[2023-06-17 01:44:48,042] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:44:48,048] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:44:48,048] [INFO] DQC Reference Directory: /var/lib/cwl/stge8a1974c-f806-43aa-ae62-b577fb382f14/dqc_reference
[2023-06-17 01:44:49,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:44:49,896] [INFO] Task started: Prodigal
[2023-06-17 01:44:49,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgdaea34b3-a645-4bb1-86b5-7d426bcb96e9/GCA_009774865.1_ASM977486v1_genomic.fna.gz | prodigal -d GCA_009774865.1_ASM977486v1_genomic.fna/cds.fna -a GCA_009774865.1_ASM977486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:45:00,709] [INFO] Task succeeded: Prodigal
[2023-06-17 01:45:00,710] [INFO] Task started: HMMsearch
[2023-06-17 01:45:00,710] [INFO] Running command: hmmsearch --tblout GCA_009774865.1_ASM977486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8a1974c-f806-43aa-ae62-b577fb382f14/dqc_reference/reference_markers.hmm GCA_009774865.1_ASM977486v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:45:00,939] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:45:00,941] [INFO] Found 6/6 markers.
[2023-06-17 01:45:00,964] [INFO] Query marker FASTA was written to GCA_009774865.1_ASM977486v1_genomic.fna/markers.fasta
[2023-06-17 01:45:00,964] [INFO] Task started: Blastn
[2023-06-17 01:45:00,964] [INFO] Running command: blastn -query GCA_009774865.1_ASM977486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a1974c-f806-43aa-ae62-b577fb382f14/dqc_reference/reference_markers.fasta -out GCA_009774865.1_ASM977486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:45:01,572] [INFO] Task succeeded: Blastn
[2023-06-17 01:45:01,577] [INFO] Selected 18 target genomes.
[2023-06-17 01:45:01,577] [INFO] Target genome list was writen to GCA_009774865.1_ASM977486v1_genomic.fna/target_genomes.txt
[2023-06-17 01:45:01,582] [INFO] Task started: fastANI
[2023-06-17 01:45:01,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaea34b3-a645-4bb1-86b5-7d426bcb96e9/GCA_009774865.1_ASM977486v1_genomic.fna.gz --refList GCA_009774865.1_ASM977486v1_genomic.fna/target_genomes.txt --output GCA_009774865.1_ASM977486v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:45:12,206] [INFO] Task succeeded: fastANI
[2023-06-17 01:45:12,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8a1974c-f806-43aa-ae62-b577fb382f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:45:12,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8a1974c-f806-43aa-ae62-b577fb382f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:45:12,219] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:45:12,219] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:45:12,220] [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 communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	78.4061	166	570	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	78.3427	177	570	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	78.2781	178	570	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	78.2616	181	570	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	78.2582	174	570	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	78.2451	176	570	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	78.2109	179	570	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	78.0432	159	570	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	77.8096	140	570	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	77.7808	173	570	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	77.7598	172	570	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	77.7237	181	570	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	77.576	106	570	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.5326	54	570	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:45:12,222] [INFO] DFAST Taxonomy check result was written to GCA_009774865.1_ASM977486v1_genomic.fna/tc_result.tsv
[2023-06-17 01:45:12,222] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:45:12,222] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:45:12,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8a1974c-f806-43aa-ae62-b577fb382f14/dqc_reference/checkm_data
[2023-06-17 01:45:12,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:45:12,252] [INFO] Task started: CheckM
[2023-06-17 01:45:12,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009774865.1_ASM977486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009774865.1_ASM977486v1_genomic.fna/checkm_input GCA_009774865.1_ASM977486v1_genomic.fna/checkm_result
[2023-06-17 01:45:45,887] [INFO] Task succeeded: CheckM
[2023-06-17 01:45:45,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:45:45,911] [INFO] ===== Completeness check finished =====
[2023-06-17 01:45:45,911] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:45:45,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009774865.1_ASM977486v1_genomic.fna/markers.fasta)
[2023-06-17 01:45:45,912] [INFO] Task started: Blastn
[2023-06-17 01:45:45,912] [INFO] Running command: blastn -query GCA_009774865.1_ASM977486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a1974c-f806-43aa-ae62-b577fb382f14/dqc_reference/reference_markers_gtdb.fasta -out GCA_009774865.1_ASM977486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:45:46,837] [INFO] Task succeeded: Blastn
[2023-06-17 01:45:46,842] [INFO] Selected 18 target genomes.
[2023-06-17 01:45:46,843] [INFO] Target genome list was writen to GCA_009774865.1_ASM977486v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:45:46,858] [INFO] Task started: fastANI
[2023-06-17 01:45:46,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaea34b3-a645-4bb1-86b5-7d426bcb96e9/GCA_009774865.1_ASM977486v1_genomic.fna.gz --refList GCA_009774865.1_ASM977486v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009774865.1_ASM977486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:45:54,723] [INFO] Task succeeded: fastANI
[2023-06-17 01:45:54,740] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:45:54,741] [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_910574205.1	s__Alistipes sp002362235	98.5187	522	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.85	98.52	0.94	0.92	5	conclusive
GCA_017936685.1	s__Alistipes sp017936685	82.0264	379	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774895.1	s__Alistipes sp009774895	78.6474	142	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.77	98.77	0.97	0.97	2	-
GCA_900544265.1	s__Alistipes merdavium	78.624	186	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_910587675.1	s__Alistipes sp910587675	78.6042	196	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014796635.1	s__Alistipes sp014796635	78.4546	101	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542665.1	s__Alistipes communis	78.4303	165	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.74	98.62	0.92	0.87	10	-
GCF_900290115.1	s__Alistipes excrementigallinarum	78.3781	188	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
GCF_000210575.1	s__Alistipes shahii	78.2616	181	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCF_000312145.1	s__Alistipes senegalensis	78.2451	176	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_910577475.1	s__Alistipes sp910577475	78.215	169	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552955.1	s__Alistipes sp900552955	78.2036	135	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546065.1	s__Alistipes merdipullorum	78.116	189	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.89	97.88	0.91	0.90	3	-
GCA_900541585.1	s__Alistipes sp900541585	77.9115	160	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_905214725.1	s__Alistipes sp905214725	77.8285	120	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416915.1	s__Alistipes sp017416915	77.8142	118	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465055.1	s__Alistipes sp017465055	77.0826	98	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937765.1	s__Alistipes sp017937765	77.0357	103	570	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:45:54,743] [INFO] GTDB search result was written to GCA_009774865.1_ASM977486v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:45:54,743] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:45:54,748] [INFO] DFAST_QC result json was written to GCA_009774865.1_ASM977486v1_genomic.fna/dqc_result.json
[2023-06-17 01:45:54,748] [INFO] DFAST_QC completed!
[2023-06-17 01:45:54,748] [INFO] Total running time: 0h1m7s