[2023-06-17 12:34:36,419] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:34:36,422] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:34:36,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg744079dc-cc3b-4d91-ba31-74b97874d8b7/dqc_reference
[2023-06-17 12:34:37,625] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:34:37,626] [INFO] Task started: Prodigal
[2023-06-17 12:34:37,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg10a2f3fc-9c67-4486-a7e5-482394ea38c2/GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna.gz | prodigal -d GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/cds.fna -a GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:34:42,155] [INFO] Task succeeded: Prodigal
[2023-06-17 12:34:42,156] [INFO] Task started: HMMsearch
[2023-06-17 12:34:42,156] [INFO] Running command: hmmsearch --tblout GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg744079dc-cc3b-4d91-ba31-74b97874d8b7/dqc_reference/reference_markers.hmm GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:34:42,365] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:34:42,367] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10a2f3fc-9c67-4486-a7e5-482394ea38c2/GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna.gz]
[2023-06-17 12:34:42,387] [INFO] Query marker FASTA was written to GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/markers.fasta
[2023-06-17 12:34:42,388] [INFO] Task started: Blastn
[2023-06-17 12:34:42,388] [INFO] Running command: blastn -query GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/markers.fasta -db /var/lib/cwl/stg744079dc-cc3b-4d91-ba31-74b97874d8b7/dqc_reference/reference_markers.fasta -out GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:34:43,027] [INFO] Task succeeded: Blastn
[2023-06-17 12:34:43,032] [INFO] Selected 10 target genomes.
[2023-06-17 12:34:43,033] [INFO] Target genome list was writen to GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/target_genomes.txt
[2023-06-17 12:34:43,035] [INFO] Task started: fastANI
[2023-06-17 12:34:43,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a2f3fc-9c67-4486-a7e5-482394ea38c2/GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna.gz --refList GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/target_genomes.txt --output GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:34:46,611] [INFO] Task succeeded: fastANI
[2023-06-17 12:34:46,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg744079dc-cc3b-4d91-ba31-74b97874d8b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:34:46,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg744079dc-cc3b-4d91-ba31-74b97874d8b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:34:46,623] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:34:46,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 12:34:46,623] [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=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.6479	262	292	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.6261	265	292	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.6156	265	292	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.0194	109	292	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.7097	106	292	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.5257	107	292	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.4548	117	292	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.4489	114	292	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.2936	103	292	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.9792	94	292	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:34:46,626] [INFO] DFAST Taxonomy check result was written to GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/tc_result.tsv
[2023-06-17 12:34:46,626] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:34:46,627] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:34:46,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg744079dc-cc3b-4d91-ba31-74b97874d8b7/dqc_reference/checkm_data
[2023-06-17 12:34:46,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:34:46,650] [INFO] Task started: CheckM
[2023-06-17 12:34:46,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/checkm_input GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/checkm_result
[2023-06-17 12:35:07,861] [INFO] Task succeeded: CheckM
[2023-06-17 12:35:07,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 15.03%
Strain heterogeneity: 5.26%
--------------------------------------------------------------------------------
[2023-06-17 12:35:07,890] [INFO] ===== Completeness check finished =====
[2023-06-17 12:35:07,891] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:35:07,891] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/markers.fasta)
[2023-06-17 12:35:07,891] [INFO] Task started: Blastn
[2023-06-17 12:35:07,891] [INFO] Running command: blastn -query GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/markers.fasta -db /var/lib/cwl/stg744079dc-cc3b-4d91-ba31-74b97874d8b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:35:08,942] [INFO] Task succeeded: Blastn
[2023-06-17 12:35:08,948] [INFO] Selected 26 target genomes.
[2023-06-17 12:35:08,948] [INFO] Target genome list was writen to GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:35:08,957] [INFO] Task started: fastANI
[2023-06-17 12:35:08,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a2f3fc-9c67-4486-a7e5-482394ea38c2/GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna.gz --refList GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/target_genomes_gtdb.txt --output GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:35:17,118] [INFO] Task succeeded: fastANI
[2023-06-17 12:35:17,143] [INFO] Found 26 fastANI hits (4 hits with ANI > circumscription radius)
[2023-06-17 12:35:17,143] [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_900547345.1	s__Collinsella sp900547345	95.6971	248	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0188	95.15	95.15	0.87	0.87	2	inconclusive
GCA_900541125.1	s__Collinsella sp900541125	95.3188	263	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2242	95.44	95.26	0.87	0.84	10	inconclusive
GCA_900545665.1	s__Collinsella sp900545665	95.3147	252	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1787	95.41	95.41	0.86	0.86	2	inconclusive
GCA_900758845.1	s__Collinsella sp900758845	95.2197	241	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.30	95.30	0.83	0.83	2	inconclusive
GCA_905216045.1	s__Collinsella sp905216045	95.0807	235	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1904	95.27	95.27	0.89	0.89	2	-
GCA_900541145.1	s__Collinsella sp900541145	94.8824	252	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1029	95.25	95.12	0.88	0.86	9	-
GCA_900544995.1	s__Collinsella sp900544995	94.7689	238	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.93	0.93	2	-
GCA_900540935.1	s__Collinsella sp900540935	94.6912	243	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.34	95.21	0.87	0.87	3	-
GCA_018373675.1	s__Collinsella sp018373675	94.6897	252	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	N/A	N/A	N/A	N/A	1	-
GCA_905215835.1	s__Collinsella sp905215835	94.6497	244	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0274	N/A	N/A	N/A	N/A	1	-
GCA_900754525.1	s__Collinsella sp900754525	94.634	234	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0709	95.23	95.09	0.81	0.78	4	-
GCA_900751755.1	s__Collinsella sp900751755	94.5724	238	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.91	99.91	0.92	0.92	2	-
GCA_900544865.1	s__Collinsella sp900544865	94.5145	251	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549745.1	s__Collinsella sp900549745	94.4001	219	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1078	95.40	95.40	0.87	0.87	2	-
GCA_900549025.1	s__Collinsella sp900549025	94.3792	227	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0692	97.49	95.13	0.83	0.77	3	-
GCA_905215945.1	s__Collinsella sp905215945	94.3478	203	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2129	96.29	95.33	0.86	0.77	4	-
GCA_900548515.1	s__Collinsella sp900548515	94.1794	239	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547285.1	s__Collinsella sp900547285	94.1179	226	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018368345.1	s__Collinsella sp018368345	93.9867	260	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761995.1	s__Collinsella sp900761995	93.7614	233	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549535.1	s__Collinsella sp900549535	93.4646	230	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470665.1	s__Collinsella sp003470665	93.3567	242	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900554645.1	s__Collinsella sp900554645	93.2959	113	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548075.1	s__Collinsella sp900548075	93.2639	210	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545445.1	s__Collinsella sp900545445	92.6947	239	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.18	95.16	0.86	0.84	3	-
GCA_900759045.1	s__Collinsella sp900759045	92.4961	228	292	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:35:17,145] [INFO] GTDB search result was written to GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/result_gtdb.tsv
[2023-06-17 12:35:17,146] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:35:17,150] [INFO] DFAST_QC result json was written to GCA_905200855.1_ERR260148-mag-bin.4_genomic.fna/dqc_result.json
[2023-06-17 12:35:17,150] [INFO] DFAST_QC completed!
[2023-06-17 12:35:17,150] [INFO] Total running time: 0h0m41s