[2023-06-28 02:21:48,773] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:21:48,775] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:21:48,775] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c74cd26-839c-4d34-9dd3-a1c4aff13c86/dqc_reference
[2023-06-28 02:21:50,161] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:21:50,162] [INFO] Task started: Prodigal
[2023-06-28 02:21:50,163] [INFO] Running command: gunzip -c /var/lib/cwl/stgf18b3d9b-4cb2-43cb-af61-96875a144bc8/GCA_944392995.1_BRZ_QV_bin83_genomic.fna.gz | prodigal -d GCA_944392995.1_BRZ_QV_bin83_genomic.fna/cds.fna -a GCA_944392995.1_BRZ_QV_bin83_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:21:54,094] [INFO] Task succeeded: Prodigal
[2023-06-28 02:21:54,095] [INFO] Task started: HMMsearch
[2023-06-28 02:21:54,095] [INFO] Running command: hmmsearch --tblout GCA_944392995.1_BRZ_QV_bin83_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c74cd26-839c-4d34-9dd3-a1c4aff13c86/dqc_reference/reference_markers.hmm GCA_944392995.1_BRZ_QV_bin83_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:21:54,382] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:21:54,383] [INFO] Found 6/6 markers.
[2023-06-28 02:21:54,421] [INFO] Query marker FASTA was written to GCA_944392995.1_BRZ_QV_bin83_genomic.fna/markers.fasta
[2023-06-28 02:21:54,422] [INFO] Task started: Blastn
[2023-06-28 02:21:54,422] [INFO] Running command: blastn -query GCA_944392995.1_BRZ_QV_bin83_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c74cd26-839c-4d34-9dd3-a1c4aff13c86/dqc_reference/reference_markers.fasta -out GCA_944392995.1_BRZ_QV_bin83_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:21:55,050] [INFO] Task succeeded: Blastn
[2023-06-28 02:21:55,055] [INFO] Selected 12 target genomes.
[2023-06-28 02:21:55,056] [INFO] Target genome list was writen to GCA_944392995.1_BRZ_QV_bin83_genomic.fna/target_genomes.txt
[2023-06-28 02:21:55,058] [INFO] Task started: fastANI
[2023-06-28 02:21:55,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18b3d9b-4cb2-43cb-af61-96875a144bc8/GCA_944392995.1_BRZ_QV_bin83_genomic.fna.gz --refList GCA_944392995.1_BRZ_QV_bin83_genomic.fna/target_genomes.txt --output GCA_944392995.1_BRZ_QV_bin83_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:22:04,532] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:04,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c74cd26-839c-4d34-9dd3-a1c4aff13c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:22:04,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c74cd26-839c-4d34-9dd3-a1c4aff13c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:22:04,544] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:22:04,544] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:22:04,544] [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
Brachyspira pilosicoli	strain=P43/6/78	GCA_000325665.1	52584	52584	type	True	91.1561	673	800	95	below_threshold
Brachyspira intermedia	strain=PWS/A	GCA_000223215.1	84377	84377	type	True	81.2387	486	800	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_000383255.1	159	159	type	True	80.7195	486	800	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_001013005.1	159	159	type	True	80.7014	481	800	95	below_threshold
Brachyspira suanatina	strain=AN4859/03	GCA_001049755.1	381802	381802	type	True	80.6296	468	800	95	below_threshold
Brachyspira hyodysenteriae	strain=B-78	GCA_001676785.2	159	159	type	True	80.5864	500	800	95	below_threshold
Brachyspira innocens	strain=B256	GCA_000384655.1	13264	13264	type	True	80.4855	493	800	95	below_threshold
Brachyspira murdochii	strain=DSM 12563	GCA_000092845.1	84378	84378	type	True	80.2901	487	800	95	below_threshold
Brachyspira alvinipulli	strain=ATCC 51933	GCA_000518245.1	84379	84379	type	True	80.1844	457	800	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_001746225.1	1287055	1287055	type	True	80.152	476	800	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_002214805.1	1287055	1287055	type	True	80.1375	479	800	95	below_threshold
Brachyspira aalborgi	strain=513A	GCA_008016455.1	29522	29522	type	True	76.235	226	800	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:22:04,546] [INFO] DFAST Taxonomy check result was written to GCA_944392995.1_BRZ_QV_bin83_genomic.fna/tc_result.tsv
