[2023-06-28 00:49:35,978] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:49:35,982] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:49:35,982] [INFO] DQC Reference Directory: /var/lib/cwl/stged4372cd-2c88-442d-9b39-32a914a04bea/dqc_reference
[2023-06-28 00:49:37,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:49:37,647] [INFO] Task started: Prodigal
[2023-06-28 00:49:37,648] [INFO] Running command: gunzip -c /var/lib/cwl/stge6baee63-5422-4085-88fb-902c8c646eaf/GCA_002708355.1_ASM270835v1_genomic.fna.gz | prodigal -d GCA_002708355.1_ASM270835v1_genomic.fna/cds.fna -a GCA_002708355.1_ASM270835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:49:39,163] [INFO] Task succeeded: Prodigal
[2023-06-28 00:49:39,163] [INFO] Task started: HMMsearch
[2023-06-28 00:49:39,164] [INFO] Running command: hmmsearch --tblout GCA_002708355.1_ASM270835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged4372cd-2c88-442d-9b39-32a914a04bea/dqc_reference/reference_markers.hmm GCA_002708355.1_ASM270835v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:49:39,463] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:49:39,464] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge6baee63-5422-4085-88fb-902c8c646eaf/GCA_002708355.1_ASM270835v1_genomic.fna.gz]
[2023-06-28 00:49:39,485] [INFO] Query marker FASTA was written to GCA_002708355.1_ASM270835v1_genomic.fna/markers.fasta
[2023-06-28 00:49:39,485] [INFO] Task started: Blastn
[2023-06-28 00:49:39,485] [INFO] Running command: blastn -query GCA_002708355.1_ASM270835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged4372cd-2c88-442d-9b39-32a914a04bea/dqc_reference/reference_markers.fasta -out GCA_002708355.1_ASM270835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:49:41,543] [INFO] Task succeeded: Blastn
[2023-06-28 00:49:41,549] [INFO] Selected 17 target genomes.
[2023-06-28 00:49:41,550] [INFO] Target genome list was writen to GCA_002708355.1_ASM270835v1_genomic.fna/target_genomes.txt
[2023-06-28 00:49:41,563] [INFO] Task started: fastANI
[2023-06-28 00:49:41,563] [INFO] Running command: fastANI --query /var/lib/cwl/stge6baee63-5422-4085-88fb-902c8c646eaf/GCA_002708355.1_ASM270835v1_genomic.fna.gz --refList GCA_002708355.1_ASM270835v1_genomic.fna/target_genomes.txt --output GCA_002708355.1_ASM270835v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:49:46,713] [INFO] Task succeeded: fastANI
[2023-06-28 00:49:46,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged4372cd-2c88-442d-9b39-32a914a04bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:49:46,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged4372cd-2c88-442d-9b39-32a914a04bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:49:46,717] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:49:46,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:49:46,717] [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
--------------------------------------------------------------------------------
[2023-06-28 00:49:46,719] [INFO] DFAST Taxonomy check result was written to GCA_002708355.1_ASM270835v1_genomic.fna/tc_result.tsv
[2023-06-28 00:49:46,720] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:49:46,720] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:49:46,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged4372cd-2c88-442d-9b39-32a914a04bea/dqc_reference/checkm_data
[2023-06-28 00:49:46,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:49:46,738] [INFO] Task started: CheckM
[2023-06-28 00:49:46,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708355.1_ASM270835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708355.1_ASM270835v1_genomic.fna/checkm_input GCA_002708355.1_ASM270835v1_genomic.fna/checkm_result
[2023-06-28 00:50:00,385] [INFO] Task succeeded: CheckM
[2023-06-28 00:50:00,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:50:00,407] [INFO] ===== Completeness check finished =====
[2023-06-28 00:50:00,407] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:50:00,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708355.1_ASM270835v1_genomic.fna/markers.fasta)
[2023-06-28 00:50:00,408] [INFO] Task started: Blastn
[2023-06-28 00:50:00,408] [INFO] Running command: blastn -query GCA_002708355.1_ASM270835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged4372cd-2c88-442d-9b39-32a914a04bea/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708355.1_ASM270835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:50:01,147] [INFO] Task succeeded: Blastn
[2023-06-28 00:50:01,151] [INFO] Selected 20 target genomes.
[2023-06-28 00:50:01,151] [INFO] Target genome list was writen to GCA_002708355.1_ASM270835v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:50:01,174] [INFO] Task started: fastANI
[2023-06-28 00:50:01,174] [INFO] Running command: fastANI --query /var/lib/cwl/stge6baee63-5422-4085-88fb-902c8c646eaf/GCA_002708355.1_ASM270835v1_genomic.fna.gz --refList GCA_002708355.1_ASM270835v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708355.1_ASM270835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:50:05,470] [INFO] Task succeeded: fastANI
[2023-06-28 00:50:05,479] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:50:05,479] [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_018674175.1	s__GCA-2705445 sp018674175	88.131	210	313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	99.85	99.83	0.95	0.93	3	-
GCA_018675635.1	s__GCA-2705445 sp018675635	78.3194	136	313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	99.99	99.99	0.98	0.98	2	-
GCA_002705445.1	s__GCA-2705445 sp002705445	78.2188	99	313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	97.03	97.03	0.89	0.89	2	-
GCA_902559815.1	s__GCA-2705445 sp902559815	77.6289	96	313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595225.1	s__GCA-2705445 sp902595225	77.0559	89	313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:50:05,484] [INFO] GTDB search result was written to GCA_002708355.1_ASM270835v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:50:05,485] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:50:05,487] [INFO] DFAST_QC result json was written to GCA_002708355.1_ASM270835v1_genomic.fna/dqc_result.json
[2023-06-28 00:50:05,487] [INFO] DFAST_QC completed!
[2023-06-28 00:50:05,487] [INFO] Total running time: 0h0m30s