[2023-06-29 16:25:32,744] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:25:32,749] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:25:32,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd839db1-aa6f-4c83-9c75-e98c94cfdc75/dqc_reference
[2023-06-29 16:25:34,008] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:25:34,009] [INFO] Task started: Prodigal
[2023-06-29 16:25:34,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg053e997e-b319-4d59-a44a-803036c7eb69/GCA_910589005.1_MGBC166864_genomic.fna.gz | prodigal -d GCA_910589005.1_MGBC166864_genomic.fna/cds.fna -a GCA_910589005.1_MGBC166864_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:25:44,469] [INFO] Task succeeded: Prodigal
[2023-06-29 16:25:44,469] [INFO] Task started: HMMsearch
[2023-06-29 16:25:44,469] [INFO] Running command: hmmsearch --tblout GCA_910589005.1_MGBC166864_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd839db1-aa6f-4c83-9c75-e98c94cfdc75/dqc_reference/reference_markers.hmm GCA_910589005.1_MGBC166864_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:25:44,749] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:25:44,751] [INFO] Found 6/6 markers.
[2023-06-29 16:25:44,785] [INFO] Query marker FASTA was written to GCA_910589005.1_MGBC166864_genomic.fna/markers.fasta
[2023-06-29 16:25:44,785] [INFO] Task started: Blastn
[2023-06-29 16:25:44,785] [INFO] Running command: blastn -query GCA_910589005.1_MGBC166864_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd839db1-aa6f-4c83-9c75-e98c94cfdc75/dqc_reference/reference_markers.fasta -out GCA_910589005.1_MGBC166864_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:25:45,444] [INFO] Task succeeded: Blastn
[2023-06-29 16:25:45,449] [INFO] Selected 24 target genomes.
[2023-06-29 16:25:45,449] [INFO] Target genome list was writen to GCA_910589005.1_MGBC166864_genomic.fna/target_genomes.txt
[2023-06-29 16:25:45,452] [INFO] Task started: fastANI
[2023-06-29 16:25:45,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg053e997e-b319-4d59-a44a-803036c7eb69/GCA_910589005.1_MGBC166864_genomic.fna.gz --refList GCA_910589005.1_MGBC166864_genomic.fna/target_genomes.txt --output GCA_910589005.1_MGBC166864_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:26:02,202] [INFO] Task succeeded: fastANI
[2023-06-29 16:26:02,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd839db1-aa6f-4c83-9c75-e98c94cfdc75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:26:02,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd839db1-aa6f-4c83-9c75-e98c94cfdc75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:26:02,212] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:26:02,212] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:26:02,212] [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
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.3947	74	1317	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	75.9028	56	1317	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:26:02,214] [INFO] DFAST Taxonomy check result was written to GCA_910589005.1_MGBC166864_genomic.fna/tc_result.tsv
[2023-06-29 16:26:02,215] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:26:02,215] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:26:02,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd839db1-aa6f-4c83-9c75-e98c94cfdc75/dqc_reference/checkm_data
[2023-06-29 16:26:02,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:26:02,273] [INFO] Task started: CheckM
[2023-06-29 16:26:02,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910589005.1_MGBC166864_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910589005.1_MGBC166864_genomic.fna/checkm_input GCA_910589005.1_MGBC166864_genomic.fna/checkm_result
[2023-06-29 16:26:37,380] [INFO] Task succeeded: CheckM
[2023-06-29 16:26:37,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:26:37,402] [INFO] ===== Completeness check finished =====
[2023-06-29 16:26:37,402] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:26:37,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910589005.1_MGBC166864_genomic.fna/markers.fasta)
[2023-06-29 16:26:37,403] [INFO] Task started: Blastn
[2023-06-29 16:26:37,403] [INFO] Running command: blastn -query GCA_910589005.1_MGBC166864_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd839db1-aa6f-4c83-9c75-e98c94cfdc75/dqc_reference/reference_markers_gtdb.fasta -out GCA_910589005.1_MGBC166864_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:26:38,415] [INFO] Task succeeded: Blastn
[2023-06-29 16:26:38,419] [INFO] Selected 17 target genomes.
[2023-06-29 16:26:38,419] [INFO] Target genome list was writen to GCA_910589005.1_MGBC166864_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:26:38,457] [INFO] Task started: fastANI
[2023-06-29 16:26:38,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg053e997e-b319-4d59-a44a-803036c7eb69/GCA_910589005.1_MGBC166864_genomic.fna.gz --refList GCA_910589005.1_MGBC166864_genomic.fna/target_genomes_gtdb.txt --output GCA_910589005.1_MGBC166864_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:26:50,545] [INFO] Task succeeded: fastANI
[2023-06-29 16:26:50,559] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:26:50,559] [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_910575035.1	s__14-2 sp910575035	99.9838	1290	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.99	99.98	0.99	0.98	3	conclusive
GCA_910588965.1	s__14-2 sp910588965	80.311	597	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577785.1	s__14-2 sp910577785	80.0835	634	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403255.2	s__14-2 sp000403255	78.0803	267	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.01	99.01	0.96	0.96	2	-
GCA_000403315.2	s__14-2 sp000403315	78.0057	315	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.01	98.74	0.95	0.92	3	-
GCA_910585295.1	s__14-2 sp009774455	77.9289	259	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.41	99.41	0.81	0.81	2	-
GCA_910575555.1	s__14-2 sp011960065	77.7968	285	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.61	97.67	0.95	0.76	7	-
GCA_910580195.1	s__14-2 sp910580195	77.4011	254	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583835.1	s__14-2 sp910583835	77.2619	203	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940225.1	s__14-2 sp001940225	77.0392	99	1317	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:26:50,562] [INFO] GTDB search result was written to GCA_910589005.1_MGBC166864_genomic.fna/result_gtdb.tsv
[2023-06-29 16:26:50,562] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:26:50,566] [INFO] DFAST_QC result json was written to GCA_910589005.1_MGBC166864_genomic.fna/dqc_result.json
[2023-06-29 16:26:50,566] [INFO] DFAST_QC completed!
[2023-06-29 16:26:50,566] [INFO] Total running time: 0h1m18s