[2023-06-30 03:33:17,065] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:33:17,067] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:33:17,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d1210b5-7929-48cf-90cd-b732988b7eb5/dqc_reference
[2023-06-30 03:33:18,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:33:18,315] [INFO] Task started: Prodigal
[2023-06-30 03:33:18,315] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeab0226-0fd0-4599-95d2-ef42a3e6f536/GCA_024280545.1_ASM2428054v1_genomic.fna.gz | prodigal -d GCA_024280545.1_ASM2428054v1_genomic.fna/cds.fna -a GCA_024280545.1_ASM2428054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:33:21,338] [INFO] Task succeeded: Prodigal
[2023-06-30 03:33:21,338] [INFO] Task started: HMMsearch
[2023-06-30 03:33:21,338] [INFO] Running command: hmmsearch --tblout GCA_024280545.1_ASM2428054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d1210b5-7929-48cf-90cd-b732988b7eb5/dqc_reference/reference_markers.hmm GCA_024280545.1_ASM2428054v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:33:21,582] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:33:21,584] [INFO] Found 6/6 markers.
[2023-06-30 03:33:21,613] [INFO] Query marker FASTA was written to GCA_024280545.1_ASM2428054v1_genomic.fna/markers.fasta
[2023-06-30 03:33:21,614] [INFO] Task started: Blastn
[2023-06-30 03:33:21,614] [INFO] Running command: blastn -query GCA_024280545.1_ASM2428054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d1210b5-7929-48cf-90cd-b732988b7eb5/dqc_reference/reference_markers.fasta -out GCA_024280545.1_ASM2428054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:22,200] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:22,207] [INFO] Selected 28 target genomes.
[2023-06-30 03:33:22,207] [INFO] Target genome list was writen to GCA_024280545.1_ASM2428054v1_genomic.fna/target_genomes.txt
[2023-06-30 03:33:22,237] [INFO] Task started: fastANI
[2023-06-30 03:33:22,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeab0226-0fd0-4599-95d2-ef42a3e6f536/GCA_024280545.1_ASM2428054v1_genomic.fna.gz --refList GCA_024280545.1_ASM2428054v1_genomic.fna/target_genomes.txt --output GCA_024280545.1_ASM2428054v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:33:32,228] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:32,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d1210b5-7929-48cf-90cd-b732988b7eb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:33:32,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d1210b5-7929-48cf-90cd-b732988b7eb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:33:32,238] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:33:32,239] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:33:32,239] [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 lithotrophicum	strain=ATCC BAA-797	GCA_000987835.1	206403	206403	type	True	77.9844	82	388	95	below_threshold
Sulfurovum riftiae	strain=1812E	GCA_001595645.1	1630136	1630136	type	True	77.4804	105	388	95	below_threshold
Sulfurovum indicum	strain=ST-419	GCA_014931715.1	2779528	2779528	type	True	77.3542	97	388	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:33:32,241] [INFO] DFAST Taxonomy check result was written to GCA_024280545.1_ASM2428054v1_genomic.fna/tc_result.tsv
[2023-06-30 03:33:32,241] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:33:32,242] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:33:32,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d1210b5-7929-48cf-90cd-b732988b7eb5/dqc_reference/checkm_data
[2023-06-30 03:33:32,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:33:32,263] [INFO] Task started: CheckM
[2023-06-30 03:33:32,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024280545.1_ASM2428054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024280545.1_ASM2428054v1_genomic.fna/checkm_input GCA_024280545.1_ASM2428054v1_genomic.fna/checkm_result
[2023-06-30 03:33:50,475] [INFO] Task succeeded: CheckM
[2023-06-30 03:33:50,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 03:33:50,500] [INFO] ===== Completeness check finished =====
[2023-06-30 03:33:50,500] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:33:50,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024280545.1_ASM2428054v1_genomic.fna/markers.fasta)
[2023-06-30 03:33:50,501] [INFO] Task started: Blastn
[2023-06-30 03:33:50,501] [INFO] Running command: blastn -query GCA_024280545.1_ASM2428054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d1210b5-7929-48cf-90cd-b732988b7eb5/dqc_reference/reference_markers_gtdb.fasta -out GCA_024280545.1_ASM2428054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:51,280] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:51,302] [INFO] Selected 21 target genomes.
[2023-06-30 03:33:51,303] [INFO] Target genome list was writen to GCA_024280545.1_ASM2428054v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:33:51,316] [INFO] Task started: fastANI
[2023-06-30 03:33:51,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeab0226-0fd0-4599-95d2-ef42a3e6f536/GCA_024280545.1_ASM2428054v1_genomic.fna.gz --refList GCA_024280545.1_ASM2428054v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024280545.1_ASM2428054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:33:57,839] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:57,860] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 03:33:57,860] [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_015490315.1	s__Sulfurovum sp015490315	78.2001	99	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987835.1	s__Sulfurovum lithotrophicum	77.9844	82	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493435.1	s__Sulfurovum sp015493435	77.763	73	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	98.17	98.17	0.86	0.86	2	-
GCF_000010345.1	s__Sulfurovum sp000010345	77.5816	92	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001595645.1	s__Sulfurovum riftiae	77.4804	105	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661535.1	s__Sulfurovum sp015661535	77.4767	56	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003934925.1	s__Sulfurovum sp003934925	77.4451	93	388	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	77.3542	97	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015663065.1	s__Sulfurovum sp015663065	77.2918	65	388	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	77.2388	78	388	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	77.1825	73	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	98.37	98.02	0.82	0.76	3	-
GCA_002733215.1	s__Sulfurovum sp002733215	77.067	65	388	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	76.9934	69	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763885.1	s__Sulfurovum sp014763885	76.8829	61	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330645.1	s__Sulfurovum sp011330645	76.8633	70	388	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	76.6759	58	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048515.1	s__Sulfurovum sp011048515	76.3403	61	388	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	99.69	99.69	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-30 03:33:57,862] [INFO] GTDB search result was written to GCA_024280545.1_ASM2428054v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:33:57,863] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:33:57,867] [INFO] DFAST_QC result json was written to GCA_024280545.1_ASM2428054v1_genomic.fna/dqc_result.json
[2023-06-30 03:33:57,867] [INFO] DFAST_QC completed!
[2023-06-30 03:33:57,867] [INFO] Total running time: 0h0m41s