[2023-06-29 12:37:51,638] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:37:51,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:37:51,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c9747f1-c714-4b85-b7ae-0558bea3a5dd/dqc_reference
[2023-06-29 12:37:52,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:37:52,867] [INFO] Task started: Prodigal
[2023-06-29 12:37:52,868] [INFO] Running command: gunzip -c /var/lib/cwl/stge8935bf9-f46b-43ce-b446-6af9bf12549b/GCA_021157555.1_ASM2115755v1_genomic.fna.gz | prodigal -d GCA_021157555.1_ASM2115755v1_genomic.fna/cds.fna -a GCA_021157555.1_ASM2115755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:37:57,231] [INFO] Task succeeded: Prodigal
[2023-06-29 12:37:57,231] [INFO] Task started: HMMsearch
[2023-06-29 12:37:57,232] [INFO] Running command: hmmsearch --tblout GCA_021157555.1_ASM2115755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c9747f1-c714-4b85-b7ae-0558bea3a5dd/dqc_reference/reference_markers.hmm GCA_021157555.1_ASM2115755v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:37:57,496] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:37:57,497] [INFO] Found 6/6 markers.
[2023-06-29 12:37:57,521] [INFO] Query marker FASTA was written to GCA_021157555.1_ASM2115755v1_genomic.fna/markers.fasta
[2023-06-29 12:37:57,521] [INFO] Task started: Blastn
[2023-06-29 12:37:57,521] [INFO] Running command: blastn -query GCA_021157555.1_ASM2115755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c9747f1-c714-4b85-b7ae-0558bea3a5dd/dqc_reference/reference_markers.fasta -out GCA_021157555.1_ASM2115755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:37:58,092] [INFO] Task succeeded: Blastn
[2023-06-29 12:37:58,096] [INFO] Selected 22 target genomes.
[2023-06-29 12:37:58,096] [INFO] Target genome list was writen to GCA_021157555.1_ASM2115755v1_genomic.fna/target_genomes.txt
[2023-06-29 12:37:58,100] [INFO] Task started: fastANI
[2023-06-29 12:37:58,100] [INFO] Running command: fastANI --query /var/lib/cwl/stge8935bf9-f46b-43ce-b446-6af9bf12549b/GCA_021157555.1_ASM2115755v1_genomic.fna.gz --refList GCA_021157555.1_ASM2115755v1_genomic.fna/target_genomes.txt --output GCA_021157555.1_ASM2115755v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:38:09,056] [INFO] Task succeeded: fastANI
[2023-06-29 12:38:09,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c9747f1-c714-4b85-b7ae-0558bea3a5dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:38:09,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c9747f1-c714-4b85-b7ae-0558bea3a5dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:38:09,058] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:38:09,058] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:38:09,059] [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
--------------------------------------------------------------------------------
[2023-06-29 12:38:09,060] [INFO] DFAST Taxonomy check result was written to GCA_021157555.1_ASM2115755v1_genomic.fna/tc_result.tsv
[2023-06-29 12:38:09,061] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:38:09,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:38:09,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c9747f1-c714-4b85-b7ae-0558bea3a5dd/dqc_reference/checkm_data
[2023-06-29 12:38:09,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:38:09,095] [INFO] Task started: CheckM
[2023-06-29 12:38:09,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021157555.1_ASM2115755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021157555.1_ASM2115755v1_genomic.fna/checkm_input GCA_021157555.1_ASM2115755v1_genomic.fna/checkm_result
[2023-06-29 12:38:30,619] [INFO] Task succeeded: CheckM
[2023-06-29 12:38:30,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 12:38:30,642] [INFO] ===== Completeness check finished =====
[2023-06-29 12:38:30,642] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:38:30,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021157555.1_ASM2115755v1_genomic.fna/markers.fasta)
[2023-06-29 12:38:30,643] [INFO] Task started: Blastn
[2023-06-29 12:38:30,643] [INFO] Running command: blastn -query GCA_021157555.1_ASM2115755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c9747f1-c714-4b85-b7ae-0558bea3a5dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_021157555.1_ASM2115755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:38:31,636] [INFO] Task succeeded: Blastn
[2023-06-29 12:38:31,642] [INFO] Selected 18 target genomes.
[2023-06-29 12:38:31,643] [INFO] Target genome list was writen to GCA_021157555.1_ASM2115755v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:38:31,657] [INFO] Task started: fastANI
[2023-06-29 12:38:31,657] [INFO] Running command: fastANI --query /var/lib/cwl/stge8935bf9-f46b-43ce-b446-6af9bf12549b/GCA_021157555.1_ASM2115755v1_genomic.fna.gz --refList GCA_021157555.1_ASM2115755v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021157555.1_ASM2115755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:38:41,143] [INFO] Task succeeded: fastANI
[2023-06-29 12:38:41,150] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:38:41,151] [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
GCF_000472805.1	s__BuS5 sp000472805	83.3375	416	609	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__BuS5;g__BuS5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016735355.1	s__BuS5 sp016735355	82.2286	255	609	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__BuS5;g__BuS5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237365.1	s__B13-G4 sp014237365	76.5505	56	609	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__B13-G4	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 12:38:41,153] [INFO] GTDB search result was written to GCA_021157555.1_ASM2115755v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:38:41,154] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:38:41,157] [INFO] DFAST_QC result json was written to GCA_021157555.1_ASM2115755v1_genomic.fna/dqc_result.json
[2023-06-29 12:38:41,157] [INFO] DFAST_QC completed!
[2023-06-29 12:38:41,157] [INFO] Total running time: 0h0m50s