[2024-01-24 12:09:05,775] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgc84b4ed3-1e91-4bb7-b460-484df77a3e91/dqc_reference
[2024-01-24 12:09:06,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,956] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg04678ba9-d8fd-4375-a7c7-ca6c7c361de4/GCF_002216855.1_ASM221685v1_genomic.fna.gz | prodigal -d GCF_002216855.1_ASM221685v1_genomic.fna/cds.fna -a GCF_002216855.1_ASM221685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:11,486] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:11,487] [INFO] Task started: HMMsearch
[2024-01-24 12:09:11,487] [INFO] Running command: hmmsearch --tblout GCF_002216855.1_ASM221685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc84b4ed3-1e91-4bb7-b460-484df77a3e91/dqc_reference/reference_markers.hmm GCF_002216855.1_ASM221685v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:11,732] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:11,733] [INFO] Found 6/6 markers.
[2024-01-24 12:09:11,759] [INFO] Query marker FASTA was written to GCF_002216855.1_ASM221685v1_genomic.fna/markers.fasta
[2024-01-24 12:09:11,759] [INFO] Task started: Blastn
[2024-01-24 12:09:11,759] [INFO] Running command: blastn -query GCF_002216855.1_ASM221685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc84b4ed3-1e91-4bb7-b460-484df77a3e91/dqc_reference/reference_markers.fasta -out GCF_002216855.1_ASM221685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:12,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:12,405] [INFO] Selected 30 target genomes.
[2024-01-24 12:09:12,405] [INFO] Target genome list was writen to GCF_002216855.1_ASM221685v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:12,419] [INFO] Task started: fastANI
[2024-01-24 12:09:12,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg04678ba9-d8fd-4375-a7c7-ca6c7c361de4/GCF_002216855.1_ASM221685v1_genomic.fna.gz --refList GCF_002216855.1_ASM221685v1_genomic.fna/target_genomes.txt --output GCF_002216855.1_ASM221685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:26,367] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:26,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc84b4ed3-1e91-4bb7-b460-484df77a3e91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:26,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc84b4ed3-1e91-4bb7-b460-484df77a3e91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:26,374] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:26,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:26,375] [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
Paraphotobacterium marinum	strain=NSCS20N07D	GCA_002216855.1	1755811	1755811	type	True	100.0	863	863	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:09:26,376] [INFO] DFAST Taxonomy check result was written to GCF_002216855.1_ASM221685v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:26,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:26,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:26,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc84b4ed3-1e91-4bb7-b460-484df77a3e91/dqc_reference/checkm_data
[2024-01-24 12:09:26,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:26,405] [INFO] Task started: CheckM
[2024-01-24 12:09:26,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002216855.1_ASM221685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002216855.1_ASM221685v1_genomic.fna/checkm_input GCF_002216855.1_ASM221685v1_genomic.fna/checkm_result
[2024-01-24 12:09:46,961] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:46,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:46,985] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:46,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:46,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002216855.1_ASM221685v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:46,986] [INFO] Task started: Blastn
[2024-01-24 12:09:46,986] [INFO] Running command: blastn -query GCF_002216855.1_ASM221685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc84b4ed3-1e91-4bb7-b460-484df77a3e91/dqc_reference/reference_markers_gtdb.fasta -out GCF_002216855.1_ASM221685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:47,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:47,953] [INFO] Selected 29 target genomes.
[2024-01-24 12:09:47,953] [INFO] Target genome list was writen to GCF_002216855.1_ASM221685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:48,009] [INFO] Task started: fastANI
[2024-01-24 12:09:48,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg04678ba9-d8fd-4375-a7c7-ca6c7c361de4/GCF_002216855.1_ASM221685v1_genomic.fna.gz --refList GCF_002216855.1_ASM221685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002216855.1_ASM221685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:59,920] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:59,925] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:59,925] [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_002216855.1	s__Paraphotobacterium marinum	100.0	863	863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Paraphotobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:09:59,927] [INFO] GTDB search result was written to GCF_002216855.1_ASM221685v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:59,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:59,931] [INFO] DFAST_QC result json was written to GCF_002216855.1_ASM221685v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:59,931] [INFO] DFAST_QC completed!
[2024-01-24 12:09:59,932] [INFO] Total running time: 0h0m54s