[2023-06-28 07:57:20,125] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:57:20,128] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:57:20,128] [INFO] DQC Reference Directory: /var/lib/cwl/stga528e93e-a222-48bd-a523-3f01357dd21a/dqc_reference
[2023-06-28 07:57:21,941] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:57:21,942] [INFO] Task started: Prodigal
[2023-06-28 07:57:21,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg44c30f56-98c9-4119-977c-fa1b9b8dc2b4/GCA_017545345.1_ASM1754534v1_genomic.fna.gz | prodigal -d GCA_017545345.1_ASM1754534v1_genomic.fna/cds.fna -a GCA_017545345.1_ASM1754534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:57:37,457] [INFO] Task succeeded: Prodigal
[2023-06-28 07:57:37,458] [INFO] Task started: HMMsearch
[2023-06-28 07:57:37,458] [INFO] Running command: hmmsearch --tblout GCA_017545345.1_ASM1754534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga528e93e-a222-48bd-a523-3f01357dd21a/dqc_reference/reference_markers.hmm GCA_017545345.1_ASM1754534v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:57:37,677] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:57:37,679] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg44c30f56-98c9-4119-977c-fa1b9b8dc2b4/GCA_017545345.1_ASM1754534v1_genomic.fna.gz]
[2023-06-28 07:57:37,702] [INFO] Query marker FASTA was written to GCA_017545345.1_ASM1754534v1_genomic.fna/markers.fasta
[2023-06-28 07:57:37,703] [INFO] Task started: Blastn
[2023-06-28 07:57:37,703] [INFO] Running command: blastn -query GCA_017545345.1_ASM1754534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga528e93e-a222-48bd-a523-3f01357dd21a/dqc_reference/reference_markers.fasta -out GCA_017545345.1_ASM1754534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:57:38,209] [INFO] Task succeeded: Blastn
[2023-06-28 07:57:38,212] [INFO] Selected 9 target genomes.
[2023-06-28 07:57:38,213] [INFO] Target genome list was writen to GCA_017545345.1_ASM1754534v1_genomic.fna/target_genomes.txt
[2023-06-28 07:57:38,214] [INFO] Task started: fastANI
[2023-06-28 07:57:38,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg44c30f56-98c9-4119-977c-fa1b9b8dc2b4/GCA_017545345.1_ASM1754534v1_genomic.fna.gz --refList GCA_017545345.1_ASM1754534v1_genomic.fna/target_genomes.txt --output GCA_017545345.1_ASM1754534v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:57:42,308] [INFO] Task succeeded: fastANI
[2023-06-28 07:57:42,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga528e93e-a222-48bd-a523-3f01357dd21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:57:42,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga528e93e-a222-48bd-a523-3f01357dd21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:57:42,313] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:57:42,313] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 07:57:42,314] [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 07:57:42,317] [INFO] DFAST Taxonomy check result was written to GCA_017545345.1_ASM1754534v1_genomic.fna/tc_result.tsv
[2023-06-28 07:57:42,319] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:57:42,319] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:57:42,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga528e93e-a222-48bd-a523-3f01357dd21a/dqc_reference/checkm_data
[2023-06-28 07:57:42,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:57:42,359] [INFO] Task started: CheckM
[2023-06-28 07:57:42,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017545345.1_ASM1754534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017545345.1_ASM1754534v1_genomic.fna/checkm_input GCA_017545345.1_ASM1754534v1_genomic.fna/checkm_result
[2023-06-28 07:58:28,326] [INFO] Task succeeded: CheckM
[2023-06-28 07:58:28,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 3.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 07:58:28,351] [INFO] ===== Completeness check finished =====
[2023-06-28 07:58:28,352] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:58:28,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017545345.1_ASM1754534v1_genomic.fna/markers.fasta)
[2023-06-28 07:58:28,353] [INFO] Task started: Blastn
[2023-06-28 07:58:28,353] [INFO] Running command: blastn -query GCA_017545345.1_ASM1754534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga528e93e-a222-48bd-a523-3f01357dd21a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017545345.1_ASM1754534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:58:28,934] [INFO] Task succeeded: Blastn
[2023-06-28 07:58:28,938] [INFO] Selected 6 target genomes.
[2023-06-28 07:58:28,939] [INFO] Target genome list was writen to GCA_017545345.1_ASM1754534v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:58:28,940] [INFO] Task started: fastANI
[2023-06-28 07:58:28,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg44c30f56-98c9-4119-977c-fa1b9b8dc2b4/GCA_017545345.1_ASM1754534v1_genomic.fna.gz --refList GCA_017545345.1_ASM1754534v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017545345.1_ASM1754534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:58:32,467] [INFO] Task succeeded: fastANI
[2023-06-28 07:58:32,479] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 07:58:32,480] [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_900319865.1	s__UBA1711 sp900319865	95.4973	475	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.00	96.55	0.84	0.79	17	conclusive
GCA_900317125.1	s__UBA1711 sp900317125	87.9825	325	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	96.93	96.01	0.87	0.83	22	-
GCA_017550405.1	s__UBA1711 sp017550405	86.0173	320	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318175.1	s__UBA1711 sp900318175	81.4532	283	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.21	97.84	0.90	0.87	10	-
GCA_002354035.1	s__UBA1711 sp002354035	80.368	228	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.39	99.39	0.95	0.95	2	-
GCA_905236405.1	s__CAJOQB01 sp905236405	76.6106	60	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__CAJOQB01	95.0	97.36	97.36	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-06-28 07:58:32,508] [INFO] GTDB search result was written to GCA_017545345.1_ASM1754534v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:58:32,509] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:58:32,512] [INFO] DFAST_QC result json was written to GCA_017545345.1_ASM1754534v1_genomic.fna/dqc_result.json
[2023-06-28 07:58:32,513] [INFO] DFAST_QC completed!
[2023-06-28 07:58:32,513] [INFO] Total running time: 0h1m12s