[2023-06-29 17:08:09,032] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:08:09,035] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:08:09,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg80423e0c-32e7-4232-881c-d9f6c29efbb9/dqc_reference
[2023-06-29 17:08:10,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:08:10,707] [INFO] Task started: Prodigal
[2023-06-29 17:08:10,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9908528-2593-4764-af6e-2a271a8cff0e/GCA_932217845.1_0316_S_maxbin.018_genomic.fna.gz | prodigal -d GCA_932217845.1_0316_S_maxbin.018_genomic.fna/cds.fna -a GCA_932217845.1_0316_S_maxbin.018_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:08:19,298] [INFO] Task succeeded: Prodigal
[2023-06-29 17:08:19,299] [INFO] Task started: HMMsearch
[2023-06-29 17:08:19,299] [INFO] Running command: hmmsearch --tblout GCA_932217845.1_0316_S_maxbin.018_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80423e0c-32e7-4232-881c-d9f6c29efbb9/dqc_reference/reference_markers.hmm GCA_932217845.1_0316_S_maxbin.018_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:08:19,557] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:08:19,559] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9908528-2593-4764-af6e-2a271a8cff0e/GCA_932217845.1_0316_S_maxbin.018_genomic.fna.gz]
[2023-06-29 17:08:19,605] [INFO] Query marker FASTA was written to GCA_932217845.1_0316_S_maxbin.018_genomic.fna/markers.fasta
[2023-06-29 17:08:19,608] [INFO] Task started: Blastn
[2023-06-29 17:08:19,608] [INFO] Running command: blastn -query GCA_932217845.1_0316_S_maxbin.018_genomic.fna/markers.fasta -db /var/lib/cwl/stg80423e0c-32e7-4232-881c-d9f6c29efbb9/dqc_reference/reference_markers.fasta -out GCA_932217845.1_0316_S_maxbin.018_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:08:20,237] [INFO] Task succeeded: Blastn
[2023-06-29 17:08:20,241] [INFO] Selected 18 target genomes.
[2023-06-29 17:08:20,241] [INFO] Target genome list was writen to GCA_932217845.1_0316_S_maxbin.018_genomic.fna/target_genomes.txt
[2023-06-29 17:08:20,243] [INFO] Task started: fastANI
[2023-06-29 17:08:20,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9908528-2593-4764-af6e-2a271a8cff0e/GCA_932217845.1_0316_S_maxbin.018_genomic.fna.gz --refList GCA_932217845.1_0316_S_maxbin.018_genomic.fna/target_genomes.txt --output GCA_932217845.1_0316_S_maxbin.018_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:08:33,033] [INFO] Task succeeded: fastANI
[2023-06-29 17:08:33,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80423e0c-32e7-4232-881c-d9f6c29efbb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:08:33,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80423e0c-32e7-4232-881c-d9f6c29efbb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:08:33,043] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:08:33,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 17:08:33,044] [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
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	77.1292	81	929	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.8831	68	929	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.7291	79	929	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.6577	63	929	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.3958	52	929	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.0406	51	929	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:08:33,046] [INFO] DFAST Taxonomy check result was written to GCA_932217845.1_0316_S_maxbin.018_genomic.fna/tc_result.tsv
[2023-06-29 17:08:33,046] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:08:33,046] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:08:33,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80423e0c-32e7-4232-881c-d9f6c29efbb9/dqc_reference/checkm_data
[2023-06-29 17:08:33,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:08:33,084] [INFO] Task started: CheckM
[2023-06-29 17:08:33,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_932217845.1_0316_S_maxbin.018_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_932217845.1_0316_S_maxbin.018_genomic.fna/checkm_input GCA_932217845.1_0316_S_maxbin.018_genomic.fna/checkm_result
[2023-06-29 17:09:03,822] [INFO] Task succeeded: CheckM
[2023-06-29 17:09:03,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:09:03,846] [INFO] ===== Completeness check finished =====
[2023-06-29 17:09:03,846] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:09:03,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_932217845.1_0316_S_maxbin.018_genomic.fna/markers.fasta)
[2023-06-29 17:09:03,847] [INFO] Task started: Blastn
[2023-06-29 17:09:03,847] [INFO] Running command: blastn -query GCA_932217845.1_0316_S_maxbin.018_genomic.fna/markers.fasta -db /var/lib/cwl/stg80423e0c-32e7-4232-881c-d9f6c29efbb9/dqc_reference/reference_markers_gtdb.fasta -out GCA_932217845.1_0316_S_maxbin.018_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:09:04,660] [INFO] Task succeeded: Blastn
[2023-06-29 17:09:04,666] [INFO] Selected 9 target genomes.
[2023-06-29 17:09:04,666] [INFO] Target genome list was writen to GCA_932217845.1_0316_S_maxbin.018_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:09:04,668] [INFO] Task started: fastANI
[2023-06-29 17:09:04,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9908528-2593-4764-af6e-2a271a8cff0e/GCA_932217845.1_0316_S_maxbin.018_genomic.fna.gz --refList GCA_932217845.1_0316_S_maxbin.018_genomic.fna/target_genomes_gtdb.txt --output GCA_932217845.1_0316_S_maxbin.018_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:09:12,580] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:12,593] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:09:12,593] [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_003611805.1	s__UBA3282 sp003611805	98.9825	864	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.73	98.68	0.87	0.86	4	conclusive
GCA_910586705.1	s__UBA3282 sp910586705	88.7326	744	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588955.1	s__UBA3282 sp910588955	86.9701	737	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579505.1	s__UBA3282 sp910579505	86.8598	730	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584725.1	s__UBA3282 sp910584725	86.6591	732	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774215.1	s__UBA3282 sp009774215	86.589	642	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.90	98.90	0.87	0.87	2	-
GCA_910587715.1	s__UBA3282 sp910587715	85.434	705	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575775.1	s__UBA3282 sp910575775	84.2622	697	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.26	98.26	0.81	0.81	2	-
GCA_002491905.1	s__UBA3282 sp002491905	83.0897	654	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:09:12,595] [INFO] GTDB search result was written to GCA_932217845.1_0316_S_maxbin.018_genomic.fna/result_gtdb.tsv
[2023-06-29 17:09:12,596] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:09:12,599] [INFO] DFAST_QC result json was written to GCA_932217845.1_0316_S_maxbin.018_genomic.fna/dqc_result.json
[2023-06-29 17:09:12,600] [INFO] DFAST_QC completed!
[2023-06-29 17:09:12,600] [INFO] Total running time: 0h1m4s