[2023-06-13 10:11:16,809] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:11:16,811] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:11:16,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg97537dbf-5fb8-4100-a867-9ec2b21fbe05/dqc_reference
[2023-06-13 10:11:18,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:11:18,064] [INFO] Task started: Prodigal
[2023-06-13 10:11:18,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg108a958a-6cc6-4c8c-bcbd-f28b427142d1/GCA_022705925.1_ASM2270592v1_genomic.fna.gz | prodigal -d GCA_022705925.1_ASM2270592v1_genomic.fna/cds.fna -a GCA_022705925.1_ASM2270592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:11:21,267] [INFO] Task succeeded: Prodigal
[2023-06-13 10:11:21,268] [INFO] Task started: HMMsearch
[2023-06-13 10:11:21,268] [INFO] Running command: hmmsearch --tblout GCA_022705925.1_ASM2270592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97537dbf-5fb8-4100-a867-9ec2b21fbe05/dqc_reference/reference_markers.hmm GCA_022705925.1_ASM2270592v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:11:21,507] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:11:21,509] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg108a958a-6cc6-4c8c-bcbd-f28b427142d1/GCA_022705925.1_ASM2270592v1_genomic.fna.gz]
[2023-06-13 10:11:21,534] [INFO] Query marker FASTA was written to GCA_022705925.1_ASM2270592v1_genomic.fna/markers.fasta
[2023-06-13 10:11:21,535] [INFO] Task started: Blastn
[2023-06-13 10:11:21,535] [INFO] Running command: blastn -query GCA_022705925.1_ASM2270592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97537dbf-5fb8-4100-a867-9ec2b21fbe05/dqc_reference/reference_markers.fasta -out GCA_022705925.1_ASM2270592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:22,018] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:22,023] [INFO] Selected 11 target genomes.
[2023-06-13 10:11:22,023] [INFO] Target genome list was writen to GCA_022705925.1_ASM2270592v1_genomic.fna/target_genomes.txt
[2023-06-13 10:11:22,026] [INFO] Task started: fastANI
[2023-06-13 10:11:22,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg108a958a-6cc6-4c8c-bcbd-f28b427142d1/GCA_022705925.1_ASM2270592v1_genomic.fna.gz --refList GCA_022705925.1_ASM2270592v1_genomic.fna/target_genomes.txt --output GCA_022705925.1_ASM2270592v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:11:27,385] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:27,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97537dbf-5fb8-4100-a867-9ec2b21fbe05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:11:27,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97537dbf-5fb8-4100-a867-9ec2b21fbe05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:11:27,388] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:11:27,388] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:11:27,388] [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
--------------------------------------------------------------------------------
[2023-06-13 10:11:27,390] [INFO] DFAST Taxonomy check result was written to GCA_022705925.1_ASM2270592v1_genomic.fna/tc_result.tsv
[2023-06-13 10:11:27,390] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:11:27,391] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:11:27,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97537dbf-5fb8-4100-a867-9ec2b21fbe05/dqc_reference/checkm_data
[2023-06-13 10:11:27,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:11:27,415] [INFO] Task started: CheckM
[2023-06-13 10:11:27,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022705925.1_ASM2270592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022705925.1_ASM2270592v1_genomic.fna/checkm_input GCA_022705925.1_ASM2270592v1_genomic.fna/checkm_result
[2023-06-13 10:11:45,454] [INFO] Task succeeded: CheckM
[2023-06-13 10:11:45,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:11:45,476] [INFO] ===== Completeness check finished =====
[2023-06-13 10:11:45,477] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:11:45,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022705925.1_ASM2270592v1_genomic.fna/markers.fasta)
[2023-06-13 10:11:45,478] [INFO] Task started: Blastn
[2023-06-13 10:11:45,478] [INFO] Running command: blastn -query GCA_022705925.1_ASM2270592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97537dbf-5fb8-4100-a867-9ec2b21fbe05/dqc_reference/reference_markers_gtdb.fasta -out GCA_022705925.1_ASM2270592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:45,953] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:45,957] [INFO] Selected 17 target genomes.
[2023-06-13 10:11:45,958] [INFO] Target genome list was writen to GCA_022705925.1_ASM2270592v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:11:45,998] [INFO] Task started: fastANI
[2023-06-13 10:11:45,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg108a958a-6cc6-4c8c-bcbd-f28b427142d1/GCA_022705925.1_ASM2270592v1_genomic.fna.gz --refList GCA_022705925.1_ASM2270592v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022705925.1_ASM2270592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:11:54,606] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:54,610] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:11:54,610] [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_002329545.1	s__UBA1443 sp002329545	98.0206	327	394	d__Bacteria;p__Omnitrophota;c__Omnitrophia;o__Omnitrophales;f__UBA2337;g__UBA1443	95.0	98.01	98.01	0.82	0.82	2	conclusive
--------------------------------------------------------------------------------
[2023-06-13 10:11:54,613] [INFO] GTDB search result was written to GCA_022705925.1_ASM2270592v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:11:54,614] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:11:54,617] [INFO] DFAST_QC result json was written to GCA_022705925.1_ASM2270592v1_genomic.fna/dqc_result.json
[2023-06-13 10:11:54,617] [INFO] DFAST_QC completed!
[2023-06-13 10:11:54,617] [INFO] Total running time: 0h0m38s