[2023-06-16 20:50:58,941] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:50:58,943] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:50:58,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f111af0-e528-4756-99cd-d8c3fe345499/dqc_reference
[2023-06-16 20:51:00,064] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:51:00,065] [INFO] Task started: Prodigal
[2023-06-16 20:51:00,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg03df3167-b29b-46bd-a51c-e8be81bcddef/GCA_013607775.1_ASM1360777v1_genomic.fna.gz | prodigal -d GCA_013607775.1_ASM1360777v1_genomic.fna/cds.fna -a GCA_013607775.1_ASM1360777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:51:03,875] [INFO] Task succeeded: Prodigal
[2023-06-16 20:51:03,875] [INFO] Task started: HMMsearch
[2023-06-16 20:51:03,875] [INFO] Running command: hmmsearch --tblout GCA_013607775.1_ASM1360777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f111af0-e528-4756-99cd-d8c3fe345499/dqc_reference/reference_markers.hmm GCA_013607775.1_ASM1360777v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:51:04,071] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:51:04,073] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg03df3167-b29b-46bd-a51c-e8be81bcddef/GCA_013607775.1_ASM1360777v1_genomic.fna.gz]
[2023-06-16 20:51:04,097] [INFO] Query marker FASTA was written to GCA_013607775.1_ASM1360777v1_genomic.fna/markers.fasta
[2023-06-16 20:51:04,098] [INFO] Task started: Blastn
[2023-06-16 20:51:04,098] [INFO] Running command: blastn -query GCA_013607775.1_ASM1360777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f111af0-e528-4756-99cd-d8c3fe345499/dqc_reference/reference_markers.fasta -out GCA_013607775.1_ASM1360777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:51:04,615] [INFO] Task succeeded: Blastn
[2023-06-16 20:51:04,619] [INFO] Selected 21 target genomes.
[2023-06-16 20:51:04,619] [INFO] Target genome list was writen to GCA_013607775.1_ASM1360777v1_genomic.fna/target_genomes.txt
[2023-06-16 20:51:04,624] [INFO] Task started: fastANI
[2023-06-16 20:51:04,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg03df3167-b29b-46bd-a51c-e8be81bcddef/GCA_013607775.1_ASM1360777v1_genomic.fna.gz --refList GCA_013607775.1_ASM1360777v1_genomic.fna/target_genomes.txt --output GCA_013607775.1_ASM1360777v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:51:15,596] [INFO] Task succeeded: fastANI
[2023-06-16 20:51:15,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f111af0-e528-4756-99cd-d8c3fe345499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:51:15,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f111af0-e528-4756-99cd-d8c3fe345499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:51:15,602] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:51:15,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:51:15,602] [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	77.8124	89	615	95	below_threshold
Sulfurovum lithotrophicum	strain=ATCC BAA-797	GCA_000987835.1	206403	206403	type	True	77.5999	106	615	95	below_threshold
Sulfurovum indicum	strain=ST-419	GCA_014931715.1	2779528	2779528	type	True	77.1391	112	615	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:51:15,604] [INFO] DFAST Taxonomy check result was written to GCA_013607775.1_ASM1360777v1_genomic.fna/tc_result.tsv
[2023-06-16 20:51:15,604] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:51:15,605] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:51:15,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f111af0-e528-4756-99cd-d8c3fe345499/dqc_reference/checkm_data
[2023-06-16 20:51:15,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:51:15,631] [INFO] Task started: CheckM
[2023-06-16 20:51:15,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013607775.1_ASM1360777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013607775.1_ASM1360777v1_genomic.fna/checkm_input GCA_013607775.1_ASM1360777v1_genomic.fna/checkm_result
[2023-06-16 20:51:32,886] [INFO] Task succeeded: CheckM
[2023-06-16 20:51:32,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:51:32,902] [INFO] ===== Completeness check finished =====
[2023-06-16 20:51:32,903] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:51:32,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013607775.1_ASM1360777v1_genomic.fna/markers.fasta)
[2023-06-16 20:51:32,904] [INFO] Task started: Blastn
[2023-06-16 20:51:32,904] [INFO] Running command: blastn -query GCA_013607775.1_ASM1360777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f111af0-e528-4756-99cd-d8c3fe345499/dqc_reference/reference_markers_gtdb.fasta -out GCA_013607775.1_ASM1360777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:51:33,584] [INFO] Task succeeded: Blastn
[2023-06-16 20:51:33,587] [INFO] Selected 12 target genomes.
[2023-06-16 20:51:33,587] [INFO] Target genome list was writen to GCA_013607775.1_ASM1360777v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:51:33,594] [INFO] Task started: fastANI
[2023-06-16 20:51:33,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg03df3167-b29b-46bd-a51c-e8be81bcddef/GCA_013607775.1_ASM1360777v1_genomic.fna.gz --refList GCA_013607775.1_ASM1360777v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013607775.1_ASM1360777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:51:38,342] [INFO] Task succeeded: fastANI
[2023-06-16 20:51:38,350] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:51:38,351] [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_013607775.1	s__Sulfurovum sp013607775	100.0	608	615	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_011330645.1	s__Sulfurovum sp011330645	83.7609	303	615	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	79.4374	227	615	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139765.1	s__Sulfurovum sp013139765	78.8827	200	615	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	78.8638	155	615	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	78.8273	201	615	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	78.6563	220	615	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	78.6557	168	615	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	78.2765	162	615	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	77.5999	106	615	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	76.9783	96	615	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurovaceae;g__Sulfurovum	95.0	98.17	98.17	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-16 20:51:38,352] [INFO] GTDB search result was written to GCA_013607775.1_ASM1360777v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:51:38,353] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:51:38,355] [INFO] DFAST_QC result json was written to GCA_013607775.1_ASM1360777v1_genomic.fna/dqc_result.json
[2023-06-16 20:51:38,356] [INFO] DFAST_QC completed!
[2023-06-16 20:51:38,356] [INFO] Total running time: 0h0m39s