[2023-06-29 17:18:38,254] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:18:38,258] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:18:38,258] [INFO] DQC Reference Directory: /var/lib/cwl/stgac6403fa-29b0-4bb8-b619-8874f5faf828/dqc_reference
[2023-06-29 17:18:39,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:18:39,563] [INFO] Task started: Prodigal
[2023-06-29 17:18:39,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bd6c006-61a4-447c-b592-47fc83d4bb0a/GCA_023708985.1_ASM2370898v1_genomic.fna.gz | prodigal -d GCA_023708985.1_ASM2370898v1_genomic.fna/cds.fna -a GCA_023708985.1_ASM2370898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:18:46,375] [INFO] Task succeeded: Prodigal
[2023-06-29 17:18:46,376] [INFO] Task started: HMMsearch
[2023-06-29 17:18:46,376] [INFO] Running command: hmmsearch --tblout GCA_023708985.1_ASM2370898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac6403fa-29b0-4bb8-b619-8874f5faf828/dqc_reference/reference_markers.hmm GCA_023708985.1_ASM2370898v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:18:46,657] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:18:46,658] [INFO] Found 6/6 markers.
[2023-06-29 17:18:46,685] [INFO] Query marker FASTA was written to GCA_023708985.1_ASM2370898v1_genomic.fna/markers.fasta
[2023-06-29 17:18:46,685] [INFO] Task started: Blastn
[2023-06-29 17:18:46,685] [INFO] Running command: blastn -query GCA_023708985.1_ASM2370898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac6403fa-29b0-4bb8-b619-8874f5faf828/dqc_reference/reference_markers.fasta -out GCA_023708985.1_ASM2370898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:18:47,430] [INFO] Task succeeded: Blastn
[2023-06-29 17:18:47,433] [INFO] Selected 14 target genomes.
[2023-06-29 17:18:47,434] [INFO] Target genome list was writen to GCA_023708985.1_ASM2370898v1_genomic.fna/target_genomes.txt
[2023-06-29 17:18:47,435] [INFO] Task started: fastANI
[2023-06-29 17:18:47,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bd6c006-61a4-447c-b592-47fc83d4bb0a/GCA_023708985.1_ASM2370898v1_genomic.fna.gz --refList GCA_023708985.1_ASM2370898v1_genomic.fna/target_genomes.txt --output GCA_023708985.1_ASM2370898v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:18:54,289] [INFO] Task succeeded: fastANI
[2023-06-29 17:18:54,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac6403fa-29b0-4bb8-b619-8874f5faf828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:18:54,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac6403fa-29b0-4bb8-b619-8874f5faf828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:18:54,301] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:18:54,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 17:18:54,301] [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	93.8956	608	713	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	93.8608	600	713	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	93.8263	613	713	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.2868	240	713	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.0661	265	713	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.0513	274	713	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.9187	242	713	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.7452	233	713	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.6863	239	713	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.4443	247	713	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.0682	194	713	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.9848	221	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 17:18:54,305] [INFO] DFAST Taxonomy check result was written to GCA_023708985.1_ASM2370898v1_genomic.fna/tc_result.tsv
[2023-06-29 17:18:54,306] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:18:54,306] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:18:54,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac6403fa-29b0-4bb8-b619-8874f5faf828/dqc_reference/checkm_data
[2023-06-29 17:18:54,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:18:54,341] [INFO] Task started: CheckM
[2023-06-29 17:18:54,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708985.1_ASM2370898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708985.1_ASM2370898v1_genomic.fna/checkm_input GCA_023708985.1_ASM2370898v1_genomic.fna/checkm_result
[2023-06-29 17:19:20,037] [INFO] Task succeeded: CheckM
[2023-06-29 17:19:20,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:19:20,082] [INFO] ===== Completeness check finished =====
[2023-06-29 17:19:20,082] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:19:20,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708985.1_ASM2370898v1_genomic.fna/markers.fasta)
[2023-06-29 17:19:20,083] [INFO] Task started: Blastn
[2023-06-29 17:19:20,084] [INFO] Running command: blastn -query GCA_023708985.1_ASM2370898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac6403fa-29b0-4bb8-b619-8874f5faf828/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708985.1_ASM2370898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:19:21,459] [INFO] Task succeeded: Blastn
[2023-06-29 17:19:21,463] [INFO] Selected 34 target genomes.
