[2023-06-19 09:28:44,692] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:28:44,696] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:28:44,696] [INFO] DQC Reference Directory: /var/lib/cwl/stga659fc67-92fd-4076-9abd-e059ff46f8be/dqc_reference
[2023-06-19 09:28:46,241] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:28:46,242] [INFO] Task started: Prodigal
[2023-06-19 09:28:46,243] [INFO] Running command: gunzip -c /var/lib/cwl/stgc81040d1-6edf-453b-b0f7-331dd5321191/GCA_018435285.1_SL1_genomic.fna.gz | prodigal -d GCA_018435285.1_SL1_genomic.fna/cds.fna -a GCA_018435285.1_SL1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:28:49,039] [INFO] Task succeeded: Prodigal
[2023-06-19 09:28:49,040] [INFO] Task started: HMMsearch
[2023-06-19 09:28:49,040] [INFO] Running command: hmmsearch --tblout GCA_018435285.1_SL1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga659fc67-92fd-4076-9abd-e059ff46f8be/dqc_reference/reference_markers.hmm GCA_018435285.1_SL1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:28:49,260] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:28:49,264] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc81040d1-6edf-453b-b0f7-331dd5321191/GCA_018435285.1_SL1_genomic.fna.gz]
[2023-06-19 09:28:49,289] [INFO] Query marker FASTA was written to GCA_018435285.1_SL1_genomic.fna/markers.fasta
[2023-06-19 09:28:49,289] [INFO] Task started: Blastn
[2023-06-19 09:28:49,289] [INFO] Running command: blastn -query GCA_018435285.1_SL1_genomic.fna/markers.fasta -db /var/lib/cwl/stga659fc67-92fd-4076-9abd-e059ff46f8be/dqc_reference/reference_markers.fasta -out GCA_018435285.1_SL1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:28:49,956] [INFO] Task succeeded: Blastn
[2023-06-19 09:28:49,961] [INFO] Selected 16 target genomes.
[2023-06-19 09:28:49,961] [INFO] Target genome list was writen to GCA_018435285.1_SL1_genomic.fna/target_genomes.txt
[2023-06-19 09:28:49,967] [INFO] Task started: fastANI
[2023-06-19 09:28:49,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgc81040d1-6edf-453b-b0f7-331dd5321191/GCA_018435285.1_SL1_genomic.fna.gz --refList GCA_018435285.1_SL1_genomic.fna/target_genomes.txt --output GCA_018435285.1_SL1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:28:58,902] [INFO] Task succeeded: fastANI
[2023-06-19 09:28:58,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga659fc67-92fd-4076-9abd-e059ff46f8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:28:58,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga659fc67-92fd-4076-9abd-e059ff46f8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:28:58,906] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:28:58,906] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 09:28:58,906] [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
--------------------------------------------------------------------------------
[2023-06-19 09:28:58,908] [INFO] DFAST Taxonomy check result was written to GCA_018435285.1_SL1_genomic.fna/tc_result.tsv
[2023-06-19 09:28:58,909] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:28:58,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:28:58,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga659fc67-92fd-4076-9abd-e059ff46f8be/dqc_reference/checkm_data
[2023-06-19 09:28:58,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:28:58,939] [INFO] Task started: CheckM
[2023-06-19 09:28:58,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018435285.1_SL1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018435285.1_SL1_genomic.fna/checkm_input GCA_018435285.1_SL1_genomic.fna/checkm_result
[2023-06-19 09:29:16,591] [INFO] Task succeeded: CheckM
[2023-06-19 09:29:16,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.07%
Contamintation: 15.34%
Strain heterogeneity: 22.22%
--------------------------------------------------------------------------------
[2023-06-19 09:29:16,630] [INFO] ===== Completeness check finished =====
[2023-06-19 09:29:16,631] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:29:16,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018435285.1_SL1_genomic.fna/markers.fasta)
[2023-06-19 09:29:16,631] [INFO] Task started: Blastn
[2023-06-19 09:29:16,631] [INFO] Running command: blastn -query GCA_018435285.1_SL1_genomic.fna/markers.fasta -db /var/lib/cwl/stga659fc67-92fd-4076-9abd-e059ff46f8be/dqc_reference/reference_markers_gtdb.fasta -out GCA_018435285.1_SL1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:29:17,510] [INFO] Task succeeded: Blastn
[2023-06-19 09:29:17,515] [INFO] Selected 18 target genomes.
[2023-06-19 09:29:17,515] [INFO] Target genome list was writen to GCA_018435285.1_SL1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:29:17,524] [INFO] Task started: fastANI
[2023-06-19 09:29:17,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgc81040d1-6edf-453b-b0f7-331dd5321191/GCA_018435285.1_SL1_genomic.fna.gz --refList GCA_018435285.1_SL1_genomic.fna/target_genomes_gtdb.txt --output GCA_018435285.1_SL1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:29:24,901] [INFO] Task succeeded: fastANI
[2023-06-19 09:29:24,905] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:29:24,906] [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_012839565.1	s__T78 sp012839565	96.3102	66	71	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__T78	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-19 09:29:24,908] [INFO] GTDB search result was written to GCA_018435285.1_SL1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:29:24,912] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:29:24,919] [INFO] DFAST_QC result json was written to GCA_018435285.1_SL1_genomic.fna/dqc_result.json
[2023-06-19 09:29:24,919] [INFO] DFAST_QC completed!
[2023-06-19 09:29:24,920] [INFO] Total running time: 0h0m40s