[2023-06-04 22:31:47,404] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:31:47,409] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:31:47,409] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1e7431d-53bc-4af8-a3f7-d8976554e9cc/dqc_reference
[2023-06-04 22:31:49,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:31:49,715] [INFO] Task started: Prodigal
[2023-06-04 22:31:49,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg52618ffd-e78a-4b6f-9ce0-48df41cb8c16/GCA_902837005.1_MGYG-HGUT-04926_genomic.fna.gz | prodigal -d GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/cds.fna -a GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:31:52,651] [INFO] Task succeeded: Prodigal
[2023-06-04 22:31:52,652] [INFO] Task started: HMMsearch
[2023-06-04 22:31:52,652] [INFO] Running command: hmmsearch --tblout GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1e7431d-53bc-4af8-a3f7-d8976554e9cc/dqc_reference/reference_markers.hmm GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:31:52,850] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:31:52,851] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg52618ffd-e78a-4b6f-9ce0-48df41cb8c16/GCA_902837005.1_MGYG-HGUT-04926_genomic.fna.gz]
[2023-06-04 22:31:52,868] [INFO] Query marker FASTA was written to GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/markers.fasta
[2023-06-04 22:31:52,868] [INFO] Task started: Blastn
[2023-06-04 22:31:52,868] [INFO] Running command: blastn -query GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e7431d-53bc-4af8-a3f7-d8976554e9cc/dqc_reference/reference_markers.fasta -out GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:31:53,913] [INFO] Task succeeded: Blastn
[2023-06-04 22:31:53,918] [INFO] Selected 11 target genomes.
[2023-06-04 22:31:53,919] [INFO] Target genome list was writen to GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/target_genomes.txt
[2023-06-04 22:31:53,926] [INFO] Task started: fastANI
[2023-06-04 22:31:53,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg52618ffd-e78a-4b6f-9ce0-48df41cb8c16/GCA_902837005.1_MGYG-HGUT-04926_genomic.fna.gz --refList GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/target_genomes.txt --output GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:31:58,942] [INFO] Task succeeded: fastANI
[2023-06-04 22:31:58,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1e7431d-53bc-4af8-a3f7-d8976554e9cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:31:58,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1e7431d-53bc-4af8-a3f7-d8976554e9cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:31:58,949] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:31:58,949] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 22:31:58,949] [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
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.8491	211	230	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.7535	213	230	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.7317	213	230	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.2542	85	230	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.5488	88	230	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.2133	89	230	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:31:58,951] [INFO] DFAST Taxonomy check result was written to GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/tc_result.tsv
[2023-06-04 22:31:58,952] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:31:58,952] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:31:58,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1e7431d-53bc-4af8-a3f7-d8976554e9cc/dqc_reference/checkm_data
[2023-06-04 22:31:58,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:31:58,972] [INFO] Task started: CheckM
[2023-06-04 22:31:58,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/checkm_input GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/checkm_result
[2023-06-04 22:32:15,136] [INFO] Task succeeded: CheckM
[2023-06-04 22:32:15,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:32:15,157] [INFO] ===== Completeness check finished =====
[2023-06-04 22:32:15,157] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:32:15,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/markers.fasta)
[2023-06-04 22:32:15,158] [INFO] Task started: Blastn
[2023-06-04 22:32:15,158] [INFO] Running command: blastn -query GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e7431d-53bc-4af8-a3f7-d8976554e9cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:32:15,644] [INFO] Task succeeded: Blastn
[2023-06-04 22:32:15,648] [INFO] Selected 15 target genomes.
[2023-06-04 22:32:15,648] [INFO] Target genome list was writen to GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:32:15,716] [INFO] Task started: fastANI
[2023-06-04 22:32:15,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg52618ffd-e78a-4b6f-9ce0-48df41cb8c16/GCA_902837005.1_MGYG-HGUT-04926_genomic.fna.gz --refList GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/target_genomes_gtdb.txt --output GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:32:20,725] [INFO] Task succeeded: fastANI
[2023-06-04 22:32:20,740] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 22:32:20,740] [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_008671135.1	s__Collinsella aerofaciens_J	94.9158	199	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_900549025.1	s__Collinsella sp900549025	94.6382	179	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0692	97.49	95.13	0.83	0.77	3	-
GCA_900545055.1	s__Collinsella sp900545055	94.0666	182	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541645.1	s__Collinsella sp900541645	93.7722	196	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.32	95.32	0.85	0.85	2	-
GCF_003459245.1	s__Collinsella sp003459245	93.6936	199	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.00	95.31	0.88	0.84	13	-
GCA_900756765.1	s__Collinsella sp900756765	93.6656	172	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543945.1	s__Collinsella sp900543945	93.4497	190	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.4468	97.82	95.67	0.91	0.87	3	-
GCA_900540945.1	s__Collinsella sp900540945	93.4076	197	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.51	95.33	0.85	0.84	5	-
GCA_900761945.1	s__Collinsella sp900761945	93.3152	164	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767675.1	s__Collinsella sp900767675	92.948	193	230	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 22:32:20,745] [INFO] GTDB search result was written to GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/result_gtdb.tsv
[2023-06-04 22:32:20,746] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:32:20,750] [INFO] DFAST_QC result json was written to GCA_902837005.1_MGYG-HGUT-04926_genomic.fna/dqc_result.json
[2023-06-04 22:32:20,750] [INFO] DFAST_QC completed!
[2023-06-04 22:32:20,750] [INFO] Total running time: 0h0m33s