[2024-01-25 18:10:05,423] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:05,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:05,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3f072c8-46a1-4b1a-b84f-5c3e0d293566/dqc_reference
[2024-01-25 18:10:06,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:06,602] [INFO] Task started: Prodigal
[2024-01-25 18:10:06,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgf37200e8-be1e-46e0-b769-508e5967563e/GCF_009937995.1_ASM993799v1_genomic.fna.gz | prodigal -d GCF_009937995.1_ASM993799v1_genomic.fna/cds.fna -a GCF_009937995.1_ASM993799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:14,985] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:14,985] [INFO] Task started: HMMsearch
[2024-01-25 18:10:14,985] [INFO] Running command: hmmsearch --tblout GCF_009937995.1_ASM993799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3f072c8-46a1-4b1a-b84f-5c3e0d293566/dqc_reference/reference_markers.hmm GCF_009937995.1_ASM993799v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:15,187] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:15,188] [INFO] Found 6/6 markers.
[2024-01-25 18:10:15,213] [INFO] Query marker FASTA was written to GCF_009937995.1_ASM993799v1_genomic.fna/markers.fasta
[2024-01-25 18:10:15,214] [INFO] Task started: Blastn
[2024-01-25 18:10:15,214] [INFO] Running command: blastn -query GCF_009937995.1_ASM993799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3f072c8-46a1-4b1a-b84f-5c3e0d293566/dqc_reference/reference_markers.fasta -out GCF_009937995.1_ASM993799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:15,771] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:15,773] [INFO] Selected 24 target genomes.
[2024-01-25 18:10:15,773] [INFO] Target genome list was writen to GCF_009937995.1_ASM993799v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:15,794] [INFO] Task started: fastANI
[2024-01-25 18:10:15,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37200e8-be1e-46e0-b769-508e5967563e/GCF_009937995.1_ASM993799v1_genomic.fna.gz --refList GCF_009937995.1_ASM993799v1_genomic.fna/target_genomes.txt --output GCF_009937995.1_ASM993799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:30,222] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:30,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3f072c8-46a1-4b1a-b84f-5c3e0d293566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:30,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3f072c8-46a1-4b1a-b84f-5c3e0d293566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:30,228] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:30,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:30,228] [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
Sulfuriferula nivalis	strain=SGTM	GCA_009937995.1	2675298	2675298	type	True	100.0	1143	1144	95	conclusive
Sulfuriferula thiophila	strain=mst6	GCA_003864975.1	1781211	1781211	type	True	79.0064	265	1144	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.4336	85	1144	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	76.703	79	1144	95	below_threshold
Sulfurirhabdus autotrophica	strain=DSM 100309	GCA_004346685.1	1706046	1706046	type	True	76.6265	57	1144	95	below_threshold
Sulfurirhabdus autotrophica	strain=BiS0	GCA_003864995.1	1706046	1706046	type	True	76.4335	55	1144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:30,230] [INFO] DFAST Taxonomy check result was written to GCF_009937995.1_ASM993799v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:30,230] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:30,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:30,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3f072c8-46a1-4b1a-b84f-5c3e0d293566/dqc_reference/checkm_data
[2024-01-25 18:10:30,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:30,264] [INFO] Task started: CheckM
[2024-01-25 18:10:30,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009937995.1_ASM993799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009937995.1_ASM993799v1_genomic.fna/checkm_input GCF_009937995.1_ASM993799v1_genomic.fna/checkm_result
[2024-01-25 18:10:58,446] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:58,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:58,463] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:58,464] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:58,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009937995.1_ASM993799v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:58,464] [INFO] Task started: Blastn
[2024-01-25 18:10:58,464] [INFO] Running command: blastn -query GCF_009937995.1_ASM993799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3f072c8-46a1-4b1a-b84f-5c3e0d293566/dqc_reference/reference_markers_gtdb.fasta -out GCF_009937995.1_ASM993799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:59,257] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:59,260] [INFO] Selected 19 target genomes.
[2024-01-25 18:10:59,260] [INFO] Target genome list was writen to GCF_009937995.1_ASM993799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:59,277] [INFO] Task started: fastANI
[2024-01-25 18:10:59,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37200e8-be1e-46e0-b769-508e5967563e/GCF_009937995.1_ASM993799v1_genomic.fna.gz --refList GCF_009937995.1_ASM993799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009937995.1_ASM993799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:09,196] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:09,201] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:09,202] [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_009937995.1	s__Sulfuriferula_A nivalis	100.0	1141	1144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013140765.1	s__Sulfuriferula_A sp013140765	79.3916	345	1144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864975.1	s__Sulfuriferula_A thiophila	79.0054	267	1144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162035.1	s__Sulfuriferula_A sp002162035	78.2416	232	1144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938015.1	s__Sulfuriferula plumbiphila	77.4404	85	1144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004346685.1	s__Sulfurirhabdus autotrophica	76.6265	57	1144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae_A;g__Sulfurirhabdus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:09,203] [INFO] GTDB search result was written to GCF_009937995.1_ASM993799v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:09,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:09,206] [INFO] DFAST_QC result json was written to GCF_009937995.1_ASM993799v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:09,206] [INFO] DFAST_QC completed!
[2024-01-25 18:11:09,206] [INFO] Total running time: 0h1m4s