9987	839	1207	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	86.8961	796	1207	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	86.7426	823	1207	95	below_threshold
Paracoccus subflavus	strain=GY0581	GCA_004310345.1	2528244	2528244	type	True	85.6136	743	1207	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.6117	672	1207	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.1289	605	1207	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.2334	499	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,778] [INFO] DFAST Taxonomy check result was written to GCF_009708075.1_ASM970807v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:58,778] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:58,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:58,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71e091a3-add3-4e1d-bd2e-d8346f75357d/dqc_reference/checkm_data
[2024-01-24 13:31:58,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:58,819] [INFO] Task started: CheckM
[2024-01-24 13:31:58,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009708075.1_ASM970807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009708075.1_ASM970807v1_genomic.fna/checkm_input GCF_009708075.1_ASM970807v1_genomic.fna/checkm_result
[2024-01-24 13:32:41,067] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:41,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,098] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:41,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:41,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009708075.1_ASM970807v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:41,099] [INFO] Task started: Blastn
[2024-01-24 13:32:41,099] [INFO] Running command: blastn -query GCF_009708075.1_ASM970807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71e091a3-add3-4e1d-bd2e-d8346f75357d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009708075.1_ASM970807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:43,267] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:43,270] [INFO] Selected 8 target genomes.
[2024-01-24 13:32:43,271] [INFO] Target genome list was writen to GCF_009708075.1_ASM970807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:43,278] [INFO] Task started: fastANI
[2024-01-24 13:32:43,279] [INFO] Running command: fastANI --query /var/lib/cwl/stge6ce5ecb-fce9-4325-a5ac-916a9357ecc4/GCF_009708075.1_ASM970807v1_genomic.fna.gz --refList GCF_009708075.1_ASM970807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009708075.1_ASM970807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:51,377] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:51,385] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:51,385] [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_009708075.1	s__Paracoccus lichenicola	100.0	1203	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017315735.1	s__Paracoccus sp017315735	91.3935	929	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	88.2835	879	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631945.1	s__Paracoccus haematequi	88.0868	864	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642735.1	s__Paracoccus acridae	87.689	861	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.80	97.80	0.86	0.86	2	-
GCF_014656455.1	s__Paracoccus aerius	87.0784	846	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_900188295.1	s__Paracoccus sediminis	86.757	822	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004310345.1	s__Paracoccus subflavus	85.584	745	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:51,387] [INFO] GTDB search result was written to GCF_009708075.1_ASM970807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:51,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:51,391] [INFO] DFAST_QC result json was written to GCF_009708075.1_ASM970807v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:51,391] [INFO] DFAST_QC completed!
[2024-01-24 13:32:51,391] [INFO] Total running time: 0h1m18s