[2023-06-27 19:44:36,739] [INFO] DFAST_QC pipeline started.
[2023-06-27 19:44:36,751] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 19:44:36,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgc73bee40-11a1-4a17-8127-10d28fff4ec5/dqc_reference
[2023-06-27 19:44:39,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 19:44:39,852] [INFO] Task started: Prodigal
[2023-06-27 19:44:39,852] [INFO] Running command: gunzip -c /var/lib/cwl/stg38c1437d-1cf4-49ae-995b-2e623a4f5e3f/GCA_002724995.1_ASM272499v1_genomic.fna.gz | prodigal -d GCA_002724995.1_ASM272499v1_genomic.fna/cds.fna -a GCA_002724995.1_ASM272499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 19:44:43,115] [INFO] Task succeeded: Prodigal
[2023-06-27 19:44:43,116] [INFO] Task started: HMMsearch
[2023-06-27 19:44:43,116] [INFO] Running command: hmmsearch --tblout GCA_002724995.1_ASM272499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc73bee40-11a1-4a17-8127-10d28fff4ec5/dqc_reference/reference_markers.hmm GCA_002724995.1_ASM272499v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 19:44:43,407] [INFO] Task succeeded: HMMsearch
[2023-06-27 19:44:43,409] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg38c1437d-1cf4-49ae-995b-2e623a4f5e3f/GCA_002724995.1_ASM272499v1_genomic.fna.gz]
[2023-06-27 19:44:43,430] [INFO] Query marker FASTA was written to GCA_002724995.1_ASM272499v1_genomic.fna/markers.fasta
[2023-06-27 19:44:43,430] [INFO] Task started: Blastn
[2023-06-27 19:44:43,430] [INFO] Running command: blastn -query GCA_002724995.1_ASM272499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc73bee40-11a1-4a17-8127-10d28fff4ec5/dqc_reference/reference_markers.fasta -out GCA_002724995.1_ASM272499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:44:44,113] [INFO] Task succeeded: Blastn
[2023-06-27 19:44:44,120] [INFO] Selected 7 target genomes.
[2023-06-27 19:44:44,121] [INFO] Target genome list was writen to GCA_002724995.1_ASM272499v1_genomic.fna/target_genomes.txt
[2023-06-27 19:44:44,126] [INFO] Task started: fastANI
[2023-06-27 19:44:44,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c1437d-1cf4-49ae-995b-2e623a4f5e3f/GCA_002724995.1_ASM272499v1_genomic.fna.gz --refList GCA_002724995.1_ASM272499v1_genomic.fna/target_genomes.txt --output GCA_002724995.1_ASM272499v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 19:44:47,039] [INFO] Task succeeded: fastANI
[2023-06-27 19:44:47,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc73bee40-11a1-4a17-8127-10d28fff4ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 19:44:47,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc73bee40-11a1-4a17-8127-10d28fff4ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 19:44:47,045] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 19:44:47,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 19:44:47,046] [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 19:44:47,048] [INFO] DFAST Taxonomy check result was written to GCA_002724995.1_ASM272499v1_genomic.fna/tc_result.tsv
[2023-06-27 19:44:47,049] [INFO] ===== Taxonomy check completed =====
[2023-06-27 19:44:47,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 19:44:47,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc73bee40-11a1-4a17-8127-10d28fff4ec5/dqc_reference/checkm_data
[2023-06-27 19:44:47,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 19:44:47,071] [INFO] Task started: CheckM
[2023-06-27 19:44:47,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002724995.1_ASM272499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002724995.1_ASM272499v1_genomic.fna/checkm_input GCA_002724995.1_ASM272499v1_genomic.fna/checkm_result
[2023-06-27 19:45:04,414] [INFO] Task succeeded: CheckM
[2023-06-27 19:45:04,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 19:45:04,440] [INFO] ===== Completeness check finished =====
[2023-06-27 19:45:04,441] [INFO] ===== Start GTDB Search =====
[2023-06-27 19:45:04,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002724995.1_ASM272499v1_genomic.fna/markers.fasta)
[2023-06-27 19:45:04,441] [INFO] Task started: Blastn
[2023-06-27 19:45:04,441] [INFO] Running command: blastn -query GCA_002724995.1_ASM272499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc73bee40-11a1-4a17-8127-10d28fff4ec5/dqc_reference/reference_markers_gtdb.fasta -out GCA_002724995.1_ASM272499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:45:05,141] [INFO] Task succeeded: Blastn
[2023-06-27 19:45:05,147] [INFO] Selected 7 target genomes.
[2023-06-27 19:45:05,147] [INFO] Target genome list was writen to GCA_002724995.1_ASM272499v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 19:45:05,157] [INFO] Task started: fastANI
[2023-06-27 19:45:05,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c1437d-1cf4-49ae-995b-2e623a4f5e3f/GCA_002724995.1_ASM272499v1_genomic.fna.gz --refList GCA_002724995.1_ASM272499v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002724995.1_ASM272499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 19:45:07,202] [INFO] Task succeeded: fastANI
[2023-06-27 19:45:07,210] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 19:45:07,210] [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_002346435.1	s__UBA11657 sp002346435	88.0572	308	456	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377585.1	s__UBA11657 sp002377585	87.5098	341	456	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	99.07	98.64	0.89	0.85	4	-
GCA_002311455.1	s__UBA11657 sp002311455	81.7913	292	456	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11657;g__UBA11657	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 19:45:07,213] [INFO] GTDB search result was written to GCA_002724995.1_ASM272499v1_genomic.fna/result_gtdb.tsv
[2023-06-27 19:45:07,214] [INFO] ===== GTDB Search completed =====
[2023-06-27 19:45:07,217] [INFO] DFAST_QC result json was written to GCA_002724995.1_ASM272499v1_genomic.fna/dqc_result.json
[2023-06-27 19:45:07,217] [INFO] DFAST_QC completed!
[2023-06-27 19:45:07,217] [INFO] Total running time: 0h0m30s