[2023-06-28 12:14:24,871] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:14:24,874] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:14:24,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg910ef2ae-cb2d-489f-b341-d9c986e0809f/dqc_reference
[2023-06-28 12:14:26,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:14:26,301] [INFO] Task started: Prodigal
[2023-06-28 12:14:26,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg035aca33-cbcd-40dd-a249-1312fa6a2c6f/GCA_005801425.1_ASM580142v1_genomic.fna.gz | prodigal -d GCA_005801425.1_ASM580142v1_genomic.fna/cds.fna -a GCA_005801425.1_ASM580142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:14:38,047] [INFO] Task succeeded: Prodigal
[2023-06-28 12:14:38,048] [INFO] Task started: HMMsearch
[2023-06-28 12:14:38,048] [INFO] Running command: hmmsearch --tblout GCA_005801425.1_ASM580142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg910ef2ae-cb2d-489f-b341-d9c986e0809f/dqc_reference/reference_markers.hmm GCA_005801425.1_ASM580142v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:14:38,325] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:14:38,327] [INFO] Found 6/6 markers.
[2023-06-28 12:14:38,356] [INFO] Query marker FASTA was written to GCA_005801425.1_ASM580142v1_genomic.fna/markers.fasta
[2023-06-28 12:14:38,357] [INFO] Task started: Blastn
[2023-06-28 12:14:38,357] [INFO] Running command: blastn -query GCA_005801425.1_ASM580142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg910ef2ae-cb2d-489f-b341-d9c986e0809f/dqc_reference/reference_markers.fasta -out GCA_005801425.1_ASM580142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:14:38,937] [INFO] Task succeeded: Blastn
[2023-06-28 12:14:38,940] [INFO] Selected 25 target genomes.
[2023-06-28 12:14:38,941] [INFO] Target genome list was writen to GCA_005801425.1_ASM580142v1_genomic.fna/target_genomes.txt
[2023-06-28 12:14:38,947] [INFO] Task started: fastANI
[2023-06-28 12:14:38,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg035aca33-cbcd-40dd-a249-1312fa6a2c6f/GCA_005801425.1_ASM580142v1_genomic.fna.gz --refList GCA_005801425.1_ASM580142v1_genomic.fna/target_genomes.txt --output GCA_005801425.1_ASM580142v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:14:54,958] [INFO] Task succeeded: fastANI
[2023-06-28 12:14:54,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg910ef2ae-cb2d-489f-b341-d9c986e0809f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:14:54,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg910ef2ae-cb2d-489f-b341-d9c986e0809f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:14:54,963] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:14:54,963] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:14:54,963] [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
--------------------------------------------------------------------------------
[2023-06-28 12:14:54,965] [INFO] DFAST Taxonomy check result was written to GCA_005801425.1_ASM580142v1_genomic.fna/tc_result.tsv
[2023-06-28 12:14:54,966] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:14:54,966] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:14:54,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg910ef2ae-cb2d-489f-b341-d9c986e0809f/dqc_reference/checkm_data
[2023-06-28 12:14:54,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:14:55,016] [INFO] Task started: CheckM
[2023-06-28 12:14:55,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005801425.1_ASM580142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005801425.1_ASM580142v1_genomic.fna/checkm_input GCA_005801425.1_ASM580142v1_genomic.fna/checkm_result
[2023-06-28 12:15:34,379] [INFO] Task succeeded: CheckM
[2023-06-28 12:15:34,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:15:34,404] [INFO] ===== Completeness check finished =====
[2023-06-28 12:15:34,405] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:15:34,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005801425.1_ASM580142v1_genomic.fna/markers.fasta)
[2023-06-28 12:15:34,405] [INFO] Task started: Blastn
[2023-06-28 12:15:34,406] [INFO] Running command: blastn -query GCA_005801425.1_ASM580142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg910ef2ae-cb2d-489f-b341-d9c986e0809f/dqc_reference/reference_markers_gtdb.fasta -out GCA_005801425.1_ASM580142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:15:35,144] [INFO] Task succeeded: Blastn
[2023-06-28 12:15:35,149] [INFO] Selected 33 target genomes.
[2023-06-28 12:15:35,149] [INFO] Target genome list was writen to GCA_005801425.1_ASM580142v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:15:35,171] [INFO] Task started: fastANI
[2023-06-28 12:15:35,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg035aca33-cbcd-40dd-a249-1312fa6a2c6f/GCA_005801425.1_ASM580142v1_genomic.fna.gz --refList GCA_005801425.1_ASM580142v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005801425.1_ASM580142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:15:53,231] [INFO] Task succeeded: fastANI
[2023-06-28 12:15:53,236] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:15:53,236] [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
GCA_005801425.1	s__SYDY01 sp005801425	100.0	1054	1064	d__Bacteria;p__Myxococcota;c__XYA12-FULL-58-9;o__XYA12-FULL-58-9;f__SYDY01;g__SYDY01	95.0	99.95	99.95	0.96	0.96	2	conclusive
--------------------------------------------------------------------------------
[2023-06-28 12:15:53,238] [INFO] GTDB search result was written to GCA_005801425.1_ASM580142v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:15:53,239] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:15:53,241] [INFO] DFAST_QC result json was written to GCA_005801425.1_ASM580142v1_genomic.fna/dqc_result.json
[2023-06-28 12:15:53,241] [INFO] DFAST_QC completed!
[2023-06-28 12:15:53,241] [INFO] Total running time: 0h1m28s