[2024-01-25 20:26:05,357] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:05,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:05,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgba477752-75c3-42f4-ab8a-d963971d409f/dqc_reference
[2024-01-25 20:26:06,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:06,487] [INFO] Task started: Prodigal
[2024-01-25 20:26:06,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg8252b125-c88f-4eec-a3c5-9d7900c5c3ca/GCF_009711365.1_ASM971136v1_genomic.fna.gz | prodigal -d GCF_009711365.1_ASM971136v1_genomic.fna/cds.fna -a GCF_009711365.1_ASM971136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:22,137] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:22,137] [INFO] Task started: HMMsearch
[2024-01-25 20:26:22,137] [INFO] Running command: hmmsearch --tblout GCF_009711365.1_ASM971136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba477752-75c3-42f4-ab8a-d963971d409f/dqc_reference/reference_markers.hmm GCF_009711365.1_ASM971136v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:22,386] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:22,387] [INFO] Found 6/6 markers.
[2024-01-25 20:26:22,429] [INFO] Query marker FASTA was written to GCF_009711365.1_ASM971136v1_genomic.fna/markers.fasta
[2024-01-25 20:26:22,429] [INFO] Task started: Blastn
[2024-01-25 20:26:22,429] [INFO] Running command: blastn -query GCF_009711365.1_ASM971136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba477752-75c3-42f4-ab8a-d963971d409f/dqc_reference/reference_markers.fasta -out GCF_009711365.1_ASM971136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:22,968] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:22,971] [INFO] Selected 25 target genomes.
[2024-01-25 20:26:22,972] [INFO] Target genome list was writen to GCF_009711365.1_ASM971136v1_genomic.fna/target_genomes.txt
[2024-01-25 20:26:22,998] [INFO] Task started: fastANI
[2024-01-25 20:26:22,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg8252b125-c88f-4eec-a3c5-9d7900c5c3ca/GCF_009711365.1_ASM971136v1_genomic.fna.gz --refList GCF_009711365.1_ASM971136v1_genomic.fna/target_genomes.txt --output GCF_009711365.1_ASM971136v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:43,776] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:43,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba477752-75c3-42f4-ab8a-d963971d409f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:43,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba477752-75c3-42f4-ab8a-d963971d409f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:43,780] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:26:43,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:26:43,781] [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
Xanthovirga aplysinae	strain=RKSG123	GCA_009711365.1	2529853	2529853	type	True	100.0	1305	1329	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:26:43,782] [INFO] DFAST Taxonomy check result was written to GCF_009711365.1_ASM971136v1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:43,782] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:43,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:43,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba477752-75c3-42f4-ab8a-d963971d409f/dqc_reference/checkm_data
[2024-01-25 20:26:43,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:43,838] [INFO] Task started: CheckM
[2024-01-25 20:26:43,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711365.1_ASM971136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711365.1_ASM971136v1_genomic.fna/checkm_input GCF_009711365.1_ASM971136v1_genomic.fna/checkm_result
[2024-01-25 20:27:30,918] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:30,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:30,939] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:30,940] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:30,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711365.1_ASM971136v1_genomic.fna/markers.fasta)
[2024-01-25 20:27:30,941] [INFO] Task started: Blastn
[2024-01-25 20:27:30,941] [INFO] Running command: blastn -query GCF_009711365.1_ASM971136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba477752-75c3-42f4-ab8a-d963971d409f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711365.1_ASM971136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:31,750] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:31,753] [INFO] Selected 33 target genomes.
[2024-01-25 20:27:31,753] [INFO] Target genome list was writen to GCF_009711365.1_ASM971136v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:31,785] [INFO] Task started: fastANI
[2024-01-25 20:27:31,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg8252b125-c88f-4eec-a3c5-9d7900c5c3ca/GCF_009711365.1_ASM971136v1_genomic.fna.gz --refList GCF_009711365.1_ASM971136v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711365.1_ASM971136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:55,289] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:55,290] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:27:55,291] [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
--------------------------------------------------------------------------------
[2024-01-25 20:27:55,292] [INFO] GTDB search result was written to GCF_009711365.1_ASM971136v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:55,292] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:55,294] [INFO] DFAST_QC result json was written to GCF_009711365.1_ASM971136v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:55,294] [INFO] DFAST_QC completed!
[2024-01-25 20:27:55,294] [INFO] Total running time: 0h1m50s