[2024-01-24 11:42:20,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,305] [INFO] DQC Reference Directory: /var/lib/cwl/stgf571f3d7-ac97-48ab-87b5-465bdeea2c50/dqc_reference
[2024-01-24 11:42:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stgb83cd1d4-da89-4a10-ac06-2040d1aa241f/GCF_900199705.1_PRJEB21894_genomic.fna.gz | prodigal -d GCF_900199705.1_PRJEB21894_genomic.fna/cds.fna -a GCF_900199705.1_PRJEB21894_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:30,382] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:30,383] [INFO] Task started: HMMsearch
[2024-01-24 11:42:30,383] [INFO] Running command: hmmsearch --tblout GCF_900199705.1_PRJEB21894_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf571f3d7-ac97-48ab-87b5-465bdeea2c50/dqc_reference/reference_markers.hmm GCF_900199705.1_PRJEB21894_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:30,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:30,578] [INFO] Found 6/6 markers.
[2024-01-24 11:42:30,599] [INFO] Query marker FASTA was written to GCF_900199705.1_PRJEB21894_genomic.fna/markers.fasta
[2024-01-24 11:42:30,600] [INFO] Task started: Blastn
[2024-01-24 11:42:30,600] [INFO] Running command: blastn -query GCF_900199705.1_PRJEB21894_genomic.fna/markers.fasta -db /var/lib/cwl/stgf571f3d7-ac97-48ab-87b5-465bdeea2c50/dqc_reference/reference_markers.fasta -out GCF_900199705.1_PRJEB21894_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:31,220] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:31,224] [INFO] Selected 14 target genomes.
[2024-01-24 11:42:31,224] [INFO] Target genome list was writen to GCF_900199705.1_PRJEB21894_genomic.fna/target_genomes.txt
[2024-01-24 11:42:31,233] [INFO] Task started: fastANI
[2024-01-24 11:42:31,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgb83cd1d4-da89-4a10-ac06-2040d1aa241f/GCF_900199705.1_PRJEB21894_genomic.fna.gz --refList GCF_900199705.1_PRJEB21894_genomic.fna/target_genomes.txt --output GCF_900199705.1_PRJEB21894_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:42:37,291] [INFO] Task succeeded: fastANI
[2024-01-24 11:42:37,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf571f3d7-ac97-48ab-87b5-465bdeea2c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:42:37,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf571f3d7-ac97-48ab-87b5-465bdeea2c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:42:37,304] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:42:37,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:42:37,304] [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 provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	100.0	576	577	95	conclusive
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	81.1561	266	577	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	81.1131	270	577	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	81.1061	253	577	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.4348	224	577	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.8134	183	577	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	79.4675	184	577	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	79.3893	187	577	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	79.2625	193	577	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	79.0761	183	577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:42:37,306] [INFO] DFAST Taxonomy check result was written to GCF_900199705.1_PRJEB21894_genomic.fna/tc_result.tsv
[2024-01-24 11:42:37,306] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:42:37,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:42:37,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf571f3d7-ac97-48ab-87b5-465bdeea2c50/dqc_reference/checkm_data
[2024-01-24 11:42:37,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:42:37,326] [INFO] Task started: CheckM
[2024-01-24 11:42:37,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199705.1_PRJEB21894_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199705.1_PRJEB21894_genomic.fna/checkm_input GCF_900199705.1_PRJEB21894_genomic.fna/checkm_result
[2024-01-24 11:43:00,115] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:00,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:00,132] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:00,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:00,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199705.1_PRJEB21894_genomic.fna/markers.fasta)
[2024-01-24 11:43:00,133] [INFO] Task started: Blastn
[2024-01-24 11:43:00,134] [INFO] Running command: blastn -query GCF_900199705.1_PRJEB21894_genomic.fna/markers.fasta -db /var/lib/cwl/stgf571f3d7-ac97-48ab-87b5-465bdeea2c50/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199705.1_PRJEB21894_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:01,199] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:01,202] [INFO] Selected 20 target genomes.
[2024-01-24 11:43:01,202] [INFO] Target genome list was writen to GCF_900199705.1_PRJEB21894_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:01,219] [INFO] Task started: fastANI
[2024-01-24 11:43:01,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgb83cd1d4-da89-4a10-ac06-2040d1aa241f/GCF_900199705.1_PRJEB21894_genomic.fna.gz --refList GCF_900199705.1_PRJEB21894_genomic.fna/target_genomes_gtdb.txt --output GCF_900199705.1_PRJEB21894_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:43:08,645] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:08,672] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:43:08,672] [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_900199705.1	s__Collinsella provencensis	100.0	576	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.12	97.12	0.85	0.85	2	conclusive
GCA_900540845.1	s__Collinsella sp900540845	81.3669	269	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000156215.1	s__Collinsella stercoris	81.181	265	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.61	95.23	0.87	0.81	5	-
GCF_000156175.1	s__Collinsella intestinalis	81.1061	253	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.88	95.17	0.89	0.86	15	-
GCF_003479805.1	s__Collinsella sp003479805	81.0886	248	577	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	80.784	222	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119895.1	s__Collinsella phocaeensis	80.4264	225	577	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	80.1757	206	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
GCF_003466125.1	s__Collinsella sp003466125	80.0664	184	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.79	97.08	0.91	0.86	19	-
GCF_000225705.1	s__Collinsella tanakaei	79.8134	183	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.30	95.17	0.91	0.86	6	-
GCF_900046475.1	s__Collinsella ihuae	79.791	203	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.74	97.24	0.91	0.87	7	-
GCF_015670745.1	s__Collinsella aerofaciens_T	79.6584	178	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0363	95.05	95.05	0.90	0.90	2	-
GCA_900540945.1	s__Collinsella sp900540945	79.3862	176	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.51	95.33	0.85	0.84	5	-
GCA_900752545.1	s__Collinsella sp900752545	79.262	172	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.93	0.93	2	-
GCA_900557455.1	s__Collinsella sp900557455	79.2038	74	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759045.1	s__Collinsella sp900759045	79.192	174	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555515.1	s__Collinsella sp900555515	79.1906	119	577	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	79.1785	172	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161805.1	s__Coprousia sp002161805	79.0788	177	577	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764025.1	s__Collinsella sp900764025	78.5899	96	577	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 11:43:08,674] [INFO] GTDB search result was written to GCF_900199705.1_PRJEB21894_genomic.fna/result_gtdb.tsv
[2024-01-24 11:43:08,674] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:43:08,678] [INFO] DFAST_QC result json was written to GCF_900199705.1_PRJEB21894_genomic.fna/dqc_result.json
[2024-01-24 11:43:08,678] [INFO] DFAST_QC completed!
[2024-01-24 11:43:08,678] [INFO] Total running time: 0h0m48s