[2023-06-28 10:56:33,434] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:56:33,436] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:56:33,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg567a0577-b73d-4944-92cc-9d10eb8605c6/dqc_reference
[2023-06-28 10:56:34,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:56:34,658] [INFO] Task started: Prodigal
[2023-06-28 10:56:34,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a6ded07-a00f-460e-b06f-cf7b27e9fb7b/GCA_019310145.1_ASM1931014v1_genomic.fna.gz | prodigal -d GCA_019310145.1_ASM1931014v1_genomic.fna/cds.fna -a GCA_019310145.1_ASM1931014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:56:41,842] [INFO] Task succeeded: Prodigal
[2023-06-28 10:56:41,842] [INFO] Task started: HMMsearch
[2023-06-28 10:56:41,842] [INFO] Running command: hmmsearch --tblout GCA_019310145.1_ASM1931014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg567a0577-b73d-4944-92cc-9d10eb8605c6/dqc_reference/reference_markers.hmm GCA_019310145.1_ASM1931014v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:56:42,057] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:56:42,058] [INFO] Found 6/6 markers.
[2023-06-28 10:56:42,092] [INFO] Query marker FASTA was written to GCA_019310145.1_ASM1931014v1_genomic.fna/markers.fasta
[2023-06-28 10:56:42,092] [INFO] Task started: Blastn
[2023-06-28 10:56:42,092] [INFO] Running command: blastn -query GCA_019310145.1_ASM1931014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg567a0577-b73d-4944-92cc-9d10eb8605c6/dqc_reference/reference_markers.fasta -out GCA_019310145.1_ASM1931014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:56:42,648] [INFO] Task succeeded: Blastn
[2023-06-28 10:56:42,656] [INFO] Selected 21 target genomes.
[2023-06-28 10:56:42,656] [INFO] Target genome list was writen to GCA_019310145.1_ASM1931014v1_genomic.fna/target_genomes.txt
[2023-06-28 10:56:42,658] [INFO] Task started: fastANI
[2023-06-28 10:56:42,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a6ded07-a00f-460e-b06f-cf7b27e9fb7b/GCA_019310145.1_ASM1931014v1_genomic.fna.gz --refList GCA_019310145.1_ASM1931014v1_genomic.fna/target_genomes.txt --output GCA_019310145.1_ASM1931014v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:56:54,215] [INFO] Task succeeded: fastANI
[2023-06-28 10:56:54,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg567a0577-b73d-4944-92cc-9d10eb8605c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:56:54,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg567a0577-b73d-4944-92cc-9d10eb8605c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:56:54,217] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:56:54,217] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:56:54,218] [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 10:56:54,219] [INFO] DFAST Taxonomy check result was written to GCA_019310145.1_ASM1931014v1_genomic.fna/tc_result.tsv
[2023-06-28 10:56:54,220] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:56:54,220] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:56:54,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg567a0577-b73d-4944-92cc-9d10eb8605c6/dqc_reference/checkm_data
[2023-06-28 10:56:54,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:56:54,264] [INFO] Task started: CheckM
[2023-06-28 10:56:54,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310145.1_ASM1931014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310145.1_ASM1931014v1_genomic.fna/checkm_input GCA_019310145.1_ASM1931014v1_genomic.fna/checkm_result
[2023-06-28 10:57:20,674] [INFO] Task succeeded: CheckM
[2023-06-28 10:57:20,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 13.02%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 10:57:20,695] [INFO] ===== Completeness check finished =====
[2023-06-28 10:57:20,695] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:57:20,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310145.1_ASM1931014v1_genomic.fna/markers.fasta)
[2023-06-28 10:57:20,696] [INFO] Task started: Blastn
[2023-06-28 10:57:20,696] [INFO] Running command: blastn -query GCA_019310145.1_ASM1931014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg567a0577-b73d-4944-92cc-9d10eb8605c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310145.1_ASM1931014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:57:21,500] [INFO] Task succeeded: Blastn
[2023-06-28 10:57:21,503] [INFO] Selected 32 target genomes.
[2023-06-28 10:57:21,503] [INFO] Target genome list was writen to GCA_019310145.1_ASM1931014v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:57:21,523] [INFO] Task started: fastANI
[2023-06-28 10:57:21,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a6ded07-a00f-460e-b06f-cf7b27e9fb7b/GCA_019310145.1_ASM1931014v1_genomic.fna.gz --refList GCA_019310145.1_ASM1931014v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310145.1_ASM1931014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:57:38,656] [INFO] Task succeeded: fastANI
[2023-06-28 10:57:38,661] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:57:38,661] [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_001751005.1	s__S5133MH16 sp001751005	78.5771	62	795	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014383215.1	s__Desulfatibia_A vada	77.7236	58	795	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__Desulfatibia_A	95.0	99.39	99.39	0.84	0.84	2	-
GCA_004193595.1	s__S5133MH16 sp004193595	77.6242	79	795	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA11574;g__S5133MH16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193555.1	s__ETH-SRB1 sp004193555	76.7443	80	795	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__ETH-SRB1;g__ETH-SRB1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:57:38,663] [INFO] GTDB search result was written to GCA_019310145.1_ASM1931014v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:57:38,665] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:57:38,668] [INFO] DFAST_QC result json was written to GCA_019310145.1_ASM1931014v1_genomic.fna/dqc_result.json
[2023-06-28 10:57:38,668] [INFO] DFAST_QC completed!
[2023-06-28 10:57:38,668] [INFO] Total running time: 0h1m5s