[2023-06-29 00:19:01,240] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:19:01,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:19:01,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg25a5a052-d234-4503-9f1c-c5e9e4e635f0/dqc_reference
[2023-06-29 00:19:03,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:19:03,643] [INFO] Task started: Prodigal
[2023-06-29 00:19:03,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c59e1a0-a10c-4702-ae81-872d96cbf715/GCA_944368775.1_BRZ_LV_bin30_genomic.fna.gz | prodigal -d GCA_944368775.1_BRZ_LV_bin30_genomic.fna/cds.fna -a GCA_944368775.1_BRZ_LV_bin30_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:19:08,684] [INFO] Task succeeded: Prodigal
[2023-06-29 00:19:08,685] [INFO] Task started: HMMsearch
[2023-06-29 00:19:08,685] [INFO] Running command: hmmsearch --tblout GCA_944368775.1_BRZ_LV_bin30_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25a5a052-d234-4503-9f1c-c5e9e4e635f0/dqc_reference/reference_markers.hmm GCA_944368775.1_BRZ_LV_bin30_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:19:08,891] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:19:08,893] [INFO] Found 6/6 markers.
[2023-06-29 00:19:08,917] [INFO] Query marker FASTA was written to GCA_944368775.1_BRZ_LV_bin30_genomic.fna/markers.fasta
[2023-06-29 00:19:08,917] [INFO] Task started: Blastn
[2023-06-29 00:19:08,917] [INFO] Running command: blastn -query GCA_944368775.1_BRZ_LV_bin30_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a5a052-d234-4503-9f1c-c5e9e4e635f0/dqc_reference/reference_markers.fasta -out GCA_944368775.1_BRZ_LV_bin30_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:19:09,574] [INFO] Task succeeded: Blastn
[2023-06-29 00:19:09,580] [INFO] Selected 33 target genomes.
[2023-06-29 00:19:09,580] [INFO] Target genome list was writen to GCA_944368775.1_BRZ_LV_bin30_genomic.fna/target_genomes.txt
[2023-06-29 00:19:09,587] [INFO] Task started: fastANI
[2023-06-29 00:19:09,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c59e1a0-a10c-4702-ae81-872d96cbf715/GCA_944368775.1_BRZ_LV_bin30_genomic.fna.gz --refList GCA_944368775.1_BRZ_LV_bin30_genomic.fna/target_genomes.txt --output GCA_944368775.1_BRZ_LV_bin30_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:19:33,638] [INFO] Task succeeded: fastANI
[2023-06-29 00:19:33,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25a5a052-d234-4503-9f1c-c5e9e4e635f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:19:33,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25a5a052-d234-4503-9f1c-c5e9e4e635f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:19:33,647] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:19:33,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:19:33,648] [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
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.4223	68	582	95	below_threshold
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	74.9933	54	582	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	74.9714	53	582	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:19:33,651] [INFO] DFAST Taxonomy check result was written to GCA_944368775.1_BRZ_LV_bin30_genomic.fna/tc_result.tsv
[2023-06-29 00:19:33,652] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:19:33,652] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:19:33,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25a5a052-d234-4503-9f1c-c5e9e4e635f0/dqc_reference/checkm_data
[2023-06-29 00:19:33,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:19:33,678] [INFO] Task started: CheckM
[2023-06-29 00:19:33,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944368775.1_BRZ_LV_bin30_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944368775.1_BRZ_LV_bin30_genomic.fna/checkm_input GCA_944368775.1_BRZ_LV_bin30_genomic.fna/checkm_result
[2023-06-29 00:19:54,550] [INFO] Task succeeded: CheckM
[2023-06-29 00:19:54,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:19:54,572] [INFO] ===== Completeness check finished =====
[2023-06-29 00:19:54,572] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:19:54,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944368775.1_BRZ_LV_bin30_genomic.fna/markers.fasta)
[2023-06-29 00:19:54,573] [INFO] Task started: Blastn
[2023-06-29 00:19:54,573] [INFO] Running command: blastn -query GCA_944368775.1_BRZ_LV_bin30_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a5a052-d234-4503-9f1c-c5e9e4e635f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_944368775.1_BRZ_LV_bin30_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:19:55,605] [INFO] Task succeeded: Blastn
[2023-06-29 00:19:55,610] [INFO] Selected 11 target genomes.
[2023-06-29 00:19:55,610] [INFO] Target genome list was writen to GCA_944368775.1_BRZ_LV_bin30_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:19:55,613] [INFO] Task started: fastANI
[2023-06-29 00:19:55,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c59e1a0-a10c-4702-ae81-872d96cbf715/GCA_944368775.1_BRZ_LV_bin30_genomic.fna.gz --refList GCA_944368775.1_BRZ_LV_bin30_genomic.fna/target_genomes_gtdb.txt --output GCA_944368775.1_BRZ_LV_bin30_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:19:59,589] [INFO] Task succeeded: fastANI
[2023-06-29 00:19:59,606] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:19:59,607] [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_019114625.1	s__Borkfalkia faecigallinarum	86.2912	361	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.33	98.33	0.78	0.78	2	-
GCA_904419945.1	s__Borkfalkia sp904419945	83.3196	356	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114755.1	s__Borkfalkia faecavium	82.2172	358	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761665.1	s__Borkfalkia avicola	81.3416	269	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.39	98.30	0.86	0.81	7	-
GCA_019115565.1	s__Borkfalkia excrementipullorum	80.4075	258	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.67	99.67	0.86	0.86	2	-
GCA_017886895.1	s__Borkfalkia sp017886895	80.2866	251	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761675.1	s__Borkfalkia excrementigallinarum	80.1221	231	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.80	98.79	0.81	0.79	3	-
GCA_904373255.1	s__Borkfalkia sp904373255	79.945	242	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119395.1	s__Borkfalkia stercoripullorum	79.6532	234	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.97	99.97	0.95	0.95	2	-
GCA_019114245.1	s__Borkfalkia faecipullorum	79.1184	235	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.25	98.23	0.86	0.84	3	-
GCA_019115995.1	s__Borkfalkia avistercoris	79.0394	214	582	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.93	99.93	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-29 00:19:59,609] [INFO] GTDB search result was written to GCA_944368775.1_BRZ_LV_bin30_genomic.fna/result_gtdb.tsv
[2023-06-29 00:19:59,610] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:19:59,614] [INFO] DFAST_QC result json was written to GCA_944368775.1_BRZ_LV_bin30_genomic.fna/dqc_result.json
[2023-06-29 00:19:59,614] [INFO] DFAST_QC completed!
[2023-06-29 00:19:59,614] [INFO] Total running time: 0h0m58s