[2023-06-28 17:02:53,785] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:02:53,788] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:02:53,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg03d05b49-c27c-494e-90f3-3faa39b159ba/dqc_reference
[2023-06-28 17:02:55,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:02:55,062] [INFO] Task started: Prodigal
[2023-06-28 17:02:55,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg35bc34c3-d15f-48f9-9150-d7eaf8a01ef4/GCA_944324025.1_BRZ_BQ_bin76_genomic.fna.gz | prodigal -d GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/cds.fna -a GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:02:58,683] [INFO] Task succeeded: Prodigal
[2023-06-28 17:02:58,683] [INFO] Task started: HMMsearch
[2023-06-28 17:02:58,683] [INFO] Running command: hmmsearch --tblout GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03d05b49-c27c-494e-90f3-3faa39b159ba/dqc_reference/reference_markers.hmm GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:02:58,916] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:02:58,918] [INFO] Found 6/6 markers.
[2023-06-28 17:02:58,945] [INFO] Query marker FASTA was written to GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/markers.fasta
[2023-06-28 17:02:58,945] [INFO] Task started: Blastn
[2023-06-28 17:02:58,945] [INFO] Running command: blastn -query GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d05b49-c27c-494e-90f3-3faa39b159ba/dqc_reference/reference_markers.fasta -out GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:02:59,539] [INFO] Task succeeded: Blastn
[2023-06-28 17:02:59,545] [INFO] Selected 23 target genomes.
[2023-06-28 17:02:59,546] [INFO] Target genome list was writen to GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/target_genomes.txt
[2023-06-28 17:02:59,556] [INFO] Task started: fastANI
[2023-06-28 17:02:59,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg35bc34c3-d15f-48f9-9150-d7eaf8a01ef4/GCA_944324025.1_BRZ_BQ_bin76_genomic.fna.gz --refList GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/target_genomes.txt --output GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:03:10,291] [INFO] Task succeeded: fastANI
[2023-06-28 17:03:10,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03d05b49-c27c-494e-90f3-3faa39b159ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:03:10,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03d05b49-c27c-494e-90f3-3faa39b159ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:03:10,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:03:10,294] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:03:10,294] [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 17:03:10,297] [INFO] DFAST Taxonomy check result was written to GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/tc_result.tsv
[2023-06-28 17:03:10,298] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:03:10,299] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:03:10,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03d05b49-c27c-494e-90f3-3faa39b159ba/dqc_reference/checkm_data
[2023-06-28 17:03:10,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:03:10,327] [INFO] Task started: CheckM
[2023-06-28 17:03:10,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/checkm_input GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/checkm_result
[2023-06-28 17:03:29,221] [INFO] Task succeeded: CheckM
[2023-06-28 17:03:29,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:03:29,249] [INFO] ===== Completeness check finished =====
[2023-06-28 17:03:29,249] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:03:29,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/markers.fasta)
[2023-06-28 17:03:29,250] [INFO] Task started: Blastn
[2023-06-28 17:03:29,250] [INFO] Running command: blastn -query GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d05b49-c27c-494e-90f3-3faa39b159ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:03:30,150] [INFO] Task succeeded: Blastn
[2023-06-28 17:03:30,155] [INFO] Selected 10 target genomes.
[2023-06-28 17:03:30,155] [INFO] Target genome list was writen to GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:03:30,162] [INFO] Task started: fastANI
[2023-06-28 17:03:30,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg35bc34c3-d15f-48f9-9150-d7eaf8a01ef4/GCA_944324025.1_BRZ_BQ_bin76_genomic.fna.gz --refList GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/target_genomes_gtdb.txt --output GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:03:34,636] [INFO] Task succeeded: fastANI
[2023-06-28 17:03:34,650] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:03:34,650] [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_900548405.1	s__Stercorousia sp001917115	97.7171	551	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.35	95.50	0.91	0.85	8	conclusive
GCA_900752845.1	s__Stercorousia sp900752845	85.5368	428	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.76	99.76	0.83	0.83	2	-
GCA_000433095.1	s__Stercorousia sp000433095	85.1404	517	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.53	99.13	0.95	0.93	3	-
GCA_000438175.1	s__Stercorousia faecigallinarum	79.8427	375	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.53	97.95	0.88	0.85	4	-
GCA_900761225.1	s__Stercorousia sp900761225	79.5878	336	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437435.1	s__Stercorousia sp000437435	79.4201	352	633	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	79.1844	339	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555175.1	s__Stercorousia sp900555175	79.0647	202	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.94	0.94	2	-
GCA_910588555.1	s__Stercorousia sp910588555	78.9795	290	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001765415.1	s__Stercorousia sp001765415	78.4681	274	633	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.74	98.70	0.94	0.93	5	-
--------------------------------------------------------------------------------
[2023-06-28 17:03:34,652] [INFO] GTDB search result was written to GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/result_gtdb.tsv
[2023-06-28 17:03:34,653] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:03:34,656] [INFO] DFAST_QC result json was written to GCA_944324025.1_BRZ_BQ_bin76_genomic.fna/dqc_result.json
[2023-06-28 17:03:34,656] [INFO] DFAST_QC completed!
[2023-06-28 17:03:34,656] [INFO] Total running time: 0h0m41s