[2024-01-24 13:28:19,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:19,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:19,080] [INFO] DQC Reference Directory: /var/lib/cwl/stgc907e121-fd12-4f0d-a08f-1411c5fc8943/dqc_reference
[2024-01-24 13:28:20,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,467] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg17e5b703-ab3a-47be-ba63-9f0b89f662b8/GCF_000428585.1_ASM42858v1_genomic.fna.gz | prodigal -d GCF_000428585.1_ASM42858v1_genomic.fna/cds.fna -a GCF_000428585.1_ASM42858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:31,881] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:31,882] [INFO] Task started: HMMsearch
[2024-01-24 13:28:31,882] [INFO] Running command: hmmsearch --tblout GCF_000428585.1_ASM42858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc907e121-fd12-4f0d-a08f-1411c5fc8943/dqc_reference/reference_markers.hmm GCF_000428585.1_ASM42858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:32,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:32,255] [INFO] Found 6/6 markers.
[2024-01-24 13:28:32,335] [INFO] Query marker FASTA was written to GCF_000428585.1_ASM42858v1_genomic.fna/markers.fasta
[2024-01-24 13:28:32,336] [INFO] Task started: Blastn
[2024-01-24 13:28:32,336] [INFO] Running command: blastn -query GCF_000428585.1_ASM42858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc907e121-fd12-4f0d-a08f-1411c5fc8943/dqc_reference/reference_markers.fasta -out GCF_000428585.1_ASM42858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:33,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:33,216] [INFO] Selected 30 target genomes.
[2024-01-24 13:28:33,216] [INFO] Target genome list was writen to GCF_000428585.1_ASM42858v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:33,227] [INFO] Task started: fastANI
[2024-01-24 13:28:33,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg17e5b703-ab3a-47be-ba63-9f0b89f662b8/GCF_000428585.1_ASM42858v1_genomic.fna.gz --refList GCF_000428585.1_ASM42858v1_genomic.fna/target_genomes.txt --output GCF_000428585.1_ASM42858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:55,556] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:55,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc907e121-fd12-4f0d-a08f-1411c5fc8943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:55,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc907e121-fd12-4f0d-a08f-1411c5fc8943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:55,561] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:55,561] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:55,561] [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
Zooshikella ganghwensis	strain=DSM 15267	GCA_000428585.1	202772	202772	type	True	100.0	1708	1724	95	conclusive
Spartinivicinus ruber	strain=S2-4-1H	GCA_011009015.1	2683272	2683272	type	True	77.0734	142	1724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:55,563] [INFO] DFAST Taxonomy check result was written to GCF_000428585.1_ASM42858v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:55,563] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:55,564] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:55,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc907e121-fd12-4f0d-a08f-1411c5fc8943/dqc_reference/checkm_data
[2024-01-24 13:28:55,565] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:55,625] [INFO] Task started: CheckM
[2024-01-24 13:28:55,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428585.1_ASM42858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428585.1_ASM42858v1_genomic.fna/checkm_input GCF_000428585.1_ASM42858v1_genomic.fna/checkm_result
[2024-01-24 13:29:34,110] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:34,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:34,130] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:34,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:34,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428585.1_ASM42858v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:34,131] [INFO] Task started: Blastn
[2024-01-24 13:29:34,131] [INFO] Running command: blastn -query GCF_000428585.1_ASM42858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc907e121-fd12-4f0d-a08f-1411c5fc8943/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428585.1_ASM42858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:35,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:35,171] [INFO] Selected 23 target genomes.
[2024-01-24 13:29:35,171] [INFO] Target genome list was writen to GCF_000428585.1_ASM42858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:35,205] [INFO] Task started: fastANI
[2024-01-24 13:29:35,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg17e5b703-ab3a-47be-ba63-9f0b89f662b8/GCF_000428585.1_ASM42858v1_genomic.fna.gz --refList GCF_000428585.1_ASM42858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428585.1_ASM42858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:53,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:53,133] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:53,133] [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_000428585.1	s__Zooshikella ganghwensis	100.0	1708	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Zooshikella	95.0	97.38	97.05	0.91	0.90	4	conclusive
GCF_018837975.1	s__Zooshikella sp018837975	83.7629	1259	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Zooshikella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425485.1	s__Spartinivicinus sp013425485	77.2332	132	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Spartinivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011009015.1	s__Spartinivicinus ruber	77.0943	141	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Spartinivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:53,136] [INFO] GTDB search result was written to GCF_000428585.1_ASM42858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:53,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:53,143] [INFO] DFAST_QC result json was written to GCF_000428585.1_ASM42858v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:53,144] [INFO] DFAST_QC completed!
[2024-01-24 13:29:53,144] [INFO] Total running time: 0h1m34s