[2024-01-24 14:19:18,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg7378da69-46da-4854-b43c-08256f6d4216/dqc_reference
[2024-01-24 14:19:20,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,146] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,147] [INFO] Running command: gunzip -c /var/lib/cwl/stgde38b84e-a7a1-4d29-ad87-942a9c0db681/GCF_900176655.1_PRJEB20374_genomic.fna.gz | prodigal -d GCF_900176655.1_PRJEB20374_genomic.fna/cds.fna -a GCF_900176655.1_PRJEB20374_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:26,743] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:26,744] [INFO] Task started: HMMsearch
[2024-01-24 14:19:26,744] [INFO] Running command: hmmsearch --tblout GCF_900176655.1_PRJEB20374_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7378da69-46da-4854-b43c-08256f6d4216/dqc_reference/reference_markers.hmm GCF_900176655.1_PRJEB20374_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:26,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:26,972] [INFO] Found 6/6 markers.
[2024-01-24 14:19:26,997] [INFO] Query marker FASTA was written to GCF_900176655.1_PRJEB20374_genomic.fna/markers.fasta
[2024-01-24 14:19:26,997] [INFO] Task started: Blastn
[2024-01-24 14:19:26,998] [INFO] Running command: blastn -query GCF_900176655.1_PRJEB20374_genomic.fna/markers.fasta -db /var/lib/cwl/stg7378da69-46da-4854-b43c-08256f6d4216/dqc_reference/reference_markers.fasta -out GCF_900176655.1_PRJEB20374_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:27,816] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:27,819] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:27,819] [INFO] Target genome list was writen to GCF_900176655.1_PRJEB20374_genomic.fna/target_genomes.txt
[2024-01-24 14:19:27,824] [INFO] Task started: fastANI
[2024-01-24 14:19:27,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgde38b84e-a7a1-4d29-ad87-942a9c0db681/GCF_900176655.1_PRJEB20374_genomic.fna.gz --refList GCF_900176655.1_PRJEB20374_genomic.fna/target_genomes.txt --output GCF_900176655.1_PRJEB20374_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:35,306] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:35,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7378da69-46da-4854-b43c-08256f6d4216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:35,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7378da69-46da-4854-b43c-08256f6d4216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:35,317] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:35,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:35,318] [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 vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	99.9999	709	711	95	conclusive
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	80.3046	288	711	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.9062	251	711	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.7615	256	711	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.7241	268	711	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.67	272	711	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.6062	222	711	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	79.2736	202	711	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.957	228	711	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.461	189	711	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.1852	174	711	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	75.3127	55	711	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:35,319] [INFO] DFAST Taxonomy check result was written to GCF_900176655.1_PRJEB20374_genomic.fna/tc_result.tsv
[2024-01-24 14:19:35,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:35,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:35,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7378da69-46da-4854-b43c-08256f6d4216/dqc_reference/checkm_data
[2024-01-24 14:19:35,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:35,346] [INFO] Task started: CheckM
[2024-01-24 14:19:35,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176655.1_PRJEB20374_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176655.1_PRJEB20374_genomic.fna/checkm_input GCF_900176655.1_PRJEB20374_genomic.fna/checkm_result
[2024-01-24 14:20:01,197] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:01,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:01,219] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:01,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:01,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176655.1_PRJEB20374_genomic.fna/markers.fasta)
[2024-01-24 14:20:01,220] [INFO] Task started: Blastn
[2024-01-24 14:20:01,220] [INFO] Running command: blastn -query GCF_900176655.1_PRJEB20374_genomic.fna/markers.fasta -db /var/lib/cwl/stg7378da69-46da-4854-b43c-08256f6d4216/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176655.1_PRJEB20374_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:02,476] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:02,480] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:02,480] [INFO] Target genome list was writen to GCF_900176655.1_PRJEB20374_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:02,496] [INFO] Task started: fastANI
[2024-01-24 14:20:02,497] [INFO] Running command: fastANI --query /var/lib/cwl/stgde38b84e-a7a1-4d29-ad87-942a9c0db681/GCF_900176655.1_PRJEB20374_genomic.fna.gz --refList GCF_900176655.1_PRJEB20374_genomic.fna/target_genomes_gtdb.txt --output GCF_900176655.1_PRJEB20374_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:09,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:09,878] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:09,879] [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_900176655.1	s__Collinsella vaginalis	99.9999	709	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.31	99.31	0.99	0.99	2	conclusive
GCA_015062655.1	s__Collinsella sp015062655	83.5223	420	711	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	80.3064	288	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902501965.1	s__Collinsella sp900556495	80.0273	314	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.47	98.05	0.92	0.92	3	-
GCA_000333815.1	s__Enorma sp000333815	79.9921	244	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCA_019117005.1	s__Collinsella stercoripullorum	79.9816	298	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_016902615.1	s__Collinsella tanakaei_A	79.7672	268	711	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	79.7417	257	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCF_002159765.1	s__Coprousia sp002159765	79.6572	248	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	97.90	97.74	0.89	0.88	3	-
GCF_016900375.1	s__Collinsella sp002305035	79.6251	300	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCF_000156215.1	s__Collinsella stercoris	79.5994	275	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.61	95.23	0.87	0.81	5	-
GCF_008014645.1	s__Collinsella sp008014645	79.388	232	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
GCF_016901575.1	s__Limicola phocaeensis_A	79.3599	232	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003479805.1	s__Collinsella sp003479805	79.3031	225	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.77	98.33	0.94	0.90	6	-
GCF_002159335.1	s__Coprousia sp002159335	79.0055	242	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	98.10	98.10	0.94	0.94	2	-
GCA_900555585.1	s__Collinsella sp900555585	78.6523	114	711	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:09,880] [INFO] GTDB search result was written to GCF_900176655.1_PRJEB20374_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:09,881] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:09,885] [INFO] DFAST_QC result json was written to GCF_900176655.1_PRJEB20374_genomic.fna/dqc_result.json
[2024-01-24 14:20:09,885] [INFO] DFAST_QC completed!
[2024-01-24 14:20:09,885] [INFO] Total running time: 0h0m51s