[2024-01-24 12:22:48,482] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,484] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgba51cd60-b229-4acf-8b0a-db347678ecf3/dqc_reference
[2024-01-24 12:22:49,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,706] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,707] [INFO] Running command: gunzip -c /var/lib/cwl/stge9503593-4a06-4269-80f9-c4ba8d59bda4/GCF_030347965.1_ASM3034796v1_genomic.fna.gz | prodigal -d GCF_030347965.1_ASM3034796v1_genomic.fna/cds.fna -a GCF_030347965.1_ASM3034796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:55,077] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:55,077] [INFO] Task started: HMMsearch
[2024-01-24 12:22:55,077] [INFO] Running command: hmmsearch --tblout GCF_030347965.1_ASM3034796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba51cd60-b229-4acf-8b0a-db347678ecf3/dqc_reference/reference_markers.hmm GCF_030347965.1_ASM3034796v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:55,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:55,350] [INFO] Found 6/6 markers.
[2024-01-24 12:22:55,373] [INFO] Query marker FASTA was written to GCF_030347965.1_ASM3034796v1_genomic.fna/markers.fasta
[2024-01-24 12:22:55,373] [INFO] Task started: Blastn
[2024-01-24 12:22:55,373] [INFO] Running command: blastn -query GCF_030347965.1_ASM3034796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba51cd60-b229-4acf-8b0a-db347678ecf3/dqc_reference/reference_markers.fasta -out GCF_030347965.1_ASM3034796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:55,984] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:55,988] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:55,988] [INFO] Target genome list was writen to GCF_030347965.1_ASM3034796v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:55,994] [INFO] Task started: fastANI
[2024-01-24 12:22:55,995] [INFO] Running command: fastANI --query /var/lib/cwl/stge9503593-4a06-4269-80f9-c4ba8d59bda4/GCF_030347965.1_ASM3034796v1_genomic.fna.gz --refList GCF_030347965.1_ASM3034796v1_genomic.fna/target_genomes.txt --output GCF_030347965.1_ASM3034796v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:04,215] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:04,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba51cd60-b229-4acf-8b0a-db347678ecf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:04,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba51cd60-b229-4acf-8b0a-db347678ecf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:04,222] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:04,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:04,222] [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	77.3845	112	720	95	below_threshold
Sulfurovum riftiae	strain=1812E	GCA_001595645.1	1630136	1630136	type	True	77.2165	103	720	95	below_threshold
Sulfurovum lithotrophicum	strain=ATCC BAA-797	GCA_000987835.1	206403	206403	type	True	77.1393	99	720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,224] [INFO] DFAST Taxonomy check result was written to GCF_030347965.1_ASM3034796v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:04,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:04,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:04,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba51cd60-b229-4acf-8b0a-db347678ecf3/dqc_reference/checkm_data
[2024-01-24 12:23:04,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:04,260] [INFO] Task started: CheckM
[2024-01-24 12:23:04,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030347965.1_ASM3034796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030347965.1_ASM3034796v1_genomic.fna/checkm_input GCF_030347965.1_ASM3034796v1_genomic.fna/checkm_result
[2024-01-24 12:23:27,919] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:27,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:27,943] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:27,943] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:27,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030347965.1_ASM3034796v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:27,944] [INFO] Task started: Blastn
[2024-01-24 12:23:27,945] [INFO] Running command: blastn -query GCF_030347965.1_ASM3034796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba51cd60-b229-4acf-8b0a-db347678ecf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030347965.1_ASM3034796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:28,738] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:28,741] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:28,741] [INFO] Target genome list was writen to GCF_030347965.1_ASM3034796v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:28,752] [INFO] Task started: fastANI
[2024-01-24 12:23:28,753] [INFO] Running command: fastANI --query /var/lib/cwl/stge9503593-4a06-4269-80f9-c4ba8d59bda4/GCF_030347965.1_ASM3034796v1_genomic.fna.gz --refList GCF_030347965.1_ASM3034796v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030347965.1_ASM3034796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:33,602] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:33,618] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:33,619] [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_014763885.1	s__Sulfurovum sp014763885	81.375	403	720	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	81.0352	393	720	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	99.69	99.69	0.91	0.91	2	-
GCF_000296775.1	s__Sulfurovum sp000296775	78.3832	174	720	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	77.9283	107	720	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	77.9105	123	720	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	77.4993	114	720	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	77.4632	61	720	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	77.3486	102	720	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	77.2725	80	720	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	77.2165	103	720	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403155.1	s__Sulfurovum sp002403155	77.0531	69	720	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	99.21	99.17	0.94	0.94	3	-
GCA_002742845.1	s__Sulfurovum sp002742845	77.0317	78	720	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	99.36	99.36	0.97	0.96	3	-
GCA_011330645.1	s__Sulfurovum sp011330645	76.9397	93	720	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	76.834	92	720	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	98.17	98.17	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:33,620] [INFO] GTDB search result was written to GCF_030347965.1_ASM3034796v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:33,621] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:33,625] [INFO] DFAST_QC result json was written to GCF_030347965.1_ASM3034796v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:33,625] [INFO] DFAST_QC completed!
[2024-01-24 12:23:33,625] [INFO] Total running time: 0h0m45s