[2024-01-24 13:41:18,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:18,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:18,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg52edd9ad-c9a0-4037-9779-9fb3429dc56b/dqc_reference
[2024-01-24 13:41:20,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:20,242] [INFO] Task started: Prodigal
[2024-01-24 13:41:20,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e6c4588-9ee6-42d5-ba39-cb618ab5e561/GCF_014145225.1_ASM1414522v1_genomic.fna.gz | prodigal -d GCF_014145225.1_ASM1414522v1_genomic.fna/cds.fna -a GCF_014145225.1_ASM1414522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:28,880] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:28,880] [INFO] Task started: HMMsearch
[2024-01-24 13:41:28,880] [INFO] Running command: hmmsearch --tblout GCF_014145225.1_ASM1414522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52edd9ad-c9a0-4037-9779-9fb3429dc56b/dqc_reference/reference_markers.hmm GCF_014145225.1_ASM1414522v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:29,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:29,238] [INFO] Found 6/6 markers.
[2024-01-24 13:41:29,272] [INFO] Query marker FASTA was written to GCF_014145225.1_ASM1414522v1_genomic.fna/markers.fasta
[2024-01-24 13:41:29,273] [INFO] Task started: Blastn
[2024-01-24 13:41:29,273] [INFO] Running command: blastn -query GCF_014145225.1_ASM1414522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52edd9ad-c9a0-4037-9779-9fb3429dc56b/dqc_reference/reference_markers.fasta -out GCF_014145225.1_ASM1414522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,976] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:29,977] [INFO] Target genome list was writen to GCF_014145225.1_ASM1414522v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:29,986] [INFO] Task started: fastANI
[2024-01-24 13:41:29,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e6c4588-9ee6-42d5-ba39-cb618ab5e561/GCF_014145225.1_ASM1414522v1_genomic.fna.gz --refList GCF_014145225.1_ASM1414522v1_genomic.fna/target_genomes.txt --output GCF_014145225.1_ASM1414522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:44,101] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:44,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52edd9ad-c9a0-4037-9779-9fb3429dc56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:44,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52edd9ad-c9a0-4037-9779-9fb3429dc56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:44,106] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:44,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:44,106] [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
Thiospirillum jenense	strain=DSM 216	GCA_014145225.1	1653858	1653858	type	True	100.0	1019	1020	95	conclusive
Chromatium okenii	strain=DSM 169	GCA_016583745.1	61644	61644	type	True	77.2709	128	1020	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,107] [INFO] DFAST Taxonomy check result was written to GCF_014145225.1_ASM1414522v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:44,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:44,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:44,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52edd9ad-c9a0-4037-9779-9fb3429dc56b/dqc_reference/checkm_data
[2024-01-24 13:41:44,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:44,147] [INFO] Task started: CheckM
[2024-01-24 13:41:44,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145225.1_ASM1414522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145225.1_ASM1414522v1_genomic.fna/checkm_input GCF_014145225.1_ASM1414522v1_genomic.fna/checkm_result
[2024-01-24 13:42:15,446] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,470] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145225.1_ASM1414522v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,471] [INFO] Task started: Blastn
[2024-01-24 13:42:15,472] [INFO] Running command: blastn -query GCF_014145225.1_ASM1414522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52edd9ad-c9a0-4037-9779-9fb3429dc56b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145225.1_ASM1414522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:16,274] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:16,279] [INFO] Selected 29 target genomes.
[2024-01-24 13:42:16,279] [INFO] Target genome list was writen to GCF_014145225.1_ASM1414522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:16,304] [INFO] Task started: fastANI
[2024-01-24 13:42:16,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e6c4588-9ee6-42d5-ba39-cb618ab5e561/GCF_014145225.1_ASM1414522v1_genomic.fna.gz --refList GCF_014145225.1_ASM1414522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145225.1_ASM1414522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:31,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:31,167] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:31,167] [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_014145225.1	s__Thiospirillum jenense	100.0	1019	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:42:31,169] [INFO] GTDB search result was written to GCF_014145225.1_ASM1414522v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:31,170] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:31,172] [INFO] DFAST_QC result json was written to GCF_014145225.1_ASM1414522v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:31,172] [INFO] DFAST_QC completed!
[2024-01-24 13:42:31,173] [INFO] Total running time: 0h1m12s