[2023-06-28 18:45:40,373] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:45:40,377] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:45:40,378] [INFO] DQC Reference Directory: /var/lib/cwl/stge726ecbf-3631-44c5-a956-a2a2220eefeb/dqc_reference
[2023-06-28 18:45:41,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:45:41,725] [INFO] Task started: Prodigal
[2023-06-28 18:45:41,725] [INFO] Running command: gunzip -c /var/lib/cwl/stgb991cf9c-3ff4-45e1-bd04-6841d8912060/GCA_020525005.1_ASM2052500v1_genomic.fna.gz | prodigal -d GCA_020525005.1_ASM2052500v1_genomic.fna/cds.fna -a GCA_020525005.1_ASM2052500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:45:44,839] [INFO] Task succeeded: Prodigal
[2023-06-28 18:45:44,840] [INFO] Task started: HMMsearch
[2023-06-28 18:45:44,840] [INFO] Running command: hmmsearch --tblout GCA_020525005.1_ASM2052500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge726ecbf-3631-44c5-a956-a2a2220eefeb/dqc_reference/reference_markers.hmm GCA_020525005.1_ASM2052500v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:45:45,069] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:45:45,070] [INFO] Found 6/6 markers.
[2023-06-28 18:45:45,093] [INFO] Query marker FASTA was written to GCA_020525005.1_ASM2052500v1_genomic.fna/markers.fasta
[2023-06-28 18:45:45,094] [INFO] Task started: Blastn
[2023-06-28 18:45:45,094] [INFO] Running command: blastn -query GCA_020525005.1_ASM2052500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge726ecbf-3631-44c5-a956-a2a2220eefeb/dqc_reference/reference_markers.fasta -out GCA_020525005.1_ASM2052500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:45:45,681] [INFO] Task succeeded: Blastn
[2023-06-28 18:45:45,684] [INFO] Selected 17 target genomes.
[2023-06-28 18:45:45,684] [INFO] Target genome list was writen to GCA_020525005.1_ASM2052500v1_genomic.fna/target_genomes.txt
[2023-06-28 18:45:45,687] [INFO] Task started: fastANI
[2023-06-28 18:45:45,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgb991cf9c-3ff4-45e1-bd04-6841d8912060/GCA_020525005.1_ASM2052500v1_genomic.fna.gz --refList GCA_020525005.1_ASM2052500v1_genomic.fna/target_genomes.txt --output GCA_020525005.1_ASM2052500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:45:51,361] [INFO] Task succeeded: fastANI
[2023-06-28 18:45:51,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge726ecbf-3631-44c5-a956-a2a2220eefeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:45:51,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge726ecbf-3631-44c5-a956-a2a2220eefeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:45:51,367] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:45:51,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:45:51,367] [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
Sulfurovum indicum	strain=ST-419	GCA_014931715.1	2779528	2779528	type	True	77.8426	112	410	95	below_threshold
Sulfurovum lithotrophicum	strain=ATCC BAA-797	GCA_000987835.1	206403	206403	type	True	77.6138	63	410	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:45:51,369] [INFO] DFAST Taxonomy check result was written to GCA_020525005.1_ASM2052500v1_genomic.fna/tc_result.tsv
[2023-06-28 18:45:51,370] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:45:51,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:45:51,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge726ecbf-3631-44c5-a956-a2a2220eefeb/dqc_reference/checkm_data
[2023-06-28 18:45:51,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:45:51,397] [INFO] Task started: CheckM
[2023-06-28 18:45:51,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020525005.1_ASM2052500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020525005.1_ASM2052500v1_genomic.fna/checkm_input GCA_020525005.1_ASM2052500v1_genomic.fna/checkm_result
[2023-06-28 18:46:09,208] [INFO] Task succeeded: CheckM
[2023-06-28 18:46:09,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:46:09,227] [INFO] ===== Completeness check finished =====
[2023-06-28 18:46:09,228] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:46:09,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020525005.1_ASM2052500v1_genomic.fna/markers.fasta)
[2023-06-28 18:46:09,229] [INFO] Task started: Blastn
[2023-06-28 18:46:09,229] [INFO] Running command: blastn -query GCA_020525005.1_ASM2052500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge726ecbf-3631-44c5-a956-a2a2220eefeb/dqc_reference/reference_markers_gtdb.fasta -out GCA_020525005.1_ASM2052500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:46:10,017] [INFO] Task succeeded: Blastn
[2023-06-28 18:46:10,022] [INFO] Selected 23 target genomes.
[2023-06-28 18:46:10,022] [INFO] Target genome list was writen to GCA_020525005.1_ASM2052500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:46:10,045] [INFO] Task started: fastANI
[2023-06-28 18:46:10,046] [INFO] Running command: fastANI --query /var/lib/cwl/stgb991cf9c-3ff4-45e1-bd04-6841d8912060/GCA_020525005.1_ASM2052500v1_genomic.fna.gz --refList GCA_020525005.1_ASM2052500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020525005.1_ASM2052500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:46:17,895] [INFO] Task succeeded: fastANI
[2023-06-28 18:46:17,911] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:46:17,912] [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
GCA_003934925.1	s__Sulfurovum sp003934925	77.8691	72	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931715.1	s__Sulfurovum indicum	77.8509	111	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493425.1	s__Sulfurovum sp015493425	77.6677	77	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	98.37	98.02	0.82	0.76	3	-
GCF_000010345.1	s__Sulfurovum sp000010345	77.5392	65	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296775.1	s__Sulfurovum sp000296775	77.028	69	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902727855.1	s__Sulfurovum sp902727855	77.0163	66	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744875.1	s__Sulfurovum sp016744875	76.9028	65	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013607775.1	s__Sulfurovum sp013607775	76.5811	88	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822805.1	s__UBA1140 sp018822805	76.5169	50	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__UBA1140	95.0	99.99	99.99	0.97	0.97	2	-
GCA_011330645.1	s__Sulfurovum sp011330645	76.5043	85	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744315.1	s__SZUA-451 sp016744315	76.1101	59	410	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__SZUA-451	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:46:17,914] [INFO] GTDB search result was written to GCA_020525005.1_ASM2052500v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:46:17,915] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:46:17,921] [INFO] DFAST_QC result json was written to GCA_020525005.1_ASM2052500v1_genomic.fna/dqc_result.json
[2023-06-28 18:46:17,922] [INFO] DFAST_QC completed!
[2023-06-28 18:46:17,922] [INFO] Total running time: 0h0m38s