[2023-06-05 00:30:10,869] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:30:10,871] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:30:10,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf708f4a-2b8c-422d-9004-8b7a6c19df15/dqc_reference
[2023-06-05 00:30:13,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:30:13,813] [INFO] Task started: Prodigal
[2023-06-05 00:30:13,814] [INFO] Running command: gunzip -c /var/lib/cwl/stgc539a3f8-5818-419b-adb2-bdd5ef55b239/GCA_001875375.1_ASM187537v1_genomic.fna.gz | prodigal -d GCA_001875375.1_ASM187537v1_genomic.fna/cds.fna -a GCA_001875375.1_ASM187537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:30:14,788] [INFO] Task succeeded: Prodigal
[2023-06-05 00:30:14,789] [INFO] Task started: HMMsearch
[2023-06-05 00:30:14,789] [INFO] Running command: hmmsearch --tblout GCA_001875375.1_ASM187537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf708f4a-2b8c-422d-9004-8b7a6c19df15/dqc_reference/reference_markers.hmm GCA_001875375.1_ASM187537v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:30:14,961] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:30:14,963] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgc539a3f8-5818-419b-adb2-bdd5ef55b239/GCA_001875375.1_ASM187537v1_genomic.fna.gz]
[2023-06-05 00:30:14,974] [INFO] Query marker FASTA was written to GCA_001875375.1_ASM187537v1_genomic.fna/markers.fasta
[2023-06-05 00:30:14,975] [INFO] Task started: Blastn
[2023-06-05 00:30:14,975] [INFO] Running command: blastn -query GCA_001875375.1_ASM187537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf708f4a-2b8c-422d-9004-8b7a6c19df15/dqc_reference/reference_markers.fasta -out GCA_001875375.1_ASM187537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:16,769] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:16,774] [INFO] Selected 5 target genomes.
[2023-06-05 00:30:16,774] [INFO] Target genome list was writen to GCA_001875375.1_ASM187537v1_genomic.fna/target_genomes.txt
[2023-06-05 00:30:16,795] [INFO] Task started: fastANI
[2023-06-05 00:30:16,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgc539a3f8-5818-419b-adb2-bdd5ef55b239/GCA_001875375.1_ASM187537v1_genomic.fna.gz --refList GCA_001875375.1_ASM187537v1_genomic.fna/target_genomes.txt --output GCA_001875375.1_ASM187537v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:30:18,852] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:18,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf708f4a-2b8c-422d-9004-8b7a6c19df15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:30:18,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf708f4a-2b8c-422d-9004-8b7a6c19df15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:30:18,855] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:30:18,855] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:30:18,855] [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
--------------------------------------------------------------------------------
[2023-06-05 00:30:18,857] [INFO] DFAST Taxonomy check result was written to GCA_001875375.1_ASM187537v1_genomic.fna/tc_result.tsv
[2023-06-05 00:30:18,857] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:30:18,857] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:30:18,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf708f4a-2b8c-422d-9004-8b7a6c19df15/dqc_reference/checkm_data
[2023-06-05 00:30:18,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:30:18,872] [INFO] Task started: CheckM
[2023-06-05 00:30:18,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001875375.1_ASM187537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001875375.1_ASM187537v1_genomic.fna/checkm_input GCA_001875375.1_ASM187537v1_genomic.fna/checkm_result
[2023-06-05 00:30:30,044] [INFO] Task succeeded: CheckM
[2023-06-05 00:30:30,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.26%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 00:30:30,065] [INFO] ===== Completeness check finished =====
[2023-06-05 00:30:30,065] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:30:30,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001875375.1_ASM187537v1_genomic.fna/markers.fasta)
[2023-06-05 00:30:30,066] [INFO] Task started: Blastn
[2023-06-05 00:30:30,066] [INFO] Running command: blastn -query GCA_001875375.1_ASM187537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf708f4a-2b8c-422d-9004-8b7a6c19df15/dqc_reference/reference_markers_gtdb.fasta -out GCA_001875375.1_ASM187537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:30,559] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:30,563] [INFO] Selected 5 target genomes.
[2023-06-05 00:30:30,564] [INFO] Target genome list was writen to GCA_001875375.1_ASM187537v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:30:30,629] [INFO] Task started: fastANI
[2023-06-05 00:30:30,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgc539a3f8-5818-419b-adb2-bdd5ef55b239/GCA_001875375.1_ASM187537v1_genomic.fna.gz --refList GCA_001875375.1_ASM187537v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001875375.1_ASM187537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:30:32,107] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:32,125] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:30:32,125] [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_001875345.1	s__CG-Epi1 sp001875345	83.4765	114	164	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845825.1	s__CG-Epi1 sp016845825	83.2926	94	164	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875365.1	s__CG-Epi1 sp001875365	82.4125	82	164	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531985.1	s__CG-Epi1 sp902531985	78.7594	53	164	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:30:32,127] [INFO] GTDB search result was written to GCA_001875375.1_ASM187537v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:30:32,128] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:30:32,131] [INFO] DFAST_QC result json was written to GCA_001875375.1_ASM187537v1_genomic.fna/dqc_result.json
[2023-06-05 00:30:32,131] [INFO] DFAST_QC completed!
[2023-06-05 00:30:32,131] [INFO] Total running time: 0h0m21s