[2023-06-05 03:38:43,582] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:38:43,585] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:38:43,585] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb1226ee-c64d-4c1e-bb4d-0aac2047e92b/dqc_reference
[2023-06-05 03:38:45,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:38:45,031] [INFO] Task started: Prodigal
[2023-06-05 03:38:45,031] [INFO] Running command: gunzip -c /var/lib/cwl/stgb28ee4f3-564d-46c9-90f9-276bd50302ac/GCA_934613705.1_ERR7745876_bin.14_genomic.fna.gz | prodigal -d GCA_934613705.1_ERR7745876_bin.14_genomic.fna/cds.fna -a GCA_934613705.1_ERR7745876_bin.14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:38:52,129] [INFO] Task succeeded: Prodigal
[2023-06-05 03:38:52,130] [INFO] Task started: HMMsearch
[2023-06-05 03:38:52,130] [INFO] Running command: hmmsearch --tblout GCA_934613705.1_ERR7745876_bin.14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb1226ee-c64d-4c1e-bb4d-0aac2047e92b/dqc_reference/reference_markers.hmm GCA_934613705.1_ERR7745876_bin.14_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:38:52,354] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:38:52,356] [INFO] Found 6/6 markers.
[2023-06-05 03:38:52,381] [INFO] Query marker FASTA was written to GCA_934613705.1_ERR7745876_bin.14_genomic.fna/markers.fasta
[2023-06-05 03:38:52,381] [INFO] Task started: Blastn
[2023-06-05 03:38:52,381] [INFO] Running command: blastn -query GCA_934613705.1_ERR7745876_bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1226ee-c64d-4c1e-bb4d-0aac2047e92b/dqc_reference/reference_markers.fasta -out GCA_934613705.1_ERR7745876_bin.14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:38:53,143] [INFO] Task succeeded: Blastn
[2023-06-05 03:38:53,147] [INFO] Selected 14 target genomes.
[2023-06-05 03:38:53,148] [INFO] Target genome list was writen to GCA_934613705.1_ERR7745876_bin.14_genomic.fna/target_genomes.txt
[2023-06-05 03:38:53,149] [INFO] Task started: fastANI
[2023-06-05 03:38:53,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28ee4f3-564d-46c9-90f9-276bd50302ac/GCA_934613705.1_ERR7745876_bin.14_genomic.fna.gz --refList GCA_934613705.1_ERR7745876_bin.14_genomic.fna/target_genomes.txt --output GCA_934613705.1_ERR7745876_bin.14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:38:58,762] [INFO] Task succeeded: fastANI
[2023-06-05 03:38:58,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb1226ee-c64d-4c1e-bb4d-0aac2047e92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:38:58,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb1226ee-c64d-4c1e-bb4d-0aac2047e92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:38:58,775] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:38:58,775] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:38:58,775] [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 burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	80.5846	302	715	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	80.4892	285	715	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.2197	303	715	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.21	298	715	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	80.1385	304	715	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.9903	277	715	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	79.626	246	715	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	79.6021	247	715	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.5846	263	715	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	79.5734	249	715	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.2863	251	715	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.0379	213	715	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	78.5098	192	715	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.2965	177	715	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:38:58,777] [INFO] DFAST Taxonomy check result was written to GCA_934613705.1_ERR7745876_bin.14_genomic.fna/tc_result.tsv
[2023-06-05 03:38:58,778] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:38:58,778] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:38:58,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb1226ee-c64d-4c1e-bb4d-0aac2047e92b/dqc_reference/checkm_data
[2023-06-05 03:38:58,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:38:58,804] [INFO] Task started: CheckM
[2023-06-05 03:38:58,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934613705.1_ERR7745876_bin.14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934613705.1_ERR7745876_bin.14_genomic.fna/checkm_input GCA_934613705.1_ERR7745876_bin.14_genomic.fna/checkm_result
[2023-06-05 03:39:24,254] [INFO] Task succeeded: CheckM
[2023-06-05 03:39:24,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:39:24,282] [INFO] ===== Completeness check finished =====
[2023-06-05 03:39:24,282] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:39:24,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934613705.1_ERR7745876_bin.14_genomic.fna/markers.fasta)
[2023-06-05 03:39:24,283] [INFO] Task started: Blastn
[2023-06-05 03:39:24,283] [INFO] Running command: blastn -query GCA_934613705.1_ERR7745876_bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1226ee-c64d-4c1e-bb4d-0aac2047e92b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934613705.1_ERR7745876_bin.14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:39:25,541] [INFO] Task succeeded: Blastn
[2023-06-05 03:39:25,546] [INFO] Selected 18 target genomes.
[2023-06-05 03:39:25,546] [INFO] Target genome list was writen to GCA_934613705.1_ERR7745876_bin.14_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:39:25,730] [INFO] Task started: fastANI
[2023-06-05 03:39:25,730] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28ee4f3-564d-46c9-90f9-276bd50302ac/GCA_934613705.1_ERR7745876_bin.14_genomic.fna.gz --refList GCA_934613705.1_ERR7745876_bin.14_genomic.fna/target_genomes_gtdb.txt --output GCA_934613705.1_ERR7745876_bin.14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:39:33,189] [INFO] Task succeeded: fastANI
[2023-06-05 03:39:33,208] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:39:33,208] [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_902501965.1	s__Collinsella sp900556495	98.9323	647	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.47	98.05	0.92	0.92	3	conclusive
GCA_015062655.1	s__Collinsella sp015062655	81.0393	332	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902150035.1	s__Enorma burkinafasonensis	80.5841	302	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900375.1	s__Collinsella sp002305035	80.5267	312	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCA_019117005.1	s__Collinsella stercoripullorum	80.4639	299	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCA_000333815.1	s__Enorma sp000333815	80.4583	288	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCF_016902615.1	s__Collinsella tanakaei_A	80.3305	296	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.95	98.95	0.92	0.92	2	-
GCF_900119895.1	s__Collinsella phocaeensis	79.9511	279	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCF_008014645.1	s__Collinsella sp008014645	79.6716	267	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
GCA_018378775.1	s__Collinsella sp018378775	79.5456	212	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.51	95.51	0.75	0.75	2	-
GCA_905215195.1	s__Collinsella sp905215195	79.4775	170	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215725.1	s__Collinsella sp905215725	79.4105	208	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0527	N/A	N/A	N/A	N/A	1	-
GCA_905215065.1	s__Collinsella sp905215065	79.3986	243	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1686	95.36	95.20	0.87	0.82	13	-
GCA_900752545.1	s__Collinsella sp900752545	79.3545	236	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.93	0.93	2	-
GCA_900543845.1	s__Collinsella sp900543845	79.3168	218	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.60	95.22	0.88	0.81	3	-
GCF_000225705.1	s__Collinsella tanakaei	79.3059	250	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.30	95.17	0.91	0.86	6	-
GCA_900552995.1	s__Collinsella sp900552995	79.2591	138	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.58	95.21	0.80	0.68	3	-
GCA_900555585.1	s__Collinsella sp900555585	78.7545	117	715	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-05 03:39:33,210] [INFO] GTDB search result was written to GCA_934613705.1_ERR7745876_bin.14_genomic.fna/result_gtdb.tsv
[2023-06-05 03:39:33,211] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:39:33,215] [INFO] DFAST_QC result json was written to GCA_934613705.1_ERR7745876_bin.14_genomic.fna/dqc_result.json
[2023-06-05 03:39:33,215] [INFO] DFAST_QC completed!
[2023-06-05 03:39:33,215] [INFO] Total running time: 0h0m50s