[2023-06-08 09:54:07,749] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:54:07,802] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:54:07,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg71956b0f-a397-49e7-bee0-080d319dbb5e/dqc_reference
[2023-06-08 09:54:10,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:54:10,084] [INFO] Task started: Prodigal
[2023-06-08 09:54:10,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg20efab45-1bd3-4f88-bcd6-1fce5b4f8229/GCA_945876115.1_TE-08apr19-104_genomic.fna.gz | prodigal -d GCA_945876115.1_TE-08apr19-104_genomic.fna/cds.fna -a GCA_945876115.1_TE-08apr19-104_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:54:14,091] [INFO] Task succeeded: Prodigal
[2023-06-08 09:54:14,091] [INFO] Task started: HMMsearch
[2023-06-08 09:54:14,091] [INFO] Running command: hmmsearch --tblout GCA_945876115.1_TE-08apr19-104_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71956b0f-a397-49e7-bee0-080d319dbb5e/dqc_reference/reference_markers.hmm GCA_945876115.1_TE-08apr19-104_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:54:14,291] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:54:14,292] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg20efab45-1bd3-4f88-bcd6-1fce5b4f8229/GCA_945876115.1_TE-08apr19-104_genomic.fna.gz]
[2023-06-08 09:54:14,319] [INFO] Query marker FASTA was written to GCA_945876115.1_TE-08apr19-104_genomic.fna/markers.fasta
[2023-06-08 09:54:14,320] [INFO] Task started: Blastn
[2023-06-08 09:54:14,320] [INFO] Running command: blastn -query GCA_945876115.1_TE-08apr19-104_genomic.fna/markers.fasta -db /var/lib/cwl/stg71956b0f-a397-49e7-bee0-080d319dbb5e/dqc_reference/reference_markers.fasta -out GCA_945876115.1_TE-08apr19-104_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:14,948] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:14,952] [INFO] Selected 4 target genomes.
[2023-06-08 09:54:14,953] [INFO] Target genome list was writen to GCA_945876115.1_TE-08apr19-104_genomic.fna/target_genomes.txt
[2023-06-08 09:54:14,954] [INFO] Task started: fastANI
[2023-06-08 09:54:14,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg20efab45-1bd3-4f88-bcd6-1fce5b4f8229/GCA_945876115.1_TE-08apr19-104_genomic.fna.gz --refList GCA_945876115.1_TE-08apr19-104_genomic.fna/target_genomes.txt --output GCA_945876115.1_TE-08apr19-104_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:54:17,296] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:17,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71956b0f-a397-49e7-bee0-080d319dbb5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:54:17,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71956b0f-a397-49e7-bee0-080d319dbb5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:54:17,299] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:54:17,299] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:54:17,299] [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
--------------------------------------------------------------------------------
[2023-06-08 09:54:17,302] [INFO] DFAST Taxonomy check result was written to GCA_945876115.1_TE-08apr19-104_genomic.fna/tc_result.tsv
[2023-06-08 09:54:17,302] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:54:17,303] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:54:17,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71956b0f-a397-49e7-bee0-080d319dbb5e/dqc_reference/checkm_data
[2023-06-08 09:54:17,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:54:17,342] [INFO] Task started: CheckM
[2023-06-08 09:54:17,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945876115.1_TE-08apr19-104_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945876115.1_TE-08apr19-104_genomic.fna/checkm_input GCA_945876115.1_TE-08apr19-104_genomic.fna/checkm_result
[2023-06-08 09:54:38,082] [INFO] Task succeeded: CheckM
[2023-06-08 09:54:38,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:54:38,104] [INFO] ===== Completeness check finished =====
[2023-06-08 09:54:38,104] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:54:38,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945876115.1_TE-08apr19-104_genomic.fna/markers.fasta)
[2023-06-08 09:54:38,106] [INFO] Task started: Blastn
[2023-06-08 09:54:38,106] [INFO] Running command: blastn -query GCA_945876115.1_TE-08apr19-104_genomic.fna/markers.fasta -db /var/lib/cwl/stg71956b0f-a397-49e7-bee0-080d319dbb5e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945876115.1_TE-08apr19-104_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:38,578] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:38,583] [INFO] Selected 16 target genomes.
[2023-06-08 09:54:38,583] [INFO] Target genome list was writen to GCA_945876115.1_TE-08apr19-104_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:54:38,588] [INFO] Task started: fastANI
[2023-06-08 09:54:38,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg20efab45-1bd3-4f88-bcd6-1fce5b4f8229/GCA_945876115.1_TE-08apr19-104_genomic.fna.gz --refList GCA_945876115.1_TE-08apr19-104_genomic.fna/target_genomes_gtdb.txt --output GCA_945876115.1_TE-08apr19-104_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:54:44,475] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:44,485] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:54:44,486] [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_903956835.1	s__UBA3015 sp903956835	91.6167	354	488	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__UBA3015;g__UBA3015	95.0	98.86	98.22	0.87	0.84	5	-
GCA_009927835.1	s__UBA3015 sp002367435	77.4703	101	488	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__UBA3015;g__UBA3015	95.0	99.27	99.08	0.77	0.68	8	-
GCA_010024525.1	s__UBA3015 sp010024525	76.9856	52	488	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__UBA3015;g__UBA3015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366885.1	s__UBA3015 sp002366885	76.1372	53	488	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__UBA3015;g__UBA3015	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:54:44,488] [INFO] GTDB search result was written to GCA_945876115.1_TE-08apr19-104_genomic.fna/result_gtdb.tsv
[2023-06-08 09:54:44,489] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:54:44,491] [INFO] DFAST_QC result json was written to GCA_945876115.1_TE-08apr19-104_genomic.fna/dqc_result.json
[2023-06-08 09:54:44,492] [INFO] DFAST_QC completed!
[2023-06-08 09:54:44,492] [INFO] Total running time: 0h0m37s