[2023-06-16 19:11:13,938] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:11:13,940] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:11:13,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a3519f-2f3a-4e53-9942-dad5478c941f/dqc_reference
[2023-06-16 19:11:15,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:11:15,114] [INFO] Task started: Prodigal
[2023-06-16 19:11:15,114] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cf26a65-0fa9-43c6-a32a-dca90f875aeb/GCA_028697315.1_ASM2869731v1_genomic.fna.gz | prodigal -d GCA_028697315.1_ASM2869731v1_genomic.fna/cds.fna -a GCA_028697315.1_ASM2869731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:11:16,686] [INFO] Task succeeded: Prodigal
[2023-06-16 19:11:16,687] [INFO] Task started: HMMsearch
[2023-06-16 19:11:16,687] [INFO] Running command: hmmsearch --tblout GCA_028697315.1_ASM2869731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a3519f-2f3a-4e53-9942-dad5478c941f/dqc_reference/reference_markers.hmm GCA_028697315.1_ASM2869731v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:11:16,841] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:11:16,842] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4cf26a65-0fa9-43c6-a32a-dca90f875aeb/GCA_028697315.1_ASM2869731v1_genomic.fna.gz]
[2023-06-16 19:11:16,855] [INFO] Query marker FASTA was written to GCA_028697315.1_ASM2869731v1_genomic.fna/markers.fasta
[2023-06-16 19:11:16,855] [INFO] Task started: Blastn
[2023-06-16 19:11:16,855] [INFO] Running command: blastn -query GCA_028697315.1_ASM2869731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a3519f-2f3a-4e53-9942-dad5478c941f/dqc_reference/reference_markers.fasta -out GCA_028697315.1_ASM2869731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:17,317] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:17,320] [INFO] Selected 9 target genomes.
[2023-06-16 19:11:17,320] [INFO] Target genome list was writen to GCA_028697315.1_ASM2869731v1_genomic.fna/target_genomes.txt
[2023-06-16 19:11:17,324] [INFO] Task started: fastANI
[2023-06-16 19:11:17,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cf26a65-0fa9-43c6-a32a-dca90f875aeb/GCA_028697315.1_ASM2869731v1_genomic.fna.gz --refList GCA_028697315.1_ASM2869731v1_genomic.fna/target_genomes.txt --output GCA_028697315.1_ASM2869731v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:11:22,536] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:22,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59a3519f-2f3a-4e53-9942-dad5478c941f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:11:22,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59a3519f-2f3a-4e53-9942-dad5478c941f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:11:22,538] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:11:22,539] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:11:22,539] [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
--------------------------------------------------------------------------------
[2023-06-16 19:11:22,540] [INFO] DFAST Taxonomy check result was written to GCA_028697315.1_ASM2869731v1_genomic.fna/tc_result.tsv
[2023-06-16 19:11:22,541] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:11:22,541] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:11:22,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a3519f-2f3a-4e53-9942-dad5478c941f/dqc_reference/checkm_data
[2023-06-16 19:11:22,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:11:22,557] [INFO] Task started: CheckM
[2023-06-16 19:11:22,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028697315.1_ASM2869731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028697315.1_ASM2869731v1_genomic.fna/checkm_input GCA_028697315.1_ASM2869731v1_genomic.fna/checkm_result
[2023-06-16 19:11:34,258] [INFO] Task succeeded: CheckM
[2023-06-16 19:11:34,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.14%
Contamintation: 1.39%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-16 19:11:34,276] [INFO] ===== Completeness check finished =====
[2023-06-16 19:11:34,276] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:11:34,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028697315.1_ASM2869731v1_genomic.fna/markers.fasta)
[2023-06-16 19:11:34,277] [INFO] Task started: Blastn
[2023-06-16 19:11:34,277] [INFO] Running command: blastn -query GCA_028697315.1_ASM2869731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a3519f-2f3a-4e53-9942-dad5478c941f/dqc_reference/reference_markers_gtdb.fasta -out GCA_028697315.1_ASM2869731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:34,725] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:34,728] [INFO] Selected 9 target genomes.
[2023-06-16 19:11:34,728] [INFO] Target genome list was writen to GCA_028697315.1_ASM2869731v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:11:34,732] [INFO] Task started: fastANI
[2023-06-16 19:11:34,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cf26a65-0fa9-43c6-a32a-dca90f875aeb/GCA_028697315.1_ASM2869731v1_genomic.fna.gz --refList GCA_028697315.1_ASM2869731v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028697315.1_ASM2869731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:11:37,420] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:37,424] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:11:37,424] [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_012719115.1	s__UBA5627 sp012719115	98.8364	192	251	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002421585.1	s__UBA5627 sp002421585	89.7646	187	251	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419135.1	s__UBA5627 sp002419135	87.7643	216	251	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520835.1	s__UBA5627 sp012520835	78.8457	122	251	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:11:37,426] [INFO] GTDB search result was written to GCA_028697315.1_ASM2869731v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:11:37,426] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:11:37,428] [INFO] DFAST_QC result json was written to GCA_028697315.1_ASM2869731v1_genomic.fna/dqc_result.json
[2023-06-16 19:11:37,429] [INFO] DFAST_QC completed!
[2023-06-16 19:11:37,429] [INFO] Total running time: 0h0m23s