[2023-06-07 21:33:18,534] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:33:18,555] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:33:18,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e3a83ef-a294-4d5c-ad0e-72ae5ff6ef35/dqc_reference
[2023-06-07 21:33:20,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:33:20,292] [INFO] Task started: Prodigal
[2023-06-07 21:33:20,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg158a2c4f-fb00-4f05-abe9-a6790bff11c0/GCA_945861815.1_MaH-09apr19-93_genomic.fna.gz | prodigal -d GCA_945861815.1_MaH-09apr19-93_genomic.fna/cds.fna -a GCA_945861815.1_MaH-09apr19-93_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:33:24,394] [INFO] Task succeeded: Prodigal
[2023-06-07 21:33:24,395] [INFO] Task started: HMMsearch
[2023-06-07 21:33:24,395] [INFO] Running command: hmmsearch --tblout GCA_945861815.1_MaH-09apr19-93_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e3a83ef-a294-4d5c-ad0e-72ae5ff6ef35/dqc_reference/reference_markers.hmm GCA_945861815.1_MaH-09apr19-93_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:33:24,588] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:33:24,590] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg158a2c4f-fb00-4f05-abe9-a6790bff11c0/GCA_945861815.1_MaH-09apr19-93_genomic.fna.gz]
[2023-06-07 21:33:24,609] [INFO] Query marker FASTA was written to GCA_945861815.1_MaH-09apr19-93_genomic.fna/markers.fasta
[2023-06-07 21:33:24,610] [INFO] Task started: Blastn
[2023-06-07 21:33:24,610] [INFO] Running command: blastn -query GCA_945861815.1_MaH-09apr19-93_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e3a83ef-a294-4d5c-ad0e-72ae5ff6ef35/dqc_reference/reference_markers.fasta -out GCA_945861815.1_MaH-09apr19-93_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:33:25,172] [INFO] Task succeeded: Blastn
[2023-06-07 21:33:25,176] [INFO] Selected 13 target genomes.
[2023-06-07 21:33:25,176] [INFO] Target genome list was writen to GCA_945861815.1_MaH-09apr19-93_genomic.fna/target_genomes.txt
[2023-06-07 21:33:25,180] [INFO] Task started: fastANI
[2023-06-07 21:33:25,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg158a2c4f-fb00-4f05-abe9-a6790bff11c0/GCA_945861815.1_MaH-09apr19-93_genomic.fna.gz --refList GCA_945861815.1_MaH-09apr19-93_genomic.fna/target_genomes.txt --output GCA_945861815.1_MaH-09apr19-93_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:33:34,394] [INFO] Task succeeded: fastANI
[2023-06-07 21:33:34,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e3a83ef-a294-4d5c-ad0e-72ae5ff6ef35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:33:34,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e3a83ef-a294-4d5c-ad0e-72ae5ff6ef35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:33:34,397] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:33:34,397] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 21:33:34,398] [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
--------------------------------------------------------------------------------
[2023-06-07 21:33:34,400] [INFO] DFAST Taxonomy check result was written to GCA_945861815.1_MaH-09apr19-93_genomic.fna/tc_result.tsv
[2023-06-07 21:33:34,400] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:33:34,401] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:33:34,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e3a83ef-a294-4d5c-ad0e-72ae5ff6ef35/dqc_reference/checkm_data
[2023-06-07 21:33:34,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:33:34,429] [INFO] Task started: CheckM
[2023-06-07 21:33:34,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945861815.1_MaH-09apr19-93_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945861815.1_MaH-09apr19-93_genomic.fna/checkm_input GCA_945861815.1_MaH-09apr19-93_genomic.fna/checkm_result
[2023-06-07 21:33:53,973] [INFO] Task succeeded: CheckM
[2023-06-07 21:33:53,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:33:53,997] [INFO] ===== Completeness check finished =====
[2023-06-07 21:33:53,998] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:33:53,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945861815.1_MaH-09apr19-93_genomic.fna/markers.fasta)
[2023-06-07 21:33:53,999] [INFO] Task started: Blastn
[2023-06-07 21:33:53,999] [INFO] Running command: blastn -query GCA_945861815.1_MaH-09apr19-93_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e3a83ef-a294-4d5c-ad0e-72ae5ff6ef35/dqc_reference/reference_markers_gtdb.fasta -out GCA_945861815.1_MaH-09apr19-93_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:33:54,606] [INFO] Task succeeded: Blastn
[2023-06-07 21:33:54,610] [INFO] Selected 18 target genomes.
[2023-06-07 21:33:54,610] [INFO] Target genome list was writen to GCA_945861815.1_MaH-09apr19-93_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:33:54,837] [INFO] Task started: fastANI
[2023-06-07 21:33:54,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg158a2c4f-fb00-4f05-abe9-a6790bff11c0/GCA_945861815.1_MaH-09apr19-93_genomic.fna.gz --refList GCA_945861815.1_MaH-09apr19-93_genomic.fna/target_genomes_gtdb.txt --output GCA_945861815.1_MaH-09apr19-93_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:34:04,360] [INFO] Task succeeded: fastANI
[2023-06-07 21:34:04,365] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 21:34:04,365] [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_016875535.1	s__VGPF01 sp016875535	80.6242	305	439	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SHYB01;f__SHYB01;g__VGPF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:34:04,367] [INFO] GTDB search result was written to GCA_945861815.1_MaH-09apr19-93_genomic.fna/result_gtdb.tsv
[2023-06-07 21:34:04,368] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:34:04,371] [INFO] DFAST_QC result json was written to GCA_945861815.1_MaH-09apr19-93_genomic.fna/dqc_result.json
[2023-06-07 21:34:04,371] [INFO] DFAST_QC completed!
[2023-06-07 21:34:04,371] [INFO] Total running time: 0h0m46s