[2024-01-24 13:18:41,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c3294c9-f7fe-48a9-b8fa-30a778d0139e/dqc_reference
[2024-01-24 13:18:42,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,673] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg835bdab1-fa26-495f-842c-2385c41f86f7/GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna.gz | prodigal -d GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/cds.fna -a GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:50,354] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:50,355] [INFO] Task started: HMMsearch
[2024-01-24 13:18:50,355] [INFO] Running command: hmmsearch --tblout GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c3294c9-f7fe-48a9-b8fa-30a778d0139e/dqc_reference/reference_markers.hmm GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:50,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:50,582] [INFO] Found 6/6 markers.
[2024-01-24 13:18:50,608] [INFO] Query marker FASTA was written to GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/markers.fasta
[2024-01-24 13:18:50,608] [INFO] Task started: Blastn
[2024-01-24 13:18:50,608] [INFO] Running command: blastn -query GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3294c9-f7fe-48a9-b8fa-30a778d0139e/dqc_reference/reference_markers.fasta -out GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:51,348] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:51,352] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:51,352] [INFO] Target genome list was writen to GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:51,368] [INFO] Task started: fastANI
[2024-01-24 13:18:51,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg835bdab1-fa26-495f-842c-2385c41f86f7/GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna.gz --refList GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/target_genomes.txt --output GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:57,279] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:57,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c3294c9-f7fe-48a9-b8fa-30a778d0139e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:57,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c3294c9-f7fe-48a9-b8fa-30a778d0139e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:57,296] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:57,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:57,297] [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 tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	99.9999	821	822	95	conclusive
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	81.4994	293	822	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.7804	287	822	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.7076	284	822	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	80.692	273	822	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	79.8704	239	822	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	79.8584	234	822	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	79.7613	238	822	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.552	188	822	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.2746	252	822	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	79.2253	222	822	95	below_threshold
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	79.0114	210	822	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.6254	153	822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:57,300] [INFO] DFAST Taxonomy check result was written to GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:57,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:57,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:57,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c3294c9-f7fe-48a9-b8fa-30a778d0139e/dqc_reference/checkm_data
[2024-01-24 13:18:57,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:57,330] [INFO] Task started: CheckM
[2024-01-24 13:18:57,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/checkm_input GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/checkm_result
[2024-01-24 13:19:24,587] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:24,588] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:24,603] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:24,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:24,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/markers.fasta)
[2024-01-24 13:19:24,604] [INFO] Task started: Blastn
[2024-01-24 13:19:24,604] [INFO] Running command: blastn -query GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3294c9-f7fe-48a9-b8fa-30a778d0139e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,044] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,048] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:26,048] [INFO] Target genome list was writen to GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:26,084] [INFO] Task started: fastANI
[2024-01-24 13:19:26,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg835bdab1-fa26-495f-842c-2385c41f86f7/GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna.gz --refList GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:33,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:33,398] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:33,398] [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_000225705.1	s__Collinsella tanakaei	99.9999	821	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.30	95.17	0.91	0.86	6	conclusive
GCA_900548365.1	s__Collinsella sp900548365	81.733	328	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCF_008014645.1	s__Collinsella sp008014645	81.7273	333	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
GCF_900119895.1	s__Collinsella phocaeensis	81.4352	290	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCF_003479805.1	s__Collinsella sp003479805	80.6886	280	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.77	98.33	0.94	0.90	6	-
GCA_900551665.1	s__Collinsella sp900551665	80.5964	224	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555555.1	s__Collinsella sp900555555	80.4743	116	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555585.1	s__Collinsella sp900555585	80.2748	132	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016900375.1	s__Collinsella sp002305035	79.8114	291	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCF_016902615.1	s__Collinsella tanakaei_A	79.6723	263	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.95	98.95	0.92	0.92	2	-
GCA_900544655.1	s__Parolsenella sp900544655	79.4293	102	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.93	99.93	0.89	0.89	2	-
GCA_015062655.1	s__Collinsella sp015062655	79.3607	229	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551185.1	s__Collinsella sp900551185	79.283	164	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0395	95.41	95.41	0.89	0.89	2	-
GCA_019117005.1	s__Collinsella stercoripullorum	79.2829	285	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_902150035.1	s__Enorma burkinafasonensis	79.276	252	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542555.1	s__Collinsella sp900542555	79.2145	219	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554325.1	s__Collinsella sp900554325	79.2007	196	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437815.1	s__Collinsella sp002437815	78.9326	218	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555745.1	s__Collinsella sp900555745	78.6252	115	822	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,400] [INFO] GTDB search result was written to GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:33,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:33,405] [INFO] DFAST_QC result json was written to GCF_000225705.1_Coll_tana_YIT_12063_V1_genomic.fna/dqc_result.json
[2024-01-24 13:19:33,405] [INFO] DFAST_QC completed!
[2024-01-24 13:19:33,405] [INFO] Total running time: 0h0m52s