[2024-01-25 17:39:20,679] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:20,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:20,680] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7354f1d-14d5-4761-b00b-8d1c05a5965e/dqc_reference
[2024-01-25 17:39:21,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:21,806] [INFO] Task started: Prodigal
[2024-01-25 17:39:21,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg29c2bb0a-1ea1-44eb-ad14-51bd16c24b15/GCF_014931715.1_ASM1493171v1_genomic.fna.gz | prodigal -d GCF_014931715.1_ASM1493171v1_genomic.fna/cds.fna -a GCF_014931715.1_ASM1493171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:26,945] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:26,946] [INFO] Task started: HMMsearch
[2024-01-25 17:39:26,946] [INFO] Running command: hmmsearch --tblout GCF_014931715.1_ASM1493171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7354f1d-14d5-4761-b00b-8d1c05a5965e/dqc_reference/reference_markers.hmm GCF_014931715.1_ASM1493171v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:27,164] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:27,165] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg29c2bb0a-1ea1-44eb-ad14-51bd16c24b15/GCF_014931715.1_ASM1493171v1_genomic.fna.gz]
[2024-01-25 17:39:27,185] [INFO] Query marker FASTA was written to GCF_014931715.1_ASM1493171v1_genomic.fna/markers.fasta
[2024-01-25 17:39:27,186] [INFO] Task started: Blastn
[2024-01-25 17:39:27,186] [INFO] Running command: blastn -query GCF_014931715.1_ASM1493171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7354f1d-14d5-4761-b00b-8d1c05a5965e/dqc_reference/reference_markers.fasta -out GCF_014931715.1_ASM1493171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:27,703] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:27,705] [INFO] Selected 14 target genomes.
[2024-01-25 17:39:27,706] [INFO] Target genome list was writen to GCF_014931715.1_ASM1493171v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:27,725] [INFO] Task started: fastANI
[2024-01-25 17:39:27,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c2bb0a-1ea1-44eb-ad14-51bd16c24b15/GCF_014931715.1_ASM1493171v1_genomic.fna.gz --refList GCF_014931715.1_ASM1493171v1_genomic.fna/target_genomes.txt --output GCF_014931715.1_ASM1493171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:35,048] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:35,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7354f1d-14d5-4761-b00b-8d1c05a5965e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:35,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7354f1d-14d5-4761-b00b-8d1c05a5965e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:35,052] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:35,053] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:35,053] [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	100.0	735	736	95	conclusive
Sulfurovum lithotrophicum	strain=ATCC BAA-797	GCA_000987835.1	206403	206403	type	True	78.5033	236	736	95	below_threshold
Sulfurovum riftiae	strain=1812E	GCA_001595645.1	1630136	1630136	type	True	78.2243	242	736	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:35,054] [INFO] DFAST Taxonomy check result was written to GCF_014931715.1_ASM1493171v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:35,055] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:35,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:35,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7354f1d-14d5-4761-b00b-8d1c05a5965e/dqc_reference/checkm_data
[2024-01-25 17:39:35,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:35,082] [INFO] Task started: CheckM
[2024-01-25 17:39:35,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014931715.1_ASM1493171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014931715.1_ASM1493171v1_genomic.fna/checkm_input GCF_014931715.1_ASM1493171v1_genomic.fna/checkm_result
[2024-01-25 17:39:55,496] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:55,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:55,513] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:55,513] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:55,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014931715.1_ASM1493171v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:55,514] [INFO] Task started: Blastn
[2024-01-25 17:39:55,514] [INFO] Running command: blastn -query GCF_014931715.1_ASM1493171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7354f1d-14d5-4761-b00b-8d1c05a5965e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014931715.1_ASM1493171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:56,268] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:56,270] [INFO] Selected 11 target genomes.
[2024-01-25 17:39:56,270] [INFO] Target genome list was writen to GCF_014931715.1_ASM1493171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:56,281] [INFO] Task started: fastANI
[2024-01-25 17:39:56,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg29c2bb0a-1ea1-44eb-ad14-51bd16c24b15/GCF_014931715.1_ASM1493171v1_genomic.fna.gz --refList GCF_014931715.1_ASM1493171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014931715.1_ASM1493171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:00,712] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:00,719] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:00,719] [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_014931715.1	s__Sulfurovum indicum	100.0	734	736	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000987835.1	s__Sulfurovum lithotrophicum	78.5602	238	736	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	78.489	203	736	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010345.1	s__Sulfurovum sp000010345	78.3198	249	736	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	78.2243	242	736	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	78.0651	182	736	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	98.37	98.02	0.82	0.76	3	-
GCA_015493435.1	s__Sulfurovum sp015493435	77.9534	178	736	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	98.17	98.17	0.86	0.86	2	-
GCA_015490315.1	s__Sulfurovum sp015490315	77.8697	124	736	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004377245.1	s__Sulfurovum sp004377245	77.5669	61	736	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	77.4717	127	736	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763895.1	s__Sulfurovum sp014763895	77.3498	117	736	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:00,721] [INFO] GTDB search result was written to GCF_014931715.1_ASM1493171v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:00,722] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:00,724] [INFO] DFAST_QC result json was written to GCF_014931715.1_ASM1493171v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:00,724] [INFO] DFAST_QC completed!
[2024-01-25 17:40:00,724] [INFO] Total running time: 0h0m40s