[2024-01-24 12:27:18,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:18,967] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:18,967] [INFO] DQC Reference Directory: /var/lib/cwl/stga0c4dfca-3b9e-4036-8adc-832d633be153/dqc_reference
[2024-01-24 12:27:20,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,101] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a1c6658-d3c0-42b8-a744-ae2d418aea04/GCF_025145285.1_ASM2514528v1_genomic.fna.gz | prodigal -d GCF_025145285.1_ASM2514528v1_genomic.fna/cds.fna -a GCF_025145285.1_ASM2514528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:41,328] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:41,329] [INFO] Task started: HMMsearch
[2024-01-24 12:27:41,329] [INFO] Running command: hmmsearch --tblout GCF_025145285.1_ASM2514528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0c4dfca-3b9e-4036-8adc-832d633be153/dqc_reference/reference_markers.hmm GCF_025145285.1_ASM2514528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:41,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:41,552] [INFO] Found 6/6 markers.
[2024-01-24 12:27:41,580] [INFO] Query marker FASTA was written to GCF_025145285.1_ASM2514528v1_genomic.fna/markers.fasta
[2024-01-24 12:27:41,580] [INFO] Task started: Blastn
[2024-01-24 12:27:41,581] [INFO] Running command: blastn -query GCF_025145285.1_ASM2514528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0c4dfca-3b9e-4036-8adc-832d633be153/dqc_reference/reference_markers.fasta -out GCF_025145285.1_ASM2514528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:42,187] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:42,272] [INFO] Selected 9 target genomes.
[2024-01-24 12:27:42,273] [INFO] Target genome list was writen to GCF_025145285.1_ASM2514528v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:42,286] [INFO] Task started: fastANI
[2024-01-24 12:27:42,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a1c6658-d3c0-42b8-a744-ae2d418aea04/GCF_025145285.1_ASM2514528v1_genomic.fna.gz --refList GCF_025145285.1_ASM2514528v1_genomic.fna/target_genomes.txt --output GCF_025145285.1_ASM2514528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:49,399] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:49,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0c4dfca-3b9e-4036-8adc-832d633be153/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:49,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0c4dfca-3b9e-4036-8adc-832d633be153/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:49,408] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:27:49,408] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:27:49,408] [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
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	100.0	1287	1289	95	conclusive
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	99.9843	1269	1289	95	conclusive
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	96.8246	978	1289	95	conclusive
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	85.8701	788	1289	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	85.0729	725	1289	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	85.0546	707	1289	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	83.5373	625	1289	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	81.8299	597	1289	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	77.0738	127	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:27:49,410] [INFO] DFAST Taxonomy check result was written to GCF_025145285.1_ASM2514528v1_genomic.fna/tc_result.tsv
[2024-01-24 12:27:49,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:49,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:49,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0c4dfca-3b9e-4036-8adc-832d633be153/dqc_reference/checkm_data
[2024-01-24 12:27:49,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:49,450] [INFO] Task started: CheckM
[2024-01-24 12:27:49,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025145285.1_ASM2514528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025145285.1_ASM2514528v1_genomic.fna/checkm_input GCF_025145285.1_ASM2514528v1_genomic.fna/checkm_result
[2024-01-24 12:28:45,225] [INFO] Task succeeded: CheckM
[2024-01-24 12:28:45,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:28:45,250] [INFO] ===== Completeness check finished =====
[2024-01-24 12:28:45,250] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:28:45,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025145285.1_ASM2514528v1_genomic.fna/markers.fasta)
[2024-01-24 12:28:45,251] [INFO] Task started: Blastn
[2024-01-24 12:28:45,251] [INFO] Running command: blastn -query GCF_025145285.1_ASM2514528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0c4dfca-3b9e-4036-8adc-832d633be153/dqc_reference/reference_markers_gtdb.fasta -out GCF_025145285.1_ASM2514528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:46,176] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:46,180] [INFO] Selected 14 target genomes.
[2024-01-24 12:28:46,180] [INFO] Target genome list was writen to GCF_025145285.1_ASM2514528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:28:46,227] [INFO] Task started: fastANI
[2024-01-24 12:28:46,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a1c6658-d3c0-42b8-a744-ae2d418aea04/GCF_025145285.1_ASM2514528v1_genomic.fna.gz --refList GCF_025145285.1_ASM2514528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025145285.1_ASM2514528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:54,865] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:54,875] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:54,876] [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
GCF_000374505.1	s__Alistipes onderdonkii	99.9843	1269	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	conclusive
GCF_000265365.1	s__Alistipes finegoldii	85.857	787	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCA_902388705.1	s__Alistipes sp902388705	85.2338	751	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.98	97.96	0.93	0.92	3	-
GCF_000210575.1	s__Alistipes shahii	85.0546	707	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCF_900083545.1	s__Alistipes provencensis	83.0153	600	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900541585.1	s__Alistipes sp900541585	82.6732	576	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCF_900107675.1	s__Alistipes timonensis	82.4103	576	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.44	0.92	0.87	7	-
GCA_001941065.1	s__Alistipes sp001941065	82.2851	569	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015553985.1	s__Alistipes sp900549305	81.8427	591	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.80	98.50	0.91	0.87	6	-
GCA_019115605.1	s__Alistipes faecigallinarum	81.1975	435	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900021155.1	s__Alistipes excrementavium	80.9081	441	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.37	98.83	0.93	0.90	7	-
GCF_900290115.1	s__Alistipes excrementigallinarum	80.6079	464	1289	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:28:54,880] [INFO] GTDB search result was written to GCF_025145285.1_ASM2514528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:54,880] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:54,883] [INFO] DFAST_QC result json was written to GCF_025145285.1_ASM2514528v1_genomic.fna/dqc_result.json
[2024-01-24 12:28:54,884] [INFO] DFAST_QC completed!
[2024-01-24 12:28:54,884] [INFO] Total running time: 0h1m36s