[2024-01-24 13:31:56,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:56,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:56,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg3787d34e-831d-4696-be58-e657f4cc31d8/dqc_reference
[2024-01-24 13:31:57,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:57,975] [INFO] Task started: Prodigal
[2024-01-24 13:31:57,975] [INFO] Running command: gunzip -c /var/lib/cwl/stga6e23ae9-7dfd-4293-9063-c341feb78bda/GCF_030347995.1_ASM3034799v1_genomic.fna.gz | prodigal -d GCF_030347995.1_ASM3034799v1_genomic.fna/cds.fna -a GCF_030347995.1_ASM3034799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:03,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:03,449] [INFO] Task started: HMMsearch
[2024-01-24 13:32:03,450] [INFO] Running command: hmmsearch --tblout GCF_030347995.1_ASM3034799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3787d34e-831d-4696-be58-e657f4cc31d8/dqc_reference/reference_markers.hmm GCF_030347995.1_ASM3034799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:03,683] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:03,684] [INFO] Found 6/6 markers.
[2024-01-24 13:32:03,708] [INFO] Query marker FASTA was written to GCF_030347995.1_ASM3034799v1_genomic.fna/markers.fasta
[2024-01-24 13:32:03,709] [INFO] Task started: Blastn
[2024-01-24 13:32:03,709] [INFO] Running command: blastn -query GCF_030347995.1_ASM3034799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3787d34e-831d-4696-be58-e657f4cc31d8/dqc_reference/reference_markers.fasta -out GCF_030347995.1_ASM3034799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:04,331] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:04,335] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:04,336] [INFO] Target genome list was writen to GCF_030347995.1_ASM3034799v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:04,344] [INFO] Task started: fastANI
[2024-01-24 13:32:04,345] [INFO] Running command: fastANI --query /var/lib/cwl/stga6e23ae9-7dfd-4293-9063-c341feb78bda/GCF_030347995.1_ASM3034799v1_genomic.fna.gz --refList GCF_030347995.1_ASM3034799v1_genomic.fna/target_genomes.txt --output GCF_030347995.1_ASM3034799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:11,222] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:11,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3787d34e-831d-4696-be58-e657f4cc31d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:11,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3787d34e-831d-4696-be58-e657f4cc31d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:11,228] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:11,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:11,229] [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 riftiae	strain=1812E	GCA_001595645.1	1630136	1630136	type	True	78.1034	136	719	95	below_threshold
Sulfurovum lithotrophicum	strain=ATCC BAA-797	GCA_000987835.1	206403	206403	type	True	77.9591	135	719	95	below_threshold
Sulfurovum indicum	strain=ST-419	GCA_014931715.1	2779528	2779528	type	True	77.7912	121	719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:11,231] [INFO] DFAST Taxonomy check result was written to GCF_030347995.1_ASM3034799v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:11,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:11,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:11,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3787d34e-831d-4696-be58-e657f4cc31d8/dqc_reference/checkm_data
[2024-01-24 13:32:11,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:11,264] [INFO] Task started: CheckM
[2024-01-24 13:32:11,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030347995.1_ASM3034799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030347995.1_ASM3034799v1_genomic.fna/checkm_input GCF_030347995.1_ASM3034799v1_genomic.fna/checkm_result
[2024-01-24 13:32:34,638] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:34,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:34,660] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:34,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:34,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030347995.1_ASM3034799v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:34,662] [INFO] Task started: Blastn
[2024-01-24 13:32:34,662] [INFO] Running command: blastn -query GCF_030347995.1_ASM3034799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3787d34e-831d-4696-be58-e657f4cc31d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_030347995.1_ASM3034799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:35,487] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:35,491] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:35,491] [INFO] Target genome list was writen to GCF_030347995.1_ASM3034799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:35,508] [INFO] Task started: fastANI
[2024-01-24 13:32:35,508] [INFO] Running command: fastANI --query /var/lib/cwl/stga6e23ae9-7dfd-4293-9063-c341feb78bda/GCF_030347995.1_ASM3034799v1_genomic.fna.gz --refList GCF_030347995.1_ASM3034799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030347995.1_ASM3034799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:41,386] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:41,402] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:41,403] [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_000296775.1	s__Sulfurovum sp000296775	97.7657	634	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004377245.1	s__Sulfurovum sp004377245	79.2654	104	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002085305.1	s__Sulfurovum sp002085305	79.138	144	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733215.1	s__Sulfurovum sp002733215	78.7615	267	719	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	78.631	196	719	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	78.3327	164	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646505.1	s__Sulfurovum sp003646505	78.3048	184	719	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	78.2744	136	719	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	78.254	187	719	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	78.1034	136	719	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	78.0294	139	719	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	77.9591	135	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391015.1	s__Sulfurovum sp011391015	77.9137	166	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015661795.1	s__Sulfurovum sp015661795	77.179	127	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978375.1	s__Sulfurovum sp003978375	77.0431	100	719	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,404] [INFO] GTDB search result was written to GCF_030347995.1_ASM3034799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:41,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:41,408] [INFO] DFAST_QC result json was written to GCF_030347995.1_ASM3034799v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:41,408] [INFO] DFAST_QC completed!
[2024-01-24 13:32:41,408] [INFO] Total running time: 0h0m45s