[2023-06-28 13:29:51,050] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:29:51,051] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:29:51,051] [INFO] DQC Reference Directory: /var/lib/cwl/stge79fb698-5c9e-4c49-ab93-842c97875498/dqc_reference
[2023-06-28 13:29:52,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:29:52,193] [INFO] Task started: Prodigal
[2023-06-28 13:29:52,193] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ae91207-966a-49b1-9139-298be3594402/GCA_019119455.1_ASM1911945v1_genomic.fna.gz | prodigal -d GCA_019119455.1_ASM1911945v1_genomic.fna/cds.fna -a GCA_019119455.1_ASM1911945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:30:02,169] [INFO] Task succeeded: Prodigal
[2023-06-28 13:30:02,170] [INFO] Task started: HMMsearch
[2023-06-28 13:30:02,170] [INFO] Running command: hmmsearch --tblout GCA_019119455.1_ASM1911945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge79fb698-5c9e-4c49-ab93-842c97875498/dqc_reference/reference_markers.hmm GCA_019119455.1_ASM1911945v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:30:02,351] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:30:02,352] [INFO] Found 6/6 markers.
[2023-06-28 13:30:02,372] [INFO] Query marker FASTA was written to GCA_019119455.1_ASM1911945v1_genomic.fna/markers.fasta
[2023-06-28 13:30:02,372] [INFO] Task started: Blastn
[2023-06-28 13:30:02,372] [INFO] Running command: blastn -query GCA_019119455.1_ASM1911945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge79fb698-5c9e-4c49-ab93-842c97875498/dqc_reference/reference_markers.fasta -out GCA_019119455.1_ASM1911945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:02,949] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:02,952] [INFO] Selected 14 target genomes.
[2023-06-28 13:30:02,952] [INFO] Target genome list was writen to GCA_019119455.1_ASM1911945v1_genomic.fna/target_genomes.txt
[2023-06-28 13:30:02,955] [INFO] Task started: fastANI
[2023-06-28 13:30:02,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ae91207-966a-49b1-9139-298be3594402/GCA_019119455.1_ASM1911945v1_genomic.fna.gz --refList GCA_019119455.1_ASM1911945v1_genomic.fna/target_genomes.txt --output GCA_019119455.1_ASM1911945v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:30:12,012] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:12,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge79fb698-5c9e-4c49-ab93-842c97875498/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:30:12,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge79fb698-5c9e-4c49-ab93-842c97875498/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:30:12,020] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 13:30:12,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 13:30:12,021] [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 dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	99.0186	714	727	95	conclusive
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	83.7792	489	727	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	83.7375	500	727	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	83.7297	492	727	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	83.7271	482	727	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	83.7103	495	727	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	83.3303	488	727	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	82.0708	471	727	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	81.9497	479	727	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.8757	90	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:30:12,022] [INFO] DFAST Taxonomy check result was written to GCA_019119455.1_ASM1911945v1_genomic.fna/tc_result.tsv
[2023-06-28 13:30:12,023] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:30:12,023] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:30:12,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge79fb698-5c9e-4c49-ab93-842c97875498/dqc_reference/checkm_data
[2023-06-28 13:30:12,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:30:12,048] [INFO] Task started: CheckM
[2023-06-28 13:30:12,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019119455.1_ASM1911945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019119455.1_ASM1911945v1_genomic.fna/checkm_input GCA_019119455.1_ASM1911945v1_genomic.fna/checkm_result
[2023-06-28 13:30:41,280] [INFO] Task succeeded: CheckM
[2023-06-28 13:30:41,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:30:41,300] [INFO] ===== Completeness check finished =====
[2023-06-28 13:30:41,300] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:30:41,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019119455.1_ASM1911945v1_genomic.fna/markers.fasta)
[2023-06-28 13:30:41,301] [INFO] Task started: Blastn
[2023-06-28 13:30:41,301] [INFO] Running command: blastn -query GCA_019119455.1_ASM1911945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge79fb698-5c9e-4c49-ab93-842c97875498/dqc_reference/reference_markers_gtdb.fasta -out GCA_019119455.1_ASM1911945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:42,227] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:42,230] [INFO] Selected 17 target genomes.
[2023-06-28 13:30:42,230] [INFO] Target genome list was writen to GCA_019119455.1_ASM1911945v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:30:42,247] [INFO] Task started: fastANI
[2023-06-28 13:30:42,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ae91207-966a-49b1-9139-298be3594402/GCA_019119455.1_ASM1911945v1_genomic.fna.gz --refList GCA_019119455.1_ASM1911945v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019119455.1_ASM1911945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:30:51,654] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:51,664] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:30:51,665] [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_006542685.1	s__Alistipes dispar	99.0186	714	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	conclusive
GCA_019115605.1	s__Alistipes faecigallinarum	84.8326	475	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119615.1	s__Alistipes stercoravium	84.6269	508	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.09	99.09	0.91	0.91	2	-
GCA_000434235.1	s__Alistipes avistercoris	84.1821	472	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.12	0.90	0.84	7	-
GCF_000210575.1	s__Alistipes shahii	83.8312	486	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCA_900544265.1	s__Alistipes merdavium	83.7953	422	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_900541585.1	s__Alistipes sp900541585	83.7938	451	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCF_000312145.1	s__Alistipes senegalensis	83.7321	500	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_001941065.1	s__Alistipes sp001941065	83.0358	443	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576555.1	s__Alistipes sp910576555	82.8895	409	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161445.1	s__Alistipes cottocaccae	82.4147	444	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.26	98.26	0.94	0.94	2	-
GCA_019118605.1	s__Alistipes faecavium	82.3323	422	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374505.1	s__Alistipes onderdonkii	81.805	497	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	-
GCF_900021155.1	s__Alistipes excrementavium	81.4431	372	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.37	98.83	0.93	0.90	7	-
GCA_017651225.1	s__Cryptobacteroides sp017651225	76.0946	56	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:30:51,666] [INFO] GTDB search result was written to GCA_019119455.1_ASM1911945v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:30:51,667] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:30:51,672] [INFO] DFAST_QC result json was written to GCA_019119455.1_ASM1911945v1_genomic.fna/dqc_result.json
[2023-06-28 13:30:51,672] [INFO] DFAST_QC completed!
[2023-06-28 13:30:51,672] [INFO] Total running time: 0h1m1s