[2023-06-29 17:19:21,463] [INFO] Target genome list was writen to GCA_023708985.1_ASM2370898v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:19:21,476] [INFO] Task started: fastANI
[2023-06-29 17:19:21,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bd6c006-61a4-447c-b592-47fc83d4bb0a/GCA_023708985.1_ASM2370898v1_genomic.fna.gz --refList GCA_023708985.1_ASM2370898v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708985.1_ASM2370898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:19:37,065] [INFO] Task succeeded: fastANI
[2023-06-29 17:19:37,094] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 17:19:37,095] [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_900543945.1	s__Collinsella sp900543945	94.7128	510	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.4468	97.82	95.67	0.91	0.87	3	-
GCA_900542175.1	s__Collinsella sp900542175	94.7017	570	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0662	N/A	N/A	N/A	N/A	1	-
GCA_905215065.1	s__Collinsella sp905215065	94.6739	582	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1686	95.36	95.20	0.87	0.82	13	-
GCF_003436275.1	s__Collinsella sp003436275	94.5971	610	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.89	95.08	0.88	0.83	16	-
GCA_900542325.1	s__Collinsella sp900542325	94.5909	572	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900768435.1	s__Collinsella sp900768435	94.5279	601	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551195.1	s__Collinsella sp900551195	94.4834	387	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0222	96.98	95.23	0.92	0.90	4	-
GCA_900544755.1	s__Collinsella sp900544755	94.4552	520	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0835	100.00	100.00	0.97	0.97	2	-
GCA_900542275.1	s__Collinsella sp900542275	94.4515	569	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.82	0.82	2	-
GCA_900542945.1	s__Collinsella sp900542945	94.4467	558	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1063	100.00	100.00	0.99	0.99	2	-
GCA_905215115.1	s__Collinsella sp905215115	94.4168	500	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214435.1	s__Collinsella sp905214435	94.4065	551	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.174	95.31	95.19	0.87	0.85	5	-
GCA_900757235.1	s__Collinsella sp900757235	94.376	459	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552395.1	s__Collinsella sp900552395	94.2958	424	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.15	N/A	N/A	N/A	N/A	1	-
GCA_900551205.1	s__Collinsella sp900551205	94.2305	424	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.45	95.34	0.91	0.90	4	-
GCA_900761995.1	s__Collinsella sp900761995	94.1744	514	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757615.1	s__Collinsella sp900757615	94.0098	566	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544865.1	s__Collinsella sp900544865	93.9733	568	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541855.1	s__Collinsella sp900541855	93.9682	564	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0387	95.91	95.91	0.87	0.87	2	-
GCA_900541135.1	s__Collinsella sp900541135	93.922	579	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010509075.1	s__Collinsella aerofaciens	93.9005	609	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.99	99.98	1.00	0.99	4	-
GCA_900543515.1	s__Collinsella sp900543515	93.8475	552	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1148	100.00	100.00	0.98	0.98	2	-
GCF_015555045.1	s__Collinsella aerofaciens_W	93.7689	584	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216145.1	s__Collinsella sp905216145	93.7072	598	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543605.1	s__Collinsella sp900543605	93.697	533	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760905.1	s__Collinsella sp900760905	93.6568	551	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.28	95.28	0.83	0.83	2	-
GCA_018376905.1	s__Collinsella sp018376905	93.5988	582	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552755.1	s__Collinsella sp900552755	93.5705	446	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541885.1	s__Collinsella sp900541885	93.5617	589	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905215755.1	s__Collinsella sp905215755	93.4177	536	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0833	N/A	N/A	N/A	N/A	1	-
GCA_900765115.1	s__Collinsella sp900765115	93.3121	556	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552295.1	s__Collinsella sp900552295	93.1342	394	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015557435.1	s__Collinsella aerofaciens_Z	93.1047	590	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765185.1	s__Collinsella sp900765185	93.0614	418	713	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 17:19:37,097] [INFO] GTDB search result was written to GCA_023708985.1_ASM2370898v1_genomic.fna/result_gtdb.tsv
[2023-06-29 17:19:37,098] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:19:37,107] [INFO] DFAST_QC result json was written to GCA_023708985.1_ASM2370898v1_genomic.fna/dqc_result.json
[2023-06-29 17:19:37,107] [INFO] DFAST_QC completed!
[2023-06-29 17:19:37,107] [INFO] Total running time: 0h0m59s