[2023-06-28 16:42:54,561] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:42:54,564] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:42:54,564] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8acb969-ae25-4179-91a3-8e020cfd7de7/dqc_reference
[2023-06-28 16:42:55,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:42:55,909] [INFO] Task started: Prodigal
[2023-06-28 16:42:55,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg553ab74f-b91e-44f3-8400-6c8b1b36c7af/GCA_944324355.1_BRZ_LB_bin15_genomic.fna.gz | prodigal -d GCA_944324355.1_BRZ_LB_bin15_genomic.fna/cds.fna -a GCA_944324355.1_BRZ_LB_bin15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:42:59,269] [INFO] Task succeeded: Prodigal
[2023-06-28 16:42:59,270] [INFO] Task started: HMMsearch
[2023-06-28 16:42:59,270] [INFO] Running command: hmmsearch --tblout GCA_944324355.1_BRZ_LB_bin15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8acb969-ae25-4179-91a3-8e020cfd7de7/dqc_reference/reference_markers.hmm GCA_944324355.1_BRZ_LB_bin15_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:42:59,512] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:42:59,514] [INFO] Found 6/6 markers.
[2023-06-28 16:42:59,543] [INFO] Query marker FASTA was written to GCA_944324355.1_BRZ_LB_bin15_genomic.fna/markers.fasta
[2023-06-28 16:42:59,544] [INFO] Task started: Blastn
[2023-06-28 16:42:59,546] [INFO] Running command: blastn -query GCA_944324355.1_BRZ_LB_bin15_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8acb969-ae25-4179-91a3-8e020cfd7de7/dqc_reference/reference_markers.fasta -out GCA_944324355.1_BRZ_LB_bin15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:00,244] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:00,247] [INFO] Selected 29 target genomes.
[2023-06-28 16:43:00,248] [INFO] Target genome list was writen to GCA_944324355.1_BRZ_LB_bin15_genomic.fna/target_genomes.txt
[2023-06-28 16:43:00,265] [INFO] Task started: fastANI
[2023-06-28 16:43:00,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg553ab74f-b91e-44f3-8400-6c8b1b36c7af/GCA_944324355.1_BRZ_LB_bin15_genomic.fna.gz --refList GCA_944324355.1_BRZ_LB_bin15_genomic.fna/target_genomes.txt --output GCA_944324355.1_BRZ_LB_bin15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:43:14,377] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:14,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8acb969-ae25-4179-91a3-8e020cfd7de7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:43:14,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8acb969-ae25-4179-91a3-8e020cfd7de7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:43:14,379] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:43:14,380] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:43:14,380] [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 16:43:14,386] [INFO] DFAST Taxonomy check result was written to GCA_944324355.1_BRZ_LB_bin15_genomic.fna/tc_result.tsv
[2023-06-28 16:43:14,387] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:43:14,387] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:43:14,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8acb969-ae25-4179-91a3-8e020cfd7de7/dqc_reference/checkm_data
[2023-06-28 16:43:14,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:43:14,439] [INFO] Task started: CheckM
[2023-06-28 16:43:14,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324355.1_BRZ_LB_bin15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324355.1_BRZ_LB_bin15_genomic.fna/checkm_input GCA_944324355.1_BRZ_LB_bin15_genomic.fna/checkm_result
[2023-06-28 16:43:32,917] [INFO] Task succeeded: CheckM
[2023-06-28 16:43:32,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:43:32,950] [INFO] ===== Completeness check finished =====
[2023-06-28 16:43:32,951] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:43:32,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324355.1_BRZ_LB_bin15_genomic.fna/markers.fasta)
[2023-06-28 16:43:32,952] [INFO] Task started: Blastn
[2023-06-28 16:43:32,952] [INFO] Running command: blastn -query GCA_944324355.1_BRZ_LB_bin15_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8acb969-ae25-4179-91a3-8e020cfd7de7/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324355.1_BRZ_LB_bin15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:33,810] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:33,815] [INFO] Selected 9 target genomes.
[2023-06-28 16:43:33,815] [INFO] Target genome list was writen to GCA_944324355.1_BRZ_LB_bin15_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:43:33,821] [INFO] Task started: fastANI
[2023-06-28 16:43:33,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg553ab74f-b91e-44f3-8400-6c8b1b36c7af/GCA_944324355.1_BRZ_LB_bin15_genomic.fna.gz --refList GCA_944324355.1_BRZ_LB_bin15_genomic.fna/target_genomes_gtdb.txt --output GCA_944324355.1_BRZ_LB_bin15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:43:37,581] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:37,591] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:43:37,591] [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_905216055.1	s__Stercorousia sp905216055	98.4366	520	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900555175.1	s__Stercorousia sp900555175	93.8975	289	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.94	0.94	2	-
GCA_000437435.1	s__Stercorousia sp000437435	82.2107	415	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.52	97.52	0.91	0.91	3	-
GCA_905212085.1	s__Stercorousia sp905212085	82.205	386	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551675.1	s__Stercorousia sp900551675	81.4371	372	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900761225.1	s__Stercorousia sp900761225	80.7336	350	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438175.1	s__Stercorousia faecigallinarum	80.096	367	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.53	97.95	0.88	0.85	4	-
GCA_001765415.1	s__Stercorousia sp001765415	79.7255	316	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.74	98.70	0.94	0.93	5	-
GCA_900769355.1	s__Stercorousia sp900769355	78.9542	244	562	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:43:37,593] [INFO] GTDB search result was written to GCA_944324355.1_BRZ_LB_bin15_genomic.fna/result_gtdb.tsv
[2023-06-28 16:43:37,593] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:43:37,596] [INFO] DFAST_QC result json was written to GCA_944324355.1_BRZ_LB_bin15_genomic.fna/dqc_result.json
[2023-06-28 16:43:37,596] [INFO] DFAST_QC completed!
[2023-06-28 16:43:37,596] [INFO] Total running time: 0h0m43s