[2023-06-28 13:31:23,592] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:23,598] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:23,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c25a8f2-b160-40ca-88e5-c9176426dd82/dqc_reference
[2023-06-28 13:31:24,807] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:24,808] [INFO] Task started: Prodigal
[2023-06-28 13:31:24,808] [INFO] Running command: gunzip -c /var/lib/cwl/stg7594a976-4c72-4c8b-9864-12b484dfd4d0/GCA_012963065.1_ASM1296306v1_genomic.fna.gz | prodigal -d GCA_012963065.1_ASM1296306v1_genomic.fna/cds.fna -a GCA_012963065.1_ASM1296306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:31:27,469] [INFO] Task succeeded: Prodigal
[2023-06-28 13:31:27,469] [INFO] Task started: HMMsearch
[2023-06-28 13:31:27,469] [INFO] Running command: hmmsearch --tblout GCA_012963065.1_ASM1296306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c25a8f2-b160-40ca-88e5-c9176426dd82/dqc_reference/reference_markers.hmm GCA_012963065.1_ASM1296306v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:31:27,622] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:31:27,623] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7594a976-4c72-4c8b-9864-12b484dfd4d0/GCA_012963065.1_ASM1296306v1_genomic.fna.gz]
[2023-06-28 13:31:27,640] [INFO] Query marker FASTA was written to GCA_012963065.1_ASM1296306v1_genomic.fna/markers.fasta
[2023-06-28 13:31:27,640] [INFO] Task started: Blastn
[2023-06-28 13:31:27,640] [INFO] Running command: blastn -query GCA_012963065.1_ASM1296306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c25a8f2-b160-40ca-88e5-c9176426dd82/dqc_reference/reference_markers.fasta -out GCA_012963065.1_ASM1296306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:28,173] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:28,176] [INFO] Selected 2 target genomes.
[2023-06-28 13:31:28,176] [INFO] Target genome list was writen to GCA_012963065.1_ASM1296306v1_genomic.fna/target_genomes.txt
[2023-06-28 13:31:28,177] [INFO] Task started: fastANI
[2023-06-28 13:31:28,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg7594a976-4c72-4c8b-9864-12b484dfd4d0/GCA_012963065.1_ASM1296306v1_genomic.fna.gz --refList GCA_012963065.1_ASM1296306v1_genomic.fna/target_genomes.txt --output GCA_012963065.1_ASM1296306v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:31:29,118] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:29,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c25a8f2-b160-40ca-88e5-c9176426dd82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:31:29,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c25a8f2-b160-40ca-88e5-c9176426dd82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:31:29,120] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:31:29,121] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:31:29,121] [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 13:31:29,122] [INFO] DFAST Taxonomy check result was written to GCA_012963065.1_ASM1296306v1_genomic.fna/tc_result.tsv
[2023-06-28 13:31:29,123] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:31:29,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:31:29,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c25a8f2-b160-40ca-88e5-c9176426dd82/dqc_reference/checkm_data
[2023-06-28 13:31:29,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:31:29,144] [INFO] Task started: CheckM
[2023-06-28 13:31:29,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012963065.1_ASM1296306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012963065.1_ASM1296306v1_genomic.fna/checkm_input GCA_012963065.1_ASM1296306v1_genomic.fna/checkm_result
[2023-06-28 13:31:44,018] [INFO] Task succeeded: CheckM
[2023-06-28 13:31:44,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 28.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:31:44,036] [INFO] ===== Completeness check finished =====
[2023-06-28 13:31:44,037] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:31:44,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012963065.1_ASM1296306v1_genomic.fna/markers.fasta)
[2023-06-28 13:31:44,037] [INFO] Task started: Blastn
[2023-06-28 13:31:44,038] [INFO] Running command: blastn -query GCA_012963065.1_ASM1296306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c25a8f2-b160-40ca-88e5-c9176426dd82/dqc_reference/reference_markers_gtdb.fasta -out GCA_012963065.1_ASM1296306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:44,762] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:44,765] [INFO] Selected 12 target genomes.
[2023-06-28 13:31:44,765] [INFO] Target genome list was writen to GCA_012963065.1_ASM1296306v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:31:44,768] [INFO] Task started: fastANI
[2023-06-28 13:31:44,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg7594a976-4c72-4c8b-9864-12b484dfd4d0/GCA_012963065.1_ASM1296306v1_genomic.fna.gz --refList GCA_012963065.1_ASM1296306v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012963065.1_ASM1296306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:31:48,752] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:48,757] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:31:48,757] [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_002696685.1	s__GCA-002712965 sp002696685	94.2178	120	158	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	98.93	98.49	0.85	0.81	3	-
GCA_009391195.1	s__GCA-002712965 sp009391195	84.7911	88	158	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392815.1	s__GCA-002712965 sp009392815	79.2451	82	158	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__GCA-002712965	95.0	99.65	99.65	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-28 13:31:48,759] [INFO] GTDB search result was written to GCA_012963065.1_ASM1296306v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:31:48,759] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:31:48,762] [INFO] DFAST_QC result json was written to GCA_012963065.1_ASM1296306v1_genomic.fna/dqc_result.json
[2023-06-28 13:31:48,762] [INFO] DFAST_QC completed!
[2023-06-28 13:31:48,762] [INFO] Total running time: 0h0m25s