[2024-01-24 12:53:56,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3c8c2fc-968c-4307-bc74-533744560577/dqc_reference
[2024-01-24 12:53:57,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:57,467] [INFO] Task started: Prodigal
[2024-01-24 12:53:57,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg4464e9ca-b490-4a77-ac66-fc005192409b/GCF_900155365.1_PRJEB18748_genomic.fna.gz | prodigal -d GCF_900155365.1_PRJEB18748_genomic.fna/cds.fna -a GCF_900155365.1_PRJEB18748_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:03,414] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:03,415] [INFO] Task started: HMMsearch
[2024-01-24 12:54:03,415] [INFO] Running command: hmmsearch --tblout GCF_900155365.1_PRJEB18748_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3c8c2fc-968c-4307-bc74-533744560577/dqc_reference/reference_markers.hmm GCF_900155365.1_PRJEB18748_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:03,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:03,623] [INFO] Found 6/6 markers.
[2024-01-24 12:54:03,653] [INFO] Query marker FASTA was written to GCF_900155365.1_PRJEB18748_genomic.fna/markers.fasta
[2024-01-24 12:54:03,653] [INFO] Task started: Blastn
[2024-01-24 12:54:03,653] [INFO] Running command: blastn -query GCF_900155365.1_PRJEB18748_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3c8c2fc-968c-4307-bc74-533744560577/dqc_reference/reference_markers.fasta -out GCF_900155365.1_PRJEB18748_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:04,356] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:04,360] [INFO] Selected 14 target genomes.
[2024-01-24 12:54:04,360] [INFO] Target genome list was writen to GCF_900155365.1_PRJEB18748_genomic.fna/target_genomes.txt
[2024-01-24 12:54:04,366] [INFO] Task started: fastANI
[2024-01-24 12:54:04,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg4464e9ca-b490-4a77-ac66-fc005192409b/GCF_900155365.1_PRJEB18748_genomic.fna.gz --refList GCF_900155365.1_PRJEB18748_genomic.fna/target_genomes.txt --output GCF_900155365.1_PRJEB18748_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:10,679] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:10,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3c8c2fc-968c-4307-bc74-533744560577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:10,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3c8c2fc-968c-4307-bc74-533744560577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:10,689] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:10,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:10,690] [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 bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	100.0	619	619	95	conclusive
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	80.6608	258	619	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	80.6347	252	619	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	80.5179	251	619	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.4377	190	619	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.2776	157	619	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.229	190	619	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.2184	192	619	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.2097	168	619	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.9874	195	619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:10,692] [INFO] DFAST Taxonomy check result was written to GCF_900155365.1_PRJEB18748_genomic.fna/tc_result.tsv
[2024-01-24 12:54:10,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:10,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:10,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3c8c2fc-968c-4307-bc74-533744560577/dqc_reference/checkm_data
[2024-01-24 12:54:10,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:10,715] [INFO] Task started: CheckM
[2024-01-24 12:54:10,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155365.1_PRJEB18748_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155365.1_PRJEB18748_genomic.fna/checkm_input GCF_900155365.1_PRJEB18748_genomic.fna/checkm_result
[2024-01-24 12:54:33,732] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:33,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:33,751] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:33,752] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:33,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155365.1_PRJEB18748_genomic.fna/markers.fasta)
[2024-01-24 12:54:33,752] [INFO] Task started: Blastn
[2024-01-24 12:54:33,752] [INFO] Running command: blastn -query GCF_900155365.1_PRJEB18748_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3c8c2fc-968c-4307-bc74-533744560577/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155365.1_PRJEB18748_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:35,058] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:35,061] [INFO] Selected 28 target genomes.
[2024-01-24 12:54:35,062] [INFO] Target genome list was writen to GCF_900155365.1_PRJEB18748_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:35,129] [INFO] Task started: fastANI
[2024-01-24 12:54:35,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg4464e9ca-b490-4a77-ac66-fc005192409b/GCF_900155365.1_PRJEB18748_genomic.fna.gz --refList GCF_900155365.1_PRJEB18748_genomic.fna/target_genomes_gtdb.txt --output GCF_900155365.1_PRJEB18748_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:45,326] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:45,350] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:45,350] [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_900155365.1	s__Collinsella bouchesdurhonensis	100.0	619	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.92	95.77	0.91	0.89	8	conclusive
GCA_900755005.1	s__Collinsella sp900755005	80.687	221	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.91	99.91	0.90	0.90	2	-
GCF_901212495.1	s__Collinsella aerofaciens_H	80.6169	252	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.63	95.88	0.84	0.79	16	-
GCF_003462685.1	s__Collinsella sp003462685	80.5151	240	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.85	99.71	0.99	0.99	3	-
GCA_900754275.1	s__Collinsella sp900754275	80.4929	224	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.49	95.11	0.84	0.77	3	-
GCA_900768435.1	s__Collinsella sp900768435	80.4636	232	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018785245.1	s__Collinsella aerofaciens_AD	80.4079	241	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1928	N/A	N/A	N/A	N/A	1	-
GCA_902362275.1	s__Collinsella sp902362275	80.3803	226	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.48	97.28	0.91	0.88	7	-
GCA_018378775.1	s__Collinsella sp018378775	80.3573	226	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.51	95.51	0.75	0.75	2	-
GCA_900547805.1	s__Collinsella sp900547805	80.3554	209	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546105.1	s__Collinsella sp900546105	80.3548	222	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008671135.1	s__Collinsella aerofaciens_J	80.3516	245	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_900768795.1	s__Collinsella sp900768795	80.2933	195	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.75	98.75	0.86	0.86	2	-
GCA_900545165.1	s__Collinsella sp900545165	80.2405	212	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015670745.1	s__Collinsella aerofaciens_T	80.1044	244	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0363	95.05	95.05	0.90	0.90	2	-
GCA_905213265.1	s__Collinsella sp905213265	80.1033	228	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0059	97.43	95.01	0.89	0.85	3	-
GCA_900752345.1	s__Collinsella sp900752345	80.0659	185	619	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	80.0033	241	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.32	95.32	0.85	0.85	2	-
GCA_900765185.1	s__Collinsella sp900765185	79.8479	180	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549025.1	s__Collinsella sp900549025	79.7082	212	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0692	97.49	95.13	0.83	0.77	3	-
GCF_900119895.1	s__Collinsella phocaeensis	79.4626	189	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCF_016900375.1	s__Collinsella sp002305035	79.3186	206	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCF_900046475.1	s__Collinsella ihuae	79.2475	216	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.74	97.24	0.91	0.87	7	-
GCA_019117005.1	s__Collinsella stercoripullorum	79.0933	188	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_000225705.1	s__Collinsella tanakaei	78.9874	195	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.30	95.17	0.91	0.86	6	-
GCA_900540955.1	s__Paratractidigestivibacter sp900540955	78.8935	120	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.08	96.08	0.89	0.89	2	-
GCA_900548365.1	s__Collinsella sp900548365	78.7381	162	619	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	78.7281	191	619	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:45,352] [INFO] GTDB search result was written to GCF_900155365.1_PRJEB18748_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:45,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:45,357] [INFO] DFAST_QC result json was written to GCF_900155365.1_PRJEB18748_genomic.fna/dqc_result.json
[2024-01-24 12:54:45,357] [INFO] DFAST_QC completed!
[2024-01-24 12:54:45,357] [INFO] Total running time: 0h0m49s