[2023-06-19 00:04:44,098] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:04:44,108] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:04:44,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg25cf554e-670d-4da5-baaf-3e093c40a8db/dqc_reference
[2023-06-19 00:04:45,319] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:04:45,320] [INFO] Task started: Prodigal
[2023-06-19 00:04:45,320] [INFO] Running command: gunzip -c /var/lib/cwl/stgad4515d5-807d-4c47-b23d-2e50e26ab3d1/GCA_018653665.1_ASM1865366v1_genomic.fna.gz | prodigal -d GCA_018653665.1_ASM1865366v1_genomic.fna/cds.fna -a GCA_018653665.1_ASM1865366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:04:50,405] [INFO] Task succeeded: Prodigal
[2023-06-19 00:04:50,406] [INFO] Task started: HMMsearch
[2023-06-19 00:04:50,406] [INFO] Running command: hmmsearch --tblout GCA_018653665.1_ASM1865366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25cf554e-670d-4da5-baaf-3e093c40a8db/dqc_reference/reference_markers.hmm GCA_018653665.1_ASM1865366v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:04:50,642] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:04:50,643] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgad4515d5-807d-4c47-b23d-2e50e26ab3d1/GCA_018653665.1_ASM1865366v1_genomic.fna.gz]
[2023-06-19 00:04:50,668] [INFO] Query marker FASTA was written to GCA_018653665.1_ASM1865366v1_genomic.fna/markers.fasta
[2023-06-19 00:04:50,668] [INFO] Task started: Blastn
[2023-06-19 00:04:50,669] [INFO] Running command: blastn -query GCA_018653665.1_ASM1865366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25cf554e-670d-4da5-baaf-3e093c40a8db/dqc_reference/reference_markers.fasta -out GCA_018653665.1_ASM1865366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:04:51,191] [INFO] Task succeeded: Blastn
[2023-06-19 00:04:51,198] [INFO] Selected 5 target genomes.
[2023-06-19 00:04:51,198] [INFO] Target genome list was writen to GCA_018653665.1_ASM1865366v1_genomic.fna/target_genomes.txt
[2023-06-19 00:04:51,199] [INFO] Task started: fastANI
[2023-06-19 00:04:51,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4515d5-807d-4c47-b23d-2e50e26ab3d1/GCA_018653665.1_ASM1865366v1_genomic.fna.gz --refList GCA_018653665.1_ASM1865366v1_genomic.fna/target_genomes.txt --output GCA_018653665.1_ASM1865366v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:04:53,673] [INFO] Task succeeded: fastANI
[2023-06-19 00:04:53,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25cf554e-670d-4da5-baaf-3e093c40a8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:04:53,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25cf554e-670d-4da5-baaf-3e093c40a8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:04:53,677] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:04:53,677] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 00:04:53,677] [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
--------------------------------------------------------------------------------
[2023-06-19 00:04:53,680] [INFO] DFAST Taxonomy check result was written to GCA_018653665.1_ASM1865366v1_genomic.fna/tc_result.tsv
[2023-06-19 00:04:53,680] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:04:53,681] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:04:53,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25cf554e-670d-4da5-baaf-3e093c40a8db/dqc_reference/checkm_data
[2023-06-19 00:04:53,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:04:53,713] [INFO] Task started: CheckM
[2023-06-19 00:04:53,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018653665.1_ASM1865366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018653665.1_ASM1865366v1_genomic.fna/checkm_input GCA_018653665.1_ASM1865366v1_genomic.fna/checkm_result
[2023-06-19 00:05:16,820] [INFO] Task succeeded: CheckM
[2023-06-19 00:05:16,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:05:16,880] [INFO] ===== Completeness check finished =====
[2023-06-19 00:05:16,880] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:05:16,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018653665.1_ASM1865366v1_genomic.fna/markers.fasta)
[2023-06-19 00:05:16,881] [INFO] Task started: Blastn
[2023-06-19 00:05:16,881] [INFO] Running command: blastn -query GCA_018653665.1_ASM1865366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25cf554e-670d-4da5-baaf-3e093c40a8db/dqc_reference/reference_markers_gtdb.fasta -out GCA_018653665.1_ASM1865366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:17,340] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:17,343] [INFO] Selected 8 target genomes.
[2023-06-19 00:05:17,344] [INFO] Target genome list was writen to GCA_018653665.1_ASM1865366v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:05:17,376] [INFO] Task started: fastANI
[2023-06-19 00:05:17,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4515d5-807d-4c47-b23d-2e50e26ab3d1/GCA_018653665.1_ASM1865366v1_genomic.fna.gz --refList GCA_018653665.1_ASM1865366v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018653665.1_ASM1865366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:05:20,172] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:20,179] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:05:20,179] [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_018649825.1	s__PSPT01 sp018649825	99.4948	471	615	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__PSPT01	95.0	99.45	99.35	0.83	0.82	4	conclusive
GCA_004195635.1	s__PSPT01 sp004195635	93.4741	443	615	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__PSPT01	95.0	99.90	99.86	0.87	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-19 00:05:20,182] [INFO] GTDB search result was written to GCA_018653665.1_ASM1865366v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:05:20,182] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:05:20,185] [INFO] DFAST_QC result json was written to GCA_018653665.1_ASM1865366v1_genomic.fna/dqc_result.json
[2023-06-19 00:05:20,186] [INFO] DFAST_QC completed!
[2023-06-19 00:05:20,186] [INFO] Total running time: 0h0m36s