[2023-06-29 14:34:41,703] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:34:41,705] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:34:41,705] [INFO] DQC Reference Directory: /var/lib/cwl/stga46430c0-db8c-4bd4-be6d-ed437338485f/dqc_reference
[2023-06-29 14:34:42,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:34:42,967] [INFO] Task started: Prodigal
[2023-06-29 14:34:42,968] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6037173-2f2c-4dcf-b8c9-99963e4990a0/GCA_023708265.1_ASM2370826v1_genomic.fna.gz | prodigal -d GCA_023708265.1_ASM2370826v1_genomic.fna/cds.fna -a GCA_023708265.1_ASM2370826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:34:55,170] [INFO] Task succeeded: Prodigal
[2023-06-29 14:34:55,170] [INFO] Task started: HMMsearch
[2023-06-29 14:34:55,170] [INFO] Running command: hmmsearch --tblout GCA_023708265.1_ASM2370826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga46430c0-db8c-4bd4-be6d-ed437338485f/dqc_reference/reference_markers.hmm GCA_023708265.1_ASM2370826v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:34:55,390] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:34:55,392] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc6037173-2f2c-4dcf-b8c9-99963e4990a0/GCA_023708265.1_ASM2370826v1_genomic.fna.gz]
[2023-06-29 14:34:55,413] [INFO] Query marker FASTA was written to GCA_023708265.1_ASM2370826v1_genomic.fna/markers.fasta
[2023-06-29 14:34:55,414] [INFO] Task started: Blastn
[2023-06-29 14:34:55,414] [INFO] Running command: blastn -query GCA_023708265.1_ASM2370826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga46430c0-db8c-4bd4-be6d-ed437338485f/dqc_reference/reference_markers.fasta -out GCA_023708265.1_ASM2370826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:34:55,990] [INFO] Task succeeded: Blastn
[2023-06-29 14:34:55,995] [INFO] Selected 24 target genomes.
[2023-06-29 14:34:55,996] [INFO] Target genome list was writen to GCA_023708265.1_ASM2370826v1_genomic.fna/target_genomes.txt
[2023-06-29 14:34:56,001] [INFO] Task started: fastANI
[2023-06-29 14:34:56,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6037173-2f2c-4dcf-b8c9-99963e4990a0/GCA_023708265.1_ASM2370826v1_genomic.fna.gz --refList GCA_023708265.1_ASM2370826v1_genomic.fna/target_genomes.txt --output GCA_023708265.1_ASM2370826v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:35:12,819] [INFO] Task succeeded: fastANI
[2023-06-29 14:35:12,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga46430c0-db8c-4bd4-be6d-ed437338485f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:35:12,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga46430c0-db8c-4bd4-be6d-ed437338485f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:35:12,836] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:35:12,836] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:35:12,836] [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 shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	82.6202	115	705	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	82.5992	116	705	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	78.997	113	705	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	77.9081	115	705	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	77.2495	69	705	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	77.0318	91	705	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	76.9939	110	705	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.7431	73	705	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.6764	70	705	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	76.6696	71	705	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.6488	62	705	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	76.4632	64	705	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:35:12,839] [INFO] DFAST Taxonomy check result was written to GCA_023708265.1_ASM2370826v1_genomic.fna/tc_result.tsv
[2023-06-29 14:35:12,839] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:35:12,840] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:35:12,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga46430c0-db8c-4bd4-be6d-ed437338485f/dqc_reference/checkm_data
[2023-06-29 14:35:12,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:35:12,865] [INFO] Task started: CheckM
[2023-06-29 14:35:12,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708265.1_ASM2370826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708265.1_ASM2370826v1_genomic.fna/checkm_input GCA_023708265.1_ASM2370826v1_genomic.fna/checkm_result
[2023-06-29 14:35:49,551] [INFO] Task succeeded: CheckM
[2023-06-29 14:35:49,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:35:49,574] [INFO] ===== Completeness check finished =====
[2023-06-29 14:35:49,574] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:35:49,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708265.1_ASM2370826v1_genomic.fna/markers.fasta)
[2023-06-29 14:35:49,575] [INFO] Task started: Blastn
[2023-06-29 14:35:49,575] [INFO] Running command: blastn -query GCA_023708265.1_ASM2370826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga46430c0-db8c-4bd4-be6d-ed437338485f/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708265.1_ASM2370826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:35:50,331] [INFO] Task succeeded: Blastn
[2023-06-29 14:35:50,335] [INFO] Selected 13 target genomes.
[2023-06-29 14:35:50,336] [INFO] Target genome list was writen to GCA_023708265.1_ASM2370826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:35:50,345] [INFO] Task started: fastANI
[2023-06-29 14:35:50,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6037173-2f2c-4dcf-b8c9-99963e4990a0/GCA_023708265.1_ASM2370826v1_genomic.fna.gz --refList GCA_023708265.1_ASM2370826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708265.1_ASM2370826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:35:57,194] [INFO] Task succeeded: fastANI
[2023-06-29 14:35:57,207] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:35:57,207] [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_900104605.1	s__Tidjanibacter inops_A	99.1434	653	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	99.31	98.92	0.96	0.89	16	conclusive
GCA_019114205.1	s__Tidjanibacter gallistercoris	83.1099	472	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577285.1	s__Tidjanibacter sp910577285	82.5979	478	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116245.1	s__Tidjanibacter faecipullorum	79.1021	252	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542505.1	s__Alistipes stercorigallinarum	77.6646	80	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCF_000154465.1	s__Alistipes putredinis	77.2495	69	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.94	97.62	0.91	0.76	28	-
GCA_014982715.1	s__DSM-108975 sp014982715	77.0179	109	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576555.1	s__Alistipes sp910576555	76.9028	92	705	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	76.6426	52	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.89	97.88	0.91	0.90	3	-
GCA_900549685.1	s__Alistipes_A sp900549685	76.0659	50	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:35:57,209] [INFO] GTDB search result was written to GCA_023708265.1_ASM2370826v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:35:57,210] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:35:57,216] [INFO] DFAST_QC result json was written to GCA_023708265.1_ASM2370826v1_genomic.fna/dqc_result.json
[2023-06-29 14:35:57,216] [INFO] DFAST_QC completed!
[2023-06-29 14:35:57,216] [INFO] Total running time: 0h1m16s