[2023-06-28 07:11:01,057] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:11:01,059] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:11:01,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg77c5974d-bab1-4fac-96da-a5b1d83c80b8/dqc_reference
[2023-06-28 07:11:03,585] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:11:03,586] [INFO] Task started: Prodigal
[2023-06-28 07:11:03,586] [INFO] Running command: gunzip -c /var/lib/cwl/stgddc29bf6-3f17-483c-b705-0c59a0e8a1f2/GCA_944359075.1_BRZ_GB_bin120_genomic.fna.gz | prodigal -d GCA_944359075.1_BRZ_GB_bin120_genomic.fna/cds.fna -a GCA_944359075.1_BRZ_GB_bin120_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:11:05,561] [INFO] Task succeeded: Prodigal
[2023-06-28 07:11:05,562] [INFO] Task started: HMMsearch
[2023-06-28 07:11:05,562] [INFO] Running command: hmmsearch --tblout GCA_944359075.1_BRZ_GB_bin120_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77c5974d-bab1-4fac-96da-a5b1d83c80b8/dqc_reference/reference_markers.hmm GCA_944359075.1_BRZ_GB_bin120_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:11:05,784] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:11:05,786] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgddc29bf6-3f17-483c-b705-0c59a0e8a1f2/GCA_944359075.1_BRZ_GB_bin120_genomic.fna.gz]
[2023-06-28 07:11:05,806] [INFO] Query marker FASTA was written to GCA_944359075.1_BRZ_GB_bin120_genomic.fna/markers.fasta
[2023-06-28 07:11:05,806] [INFO] Task started: Blastn
[2023-06-28 07:11:05,806] [INFO] Running command: blastn -query GCA_944359075.1_BRZ_GB_bin120_genomic.fna/markers.fasta -db /var/lib/cwl/stg77c5974d-bab1-4fac-96da-a5b1d83c80b8/dqc_reference/reference_markers.fasta -out GCA_944359075.1_BRZ_GB_bin120_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:11:08,067] [INFO] Task succeeded: Blastn
[2023-06-28 07:11:08,071] [INFO] Selected 27 target genomes.
[2023-06-28 07:11:08,072] [INFO] Target genome list was writen to GCA_944359075.1_BRZ_GB_bin120_genomic.fna/target_genomes.txt
[2023-06-28 07:11:08,088] [INFO] Task started: fastANI
[2023-06-28 07:11:08,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgddc29bf6-3f17-483c-b705-0c59a0e8a1f2/GCA_944359075.1_BRZ_GB_bin120_genomic.fna.gz --refList GCA_944359075.1_BRZ_GB_bin120_genomic.fna/target_genomes.txt --output GCA_944359075.1_BRZ_GB_bin120_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:11:18,877] [INFO] Task succeeded: fastANI
[2023-06-28 07:11:18,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77c5974d-bab1-4fac-96da-a5b1d83c80b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:11:18,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77c5974d-bab1-4fac-96da-a5b1d83c80b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:11:18,881] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:11:18,881] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 07:11:18,881] [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 07:11:18,883] [INFO] DFAST Taxonomy check result was written to GCA_944359075.1_BRZ_GB_bin120_genomic.fna/tc_result.tsv
[2023-06-28 07:11:18,884] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:11:18,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:11:18,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77c5974d-bab1-4fac-96da-a5b1d83c80b8/dqc_reference/checkm_data
[2023-06-28 07:11:18,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:11:18,906] [INFO] Task started: CheckM
[2023-06-28 07:11:18,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944359075.1_BRZ_GB_bin120_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944359075.1_BRZ_GB_bin120_genomic.fna/checkm_input GCA_944359075.1_BRZ_GB_bin120_genomic.fna/checkm_result
[2023-06-28 07:11:33,203] [INFO] Task succeeded: CheckM
[2023-06-28 07:11:33,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:11:33,231] [INFO] ===== Completeness check finished =====
[2023-06-28 07:11:33,232] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:11:33,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944359075.1_BRZ_GB_bin120_genomic.fna/markers.fasta)
[2023-06-28 07:11:33,233] [INFO] Task started: Blastn
[2023-06-28 07:11:33,233] [INFO] Running command: blastn -query GCA_944359075.1_BRZ_GB_bin120_genomic.fna/markers.fasta -db /var/lib/cwl/stg77c5974d-bab1-4fac-96da-a5b1d83c80b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_944359075.1_BRZ_GB_bin120_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:11:33,975] [INFO] Task succeeded: Blastn
[2023-06-28 07:11:33,980] [INFO] Selected 22 target genomes.
[2023-06-28 07:11:33,981] [INFO] Target genome list was writen to GCA_944359075.1_BRZ_GB_bin120_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:11:33,996] [INFO] Task started: fastANI
[2023-06-28 07:11:33,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgddc29bf6-3f17-483c-b705-0c59a0e8a1f2/GCA_944359075.1_BRZ_GB_bin120_genomic.fna.gz --refList GCA_944359075.1_BRZ_GB_bin120_genomic.fna/target_genomes_gtdb.txt --output GCA_944359075.1_BRZ_GB_bin120_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:11:39,576] [INFO] Task succeeded: fastANI
[2023-06-28 07:11:39,583] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 07:11:39,584] [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_900542735.1	s__Scybalousia sp900542735	80.0042	215	396	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	98.00	97.98	0.84	0.82	4	-
GCA_018716115.1	s__Scybalousia intestinigallinarum	77.4676	70	396	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	99.54	99.15	0.85	0.80	3	-
GCA_002493865.1	s__Scybalousia sp002493865	77.4229	55	396	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543675.1	s__Scybalousia sp900543675	77.2518	79	396	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	97.87	97.87	0.85	0.85	2	-
GCA_910584255.1	s__Scybalousia sp910584255	77.1617	101	396	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:11:39,586] [INFO] GTDB search result was written to GCA_944359075.1_BRZ_GB_bin120_genomic.fna/result_gtdb.tsv
[2023-06-28 07:11:39,586] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:11:39,589] [INFO] DFAST_QC result json was written to GCA_944359075.1_BRZ_GB_bin120_genomic.fna/dqc_result.json
[2023-06-28 07:11:39,589] [INFO] DFAST_QC completed!
[2023-06-28 07:11:39,589] [INFO] Total running time: 0h0m39s