[2024-01-25 17:49:50,713] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg9802a9fc-f7ed-4b65-bff9-674a7364a0e2/dqc_reference
[2024-01-25 17:49:51,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:51,861] [INFO] Task started: Prodigal
[2024-01-25 17:49:51,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d4666f0-68bb-4ddf-9f30-456fdc2a5e4d/GCF_012102615.1_ASM1210261v1_genomic.fna.gz | prodigal -d GCF_012102615.1_ASM1210261v1_genomic.fna/cds.fna -a GCF_012102615.1_ASM1210261v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:58,887] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:58,888] [INFO] Task started: HMMsearch
[2024-01-25 17:49:58,888] [INFO] Running command: hmmsearch --tblout GCF_012102615.1_ASM1210261v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9802a9fc-f7ed-4b65-bff9-674a7364a0e2/dqc_reference/reference_markers.hmm GCF_012102615.1_ASM1210261v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:59,102] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:59,103] [INFO] Found 6/6 markers.
[2024-01-25 17:49:59,123] [INFO] Query marker FASTA was written to GCF_012102615.1_ASM1210261v1_genomic.fna/markers.fasta
[2024-01-25 17:49:59,124] [INFO] Task started: Blastn
[2024-01-25 17:49:59,124] [INFO] Running command: blastn -query GCF_012102615.1_ASM1210261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9802a9fc-f7ed-4b65-bff9-674a7364a0e2/dqc_reference/reference_markers.fasta -out GCF_012102615.1_ASM1210261v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:59,737] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:59,741] [INFO] Selected 22 target genomes.
[2024-01-25 17:49:59,741] [INFO] Target genome list was writen to GCF_012102615.1_ASM1210261v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:59,787] [INFO] Task started: fastANI
[2024-01-25 17:49:59,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d4666f0-68bb-4ddf-9f30-456fdc2a5e4d/GCF_012102615.1_ASM1210261v1_genomic.fna.gz --refList GCF_012102615.1_ASM1210261v1_genomic.fna/target_genomes.txt --output GCF_012102615.1_ASM1210261v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:13,986] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:13,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9802a9fc-f7ed-4b65-bff9-674a7364a0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:13,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9802a9fc-f7ed-4b65-bff9-674a7364a0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:13,991] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:50:13,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:13,991] [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
Haematospirillum jordaniae	strain=H5569	GCA_012102615.1	1549855	1549855	type	True	100.0	781	782	95	conclusive
Haematospirillum jordaniae	strain=H5569	GCA_001611975.1	1549855	1549855	type	True	99.9994	781	782	95	conclusive
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	76.6909	97	782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:13,992] [INFO] DFAST Taxonomy check result was written to GCF_012102615.1_ASM1210261v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:13,993] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:13,993] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:13,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9802a9fc-f7ed-4b65-bff9-674a7364a0e2/dqc_reference/checkm_data
[2024-01-25 17:50:13,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:14,021] [INFO] Task started: CheckM
[2024-01-25 17:50:14,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012102615.1_ASM1210261v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012102615.1_ASM1210261v1_genomic.fna/checkm_input GCF_012102615.1_ASM1210261v1_genomic.fna/checkm_result
[2024-01-25 17:50:39,461] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:39,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:39,479] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:39,479] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:39,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012102615.1_ASM1210261v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:39,480] [INFO] Task started: Blastn
[2024-01-25 17:50:39,480] [INFO] Running command: blastn -query GCF_012102615.1_ASM1210261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9802a9fc-f7ed-4b65-bff9-674a7364a0e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_012102615.1_ASM1210261v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:40,523] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:40,527] [INFO] Selected 14 target genomes.
[2024-01-25 17:50:40,527] [INFO] Target genome list was writen to GCF_012102615.1_ASM1210261v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:40,557] [INFO] Task started: fastANI
[2024-01-25 17:50:40,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d4666f0-68bb-4ddf-9f30-456fdc2a5e4d/GCF_012102615.1_ASM1210261v1_genomic.fna.gz --refList GCF_012102615.1_ASM1210261v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012102615.1_ASM1210261v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:49,114] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:49,120] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:49,120] [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_001611975.1	s__Haematospirillum jordaniae	99.9994	781	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Haematospirillum	95.0	99.88	99.28	0.99	0.98	11	conclusive
GCF_012102705.1	s__Haematospirillum sp012102705	94.0139	709	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Haematospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012102745.1	s__Haematospirillum sp012102745	93.0122	717	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Haematospirillum	95.0	99.64	99.29	0.98	0.97	3	-
GCF_000381985.1	s__Novispirillum itersonii	76.6909	97	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Novispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156605.1	s__Insolitispirillum peregrinum	76.488	62	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Insolitispirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:49,121] [INFO] GTDB search result was written to GCF_012102615.1_ASM1210261v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:49,121] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:49,123] [INFO] DFAST_QC result json was written to GCF_012102615.1_ASM1210261v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:49,124] [INFO] DFAST_QC completed!
[2024-01-25 17:50:49,124] [INFO] Total running time: 0h0m58s