[2023-06-28 12:34:08,082] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:34:08,097] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:34:08,097] [INFO] DQC Reference Directory: /var/lib/cwl/stgc888a87a-926d-4df5-8e97-d5ac06560502/dqc_reference
[2023-06-28 12:34:09,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:34:09,542] [INFO] Task started: Prodigal
[2023-06-28 12:34:09,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b987103-a0fd-4435-b2d8-73f51965b025/GCA_944320615.1_BRZ_GF_bin5_genomic.fna.gz | prodigal -d GCA_944320615.1_BRZ_GF_bin5_genomic.fna/cds.fna -a GCA_944320615.1_BRZ_GF_bin5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:34:16,985] [INFO] Task succeeded: Prodigal
[2023-06-28 12:34:16,986] [INFO] Task started: HMMsearch
[2023-06-28 12:34:16,986] [INFO] Running command: hmmsearch --tblout GCA_944320615.1_BRZ_GF_bin5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc888a87a-926d-4df5-8e97-d5ac06560502/dqc_reference/reference_markers.hmm GCA_944320615.1_BRZ_GF_bin5_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:34:17,224] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:34:17,225] [INFO] Found 6/6 markers.
[2023-06-28 12:34:17,279] [INFO] Query marker FASTA was written to GCA_944320615.1_BRZ_GF_bin5_genomic.fna/markers.fasta
[2023-06-28 12:34:17,279] [INFO] Task started: Blastn
[2023-06-28 12:34:17,280] [INFO] Running command: blastn -query GCA_944320615.1_BRZ_GF_bin5_genomic.fna/markers.fasta -db /var/lib/cwl/stgc888a87a-926d-4df5-8e97-d5ac06560502/dqc_reference/reference_markers.fasta -out GCA_944320615.1_BRZ_GF_bin5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:17,941] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:17,945] [INFO] Selected 10 target genomes.
[2023-06-28 12:34:17,945] [INFO] Target genome list was writen to GCA_944320615.1_BRZ_GF_bin5_genomic.fna/target_genomes.txt
[2023-06-28 12:34:17,946] [INFO] Task started: fastANI
[2023-06-28 12:34:17,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b987103-a0fd-4435-b2d8-73f51965b025/GCA_944320615.1_BRZ_GF_bin5_genomic.fna.gz --refList GCA_944320615.1_BRZ_GF_bin5_genomic.fna/target_genomes.txt --output GCA_944320615.1_BRZ_GF_bin5_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:34:22,845] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:22,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc888a87a-926d-4df5-8e97-d5ac06560502/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:34:22,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc888a87a-926d-4df5-8e97-d5ac06560502/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:34:22,862] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 12:34:22,863] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-28 12:34:22,863] [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
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	97.4221	647	755	95	inconclusive
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	95.992	651	755	95	inconclusive
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	81.7665	380	755	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	81.6852	365	755	95	below_threshold
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	81.5456	351	755	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.5626	246	755	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.5366	266	755	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.4906	263	755	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.9917	209	755	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.955	200	755	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:34:22,865] [INFO] DFAST Taxonomy check result was written to GCA_944320615.1_BRZ_GF_bin5_genomic.fna/tc_result.tsv
[2023-06-28 12:34:22,866] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:34:22,866] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:34:22,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc888a87a-926d-4df5-8e97-d5ac06560502/dqc_reference/checkm_data
[2023-06-28 12:34:22,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:34:22,900] [INFO] Task started: CheckM
[2023-06-28 12:34:22,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320615.1_BRZ_GF_bin5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320615.1_BRZ_GF_bin5_genomic.fna/checkm_input GCA_944320615.1_BRZ_GF_bin5_genomic.fna/checkm_result
[2023-06-28 12:34:49,127] [INFO] Task succeeded: CheckM
[2023-06-28 12:34:49,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:34:49,153] [INFO] ===== Completeness check finished =====
[2023-06-28 12:34:49,153] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:34:49,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320615.1_BRZ_GF_bin5_genomic.fna/markers.fasta)
[2023-06-28 12:34:49,154] [INFO] Task started: Blastn
[2023-06-28 12:34:49,154] [INFO] Running command: blastn -query GCA_944320615.1_BRZ_GF_bin5_genomic.fna/markers.fasta -db /var/lib/cwl/stgc888a87a-926d-4df5-8e97-d5ac06560502/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320615.1_BRZ_GF_bin5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:50,289] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:50,293] [INFO] Selected 14 target genomes.
[2023-06-28 12:34:50,293] [INFO] Target genome list was writen to GCA_944320615.1_BRZ_GF_bin5_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:34:50,307] [INFO] Task started: fastANI
[2023-06-28 12:34:50,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b987103-a0fd-4435-b2d8-73f51965b025/GCA_944320615.1_BRZ_GF_bin5_genomic.fna.gz --refList GCA_944320615.1_BRZ_GF_bin5_genomic.fna/target_genomes_gtdb.txt --output GCA_944320615.1_BRZ_GF_bin5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:34:56,673] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:56,685] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:34:56,685] [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_000311845.1	s__Enorma massiliensis	97.4221	647	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	97.43	96.04	0.89	0.84	11	conclusive
GCF_902150035.1	s__Enorma burkinafasonensis	81.6852	365	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333815.1	s__Enorma sp000333815	81.6654	379	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCA_900538305.1	s__Enorma sp900538305	81.5904	344	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186505.1	s__Enorma phocaeensis	81.5457	351	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210055.1	s__Enorma sp900751795	81.2252	285	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	99.77	99.77	0.84	0.84	2	-
GCF_002159335.1	s__Coprousia sp002159335	80.3313	311	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	98.10	98.10	0.94	0.94	2	-
GCF_016901575.1	s__Limicola phocaeensis_A	80.2387	319	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900375.1	s__Collinsella sp002305035	80.1342	302	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCF_002160065.1	s__Limicola sp002160065	80.0769	306	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715125.1	s__Coprousia avicola	80.0567	299	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161805.1	s__Coprousia sp002161805	79.9424	285	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210085.1	s__Collinsella sp905210085	78.6118	189	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549355.1	s__Collinsella sp900549355	78.3747	157	755	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.84	99.84	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:34:56,688] [INFO] GTDB search result was written to GCA_944320615.1_BRZ_GF_bin5_genomic.fna/result_gtdb.tsv
[2023-06-28 12:34:56,688] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:34:56,695] [INFO] DFAST_QC result json was written to GCA_944320615.1_BRZ_GF_bin5_genomic.fna/dqc_result.json
[2023-06-28 12:34:56,695] [INFO] DFAST_QC completed!
[2023-06-28 12:34:56,695] [INFO] Total running time: 0h0m49s