[2023-06-28 02:22:04,547] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:22:04,547] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:22:04,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c74cd26-839c-4d34-9dd3-a1c4aff13c86/dqc_reference/checkm_data
[2023-06-28 02:22:04,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:22:04,585] [INFO] Task started: CheckM
[2023-06-28 02:22:04,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944392995.1_BRZ_QV_bin83_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944392995.1_BRZ_QV_bin83_genomic.fna/checkm_input GCA_944392995.1_BRZ_QV_bin83_genomic.fna/checkm_result
[2023-06-28 02:22:25,615] [INFO] Task succeeded: CheckM
[2023-06-28 02:22:25,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.99%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 02:22:25,641] [INFO] ===== Completeness check finished =====
[2023-06-28 02:22:25,641] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:22:25,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944392995.1_BRZ_QV_bin83_genomic.fna/markers.fasta)
[2023-06-28 02:22:25,642] [INFO] Task started: Blastn
[2023-06-28 02:22:25,642] [INFO] Running command: blastn -query GCA_944392995.1_BRZ_QV_bin83_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c74cd26-839c-4d34-9dd3-a1c4aff13c86/dqc_reference/reference_markers_gtdb.fasta -out GCA_944392995.1_BRZ_QV_bin83_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:26,544] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:26,548] [INFO] Selected 12 target genomes.
[2023-06-28 02:22:26,549] [INFO] Target genome list was writen to GCA_944392995.1_BRZ_QV_bin83_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:22:26,565] [INFO] Task started: fastANI
[2023-06-28 02:22:26,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18b3d9b-4cb2-43cb-af61-96875a144bc8/GCA_944392995.1_BRZ_QV_bin83_genomic.fna.gz --refList GCA_944392995.1_BRZ_QV_bin83_genomic.fna/target_genomes_gtdb.txt --output GCA_944392995.1_BRZ_QV_bin83_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:22:36,827] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:36,842] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:22:36,842] [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_000325665.1	s__Brachyspira pilosicoli	91.1384	674	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	98.38	97.84	0.95	0.91	19	-
GCF_008016535.1	s__Brachyspira pilosicoli_A	91.0817	618	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755885.1	s__Brachyspira sp009755885	90.9278	661	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001049755.1	s__Brachyspira suanatina	80.5963	470	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676785.2	s__Brachyspira hyodysenteriae	80.5494	503	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.16	98.93	0.98	0.95	58	-
GCF_000384655.1	s__Brachyspira innocens	80.4641	495	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092845.1	s__Brachyspira murdochii	80.3024	488	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	97.81	96.97	0.94	0.93	3	-
GCF_002379365.1	s__Brachyspira sp002379365	80.227	479	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214805.1	s__Brachyspira hampsonii	80.1224	480	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.94	99.90	1.00	1.00	3	-
GCF_000518245.1	s__Brachyspira alvinipulli	80.121	464	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746205.1	s__Brachyspira hampsonii_B	80.1086	473	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316195.1	s__Brachyspira hampsonii_C	80.0016	460	800	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	98.70	97.44	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-28 02:22:36,844] [INFO] GTDB search result was written to GCA_944392995.1_BRZ_QV_bin83_genomic.fna/result_gtdb.tsv
[2023-06-28 02:22:36,845] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:22:36,850] [INFO] DFAST_QC result json was written to GCA_944392995.1_BRZ_QV_bin83_genomic.fna/dqc_result.json
[2023-06-28 02:22:36,850] [INFO] DFAST_QC completed!
[2023-06-28 02:22:36,850] [INFO] Total running time: 0h0m48s