[2023-06-27 18:56:20,095] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:56:20,097] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:56:20,098] [INFO] DQC Reference Directory: /var/lib/cwl/stg5da35b16-81ac-49e8-9b4a-3943a8f8b0d9/dqc_reference
[2023-06-27 18:56:21,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:56:21,284] [INFO] Task started: Prodigal
[2023-06-27 18:56:21,284] [INFO] Running command: gunzip -c /var/lib/cwl/stg41c2c7e2-df7f-4543-8045-3813ab03ddf4/GCA_002340895.1_ASM234089v1_genomic.fna.gz | prodigal -d GCA_002340895.1_ASM234089v1_genomic.fna/cds.fna -a GCA_002340895.1_ASM234089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:56:22,937] [INFO] Task succeeded: Prodigal
[2023-06-27 18:56:22,938] [INFO] Task started: HMMsearch
[2023-06-27 18:56:22,938] [INFO] Running command: hmmsearch --tblout GCA_002340895.1_ASM234089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5da35b16-81ac-49e8-9b4a-3943a8f8b0d9/dqc_reference/reference_markers.hmm GCA_002340895.1_ASM234089v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:56:23,138] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:56:23,140] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg41c2c7e2-df7f-4543-8045-3813ab03ddf4/GCA_002340895.1_ASM234089v1_genomic.fna.gz]
[2023-06-27 18:56:23,156] [INFO] Query marker FASTA was written to GCA_002340895.1_ASM234089v1_genomic.fna/markers.fasta
[2023-06-27 18:56:23,156] [INFO] Task started: Blastn
[2023-06-27 18:56:23,157] [INFO] Running command: blastn -query GCA_002340895.1_ASM234089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5da35b16-81ac-49e8-9b4a-3943a8f8b0d9/dqc_reference/reference_markers.fasta -out GCA_002340895.1_ASM234089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:23,706] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:23,711] [INFO] Selected 18 target genomes.
[2023-06-27 18:56:23,711] [INFO] Target genome list was writen to GCA_002340895.1_ASM234089v1_genomic.fna/target_genomes.txt
[2023-06-27 18:56:23,720] [INFO] Task started: fastANI
[2023-06-27 18:56:23,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c2c7e2-df7f-4543-8045-3813ab03ddf4/GCA_002340895.1_ASM234089v1_genomic.fna.gz --refList GCA_002340895.1_ASM234089v1_genomic.fna/target_genomes.txt --output GCA_002340895.1_ASM234089v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:56:31,174] [INFO] Task succeeded: fastANI
[2023-06-27 18:56:31,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5da35b16-81ac-49e8-9b4a-3943a8f8b0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:56:31,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5da35b16-81ac-49e8-9b4a-3943a8f8b0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:56:31,177] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:56:31,177] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 18:56:31,178] [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
--------------------------------------------------------------------------------
[2023-06-27 18:56:31,180] [INFO] DFAST Taxonomy check result was written to GCA_002340895.1_ASM234089v1_genomic.fna/tc_result.tsv
[2023-06-27 18:56:31,181] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:56:31,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:56:31,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5da35b16-81ac-49e8-9b4a-3943a8f8b0d9/dqc_reference/checkm_data
[2023-06-27 18:56:31,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:56:31,201] [INFO] Task started: CheckM
[2023-06-27 18:56:31,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002340895.1_ASM234089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002340895.1_ASM234089v1_genomic.fna/checkm_input GCA_002340895.1_ASM234089v1_genomic.fna/checkm_result
[2023-06-27 18:56:44,406] [INFO] Task succeeded: CheckM
[2023-06-27 18:56:44,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:56:44,426] [INFO] ===== Completeness check finished =====
[2023-06-27 18:56:44,426] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:56:44,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002340895.1_ASM234089v1_genomic.fna/markers.fasta)
[2023-06-27 18:56:44,427] [INFO] Task started: Blastn
[2023-06-27 18:56:44,427] [INFO] Running command: blastn -query GCA_002340895.1_ASM234089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5da35b16-81ac-49e8-9b4a-3943a8f8b0d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_002340895.1_ASM234089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:45,138] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:45,147] [INFO] Selected 16 target genomes.
[2023-06-27 18:56:45,147] [INFO] Target genome list was writen to GCA_002340895.1_ASM234089v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:56:45,150] [INFO] Task started: fastANI
[2023-06-27 18:56:45,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c2c7e2-df7f-4543-8045-3813ab03ddf4/GCA_002340895.1_ASM234089v1_genomic.fna.gz --refList GCA_002340895.1_ASM234089v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002340895.1_ASM234089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:56:50,095] [INFO] Task succeeded: fastANI
[2023-06-27 18:56:50,102] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 18:56:50,103] [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_002384685.1	s__BACL14 sp002384685	99.3264	237	268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.54	99.37	0.90	0.88	8	conclusive
GCA_000168995.1	s__BACL14 sp000168995	81.7121	215	268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	98.71	98.43	0.97	0.92	10	-
--------------------------------------------------------------------------------
[2023-06-27 18:56:50,105] [INFO] GTDB search result was written to GCA_002340895.1_ASM234089v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:56:50,106] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:56:50,109] [INFO] DFAST_QC result json was written to GCA_002340895.1_ASM234089v1_genomic.fna/dqc_result.json
[2023-06-27 18:56:50,110] [INFO] DFAST_QC completed!
[2023-06-27 18:56:50,110] [INFO] Total running time: 0h0m30s