[2023-06-30 03:29:17,331] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:29:17,338] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:29:17,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgce808e3f-fc9d-48b6-aeb0-32482c8119a1/dqc_reference
[2023-06-30 03:29:19,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:29:19,859] [INFO] Task started: Prodigal
[2023-06-30 03:29:19,860] [INFO] Running command: gunzip -c /var/lib/cwl/stgb11a1cbc-d4ba-4eb7-a410-2e6514923437/GCA_900752995.1_ERS396322_43_genomic.fna.gz | prodigal -d GCA_900752995.1_ERS396322_43_genomic.fna/cds.fna -a GCA_900752995.1_ERS396322_43_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:29:26,835] [INFO] Task succeeded: Prodigal
[2023-06-30 03:29:26,836] [INFO] Task started: HMMsearch
[2023-06-30 03:29:26,836] [INFO] Running command: hmmsearch --tblout GCA_900752995.1_ERS396322_43_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce808e3f-fc9d-48b6-aeb0-32482c8119a1/dqc_reference/reference_markers.hmm GCA_900752995.1_ERS396322_43_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:29:27,041] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:29:27,043] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb11a1cbc-d4ba-4eb7-a410-2e6514923437/GCA_900752995.1_ERS396322_43_genomic.fna.gz]
[2023-06-30 03:29:27,063] [INFO] Query marker FASTA was written to GCA_900752995.1_ERS396322_43_genomic.fna/markers.fasta
[2023-06-30 03:29:27,063] [INFO] Task started: Blastn
[2023-06-30 03:29:27,063] [INFO] Running command: blastn -query GCA_900752995.1_ERS396322_43_genomic.fna/markers.fasta -db /var/lib/cwl/stgce808e3f-fc9d-48b6-aeb0-32482c8119a1/dqc_reference/reference_markers.fasta -out GCA_900752995.1_ERS396322_43_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:29:27,555] [INFO] Task succeeded: Blastn
[2023-06-30 03:29:27,561] [INFO] Selected 13 target genomes.
[2023-06-30 03:29:27,562] [INFO] Target genome list was writen to GCA_900752995.1_ERS396322_43_genomic.fna/target_genomes.txt
[2023-06-30 03:29:27,566] [INFO] Task started: fastANI
[2023-06-30 03:29:27,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgb11a1cbc-d4ba-4eb7-a410-2e6514923437/GCA_900752995.1_ERS396322_43_genomic.fna.gz --refList GCA_900752995.1_ERS396322_43_genomic.fna/target_genomes.txt --output GCA_900752995.1_ERS396322_43_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:29:33,770] [INFO] Task succeeded: fastANI
[2023-06-30 03:29:33,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce808e3f-fc9d-48b6-aeb0-32482c8119a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:29:33,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce808e3f-fc9d-48b6-aeb0-32482c8119a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:29:33,780] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:29:33,781] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:29:33,781] [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
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	78.4793	53	448	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.6763	67	448	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:29:33,783] [INFO] DFAST Taxonomy check result was written to GCA_900752995.1_ERS396322_43_genomic.fna/tc_result.tsv
[2023-06-30 03:29:33,784] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:29:33,784] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:29:33,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce808e3f-fc9d-48b6-aeb0-32482c8119a1/dqc_reference/checkm_data
[2023-06-30 03:29:33,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:29:33,814] [INFO] Task started: CheckM
[2023-06-30 03:29:33,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900752995.1_ERS396322_43_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900752995.1_ERS396322_43_genomic.fna/checkm_input GCA_900752995.1_ERS396322_43_genomic.fna/checkm_result
[2023-06-30 03:30:00,343] [INFO] Task succeeded: CheckM
[2023-06-30 03:30:00,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:30:00,364] [INFO] ===== Completeness check finished =====
[2023-06-30 03:30:00,365] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:30:00,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900752995.1_ERS396322_43_genomic.fna/markers.fasta)
[2023-06-30 03:30:00,366] [INFO] Task started: Blastn
[2023-06-30 03:30:00,366] [INFO] Running command: blastn -query GCA_900752995.1_ERS396322_43_genomic.fna/markers.fasta -db /var/lib/cwl/stgce808e3f-fc9d-48b6-aeb0-32482c8119a1/dqc_reference/reference_markers_gtdb.fasta -out GCA_900752995.1_ERS396322_43_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:30:00,833] [INFO] Task succeeded: Blastn
[2023-06-30 03:30:00,838] [INFO] Selected 10 target genomes.
[2023-06-30 03:30:00,838] [INFO] Target genome list was writen to GCA_900752995.1_ERS396322_43_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:30:00,844] [INFO] Task started: fastANI
[2023-06-30 03:30:00,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgb11a1cbc-d4ba-4eb7-a410-2e6514923437/GCA_900752995.1_ERS396322_43_genomic.fna.gz --refList GCA_900752995.1_ERS396322_43_genomic.fna/target_genomes_gtdb.txt --output GCA_900752995.1_ERS396322_43_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:30:04,686] [INFO] Task succeeded: fastANI
[2023-06-30 03:30:04,696] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:30:04,696] [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_910587185.1	s__Paramuribaculum sp910587185	96.6118	407	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	96.59	96.53	0.88	0.86	5	conclusive
GCA_910586475.1	s__Paramuribaculum sp910586475	78.2823	98	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551515.1	s__Paramuribaculum sp900551515	77.8526	84	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802445.1	s__CAG-1031 sp014802445	77.8347	53	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-1031	95.0	98.18	98.18	0.94	0.94	2	-
GCA_014801065.1	s__Paramuribaculum sp014801065	77.7583	62	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801655.1	s__Paramuribaculum sp014801655	77.7157	76	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.11	0.75	0.73	4	-
GCA_001689535.1	s__Paramuribaculum sp001689535	77.7137	81	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.63	98.52	0.86	0.84	5	-
GCA_900759915.1	s__Paramuribaculum sp900759915	77.6928	83	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	97.33	97.33	0.87	0.87	2	-
GCF_003024805.1	s__Duncaniella muris	77.6763	67	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.34	97.90	0.87	0.80	17	-
GCA_910578305.1	s__Paramuribaculum sp910578305	77.1204	57	448	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:30:04,698] [INFO] GTDB search result was written to GCA_900752995.1_ERS396322_43_genomic.fna/result_gtdb.tsv
[2023-06-30 03:30:04,699] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:30:04,703] [INFO] DFAST_QC result json was written to GCA_900752995.1_ERS396322_43_genomic.fna/dqc_result.json
[2023-06-30 03:30:04,703] [INFO] DFAST_QC completed!
[2023-06-30 03:30:04,703] [INFO] Total running time: 0h0m47s