[2024-01-24 12:36:24,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,882] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d8b41fd-21ad-4389-ad2a-a8f1fd799a06/dqc_reference
[2024-01-24 12:36:26,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,250] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg980902a1-cd47-4cef-87f6-b2812717860a/GCF_900199545.1_PRJEB21863_genomic.fna.gz | prodigal -d GCF_900199545.1_PRJEB21863_genomic.fna/cds.fna -a GCF_900199545.1_PRJEB21863_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:37,690] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:37,690] [INFO] Task started: HMMsearch
[2024-01-24 12:36:37,690] [INFO] Running command: hmmsearch --tblout GCF_900199545.1_PRJEB21863_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d8b41fd-21ad-4389-ad2a-a8f1fd799a06/dqc_reference/reference_markers.hmm GCF_900199545.1_PRJEB21863_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:37,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:37,951] [INFO] Found 6/6 markers.
[2024-01-24 12:36:37,986] [INFO] Query marker FASTA was written to GCF_900199545.1_PRJEB21863_genomic.fna/markers.fasta
[2024-01-24 12:36:37,986] [INFO] Task started: Blastn
[2024-01-24 12:36:37,987] [INFO] Running command: blastn -query GCF_900199545.1_PRJEB21863_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d8b41fd-21ad-4389-ad2a-a8f1fd799a06/dqc_reference/reference_markers.fasta -out GCF_900199545.1_PRJEB21863_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:38,621] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:38,625] [INFO] Selected 13 target genomes.
[2024-01-24 12:36:38,626] [INFO] Target genome list was writen to GCF_900199545.1_PRJEB21863_genomic.fna/target_genomes.txt
[2024-01-24 12:36:38,636] [INFO] Task started: fastANI
[2024-01-24 12:36:38,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg980902a1-cd47-4cef-87f6-b2812717860a/GCF_900199545.1_PRJEB21863_genomic.fna.gz --refList GCF_900199545.1_PRJEB21863_genomic.fna/target_genomes.txt --output GCF_900199545.1_PRJEB21863_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:46,258] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:46,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d8b41fd-21ad-4389-ad2a-a8f1fd799a06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:46,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d8b41fd-21ad-4389-ad2a-a8f1fd799a06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:46,273] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:46,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:46,274] [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
Raoultibacter massiliensis	strain=Marseille-P2849	GCA_900199545.1	1852371	1852371	type	True	99.9985	1213	1214	95	conclusive
Raoultibacter timonensis	strain=Marseille-P3277	GCA_900240215.1	1907662	1907662	type	True	82.2645	768	1214	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	78.9169	314	1214	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	78.8546	321	1214	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	78.8279	329	1214	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	78.8003	333	1214	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	78.7042	324	1214	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	78.4124	327	1214	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	78.3815	348	1214	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	78.3771	342	1214	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	77.4621	163	1214	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	77.3966	167	1214	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	77.2006	162	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:46,275] [INFO] DFAST Taxonomy check result was written to GCF_900199545.1_PRJEB21863_genomic.fna/tc_result.tsv
[2024-01-24 12:36:46,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:46,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:46,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d8b41fd-21ad-4389-ad2a-a8f1fd799a06/dqc_reference/checkm_data
[2024-01-24 12:36:46,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:46,316] [INFO] Task started: CheckM
[2024-01-24 12:36:46,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900199545.1_PRJEB21863_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900199545.1_PRJEB21863_genomic.fna/checkm_input GCF_900199545.1_PRJEB21863_genomic.fna/checkm_result
[2024-01-24 12:37:21,380] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:21,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:21,397] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:21,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:21,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900199545.1_PRJEB21863_genomic.fna/markers.fasta)
[2024-01-24 12:37:21,399] [INFO] Task started: Blastn
[2024-01-24 12:37:21,399] [INFO] Running command: blastn -query GCF_900199545.1_PRJEB21863_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d8b41fd-21ad-4389-ad2a-a8f1fd799a06/dqc_reference/reference_markers_gtdb.fasta -out GCF_900199545.1_PRJEB21863_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:22,329] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:22,332] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:22,332] [INFO] Target genome list was writen to GCF_900199545.1_PRJEB21863_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:22,346] [INFO] Task started: fastANI
[2024-01-24 12:37:22,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg980902a1-cd47-4cef-87f6-b2812717860a/GCF_900199545.1_PRJEB21863_genomic.fna.gz --refList GCF_900199545.1_PRJEB21863_genomic.fna/target_genomes_gtdb.txt --output GCF_900199545.1_PRJEB21863_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:31,096] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:31,116] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:31,117] [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_900199545.1	s__Raoultibacter massiliensis	99.9985	1213	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900240215.1	s__Raoultibacter timonensis	82.2721	768	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter	95.0	98.77	98.77	0.93	0.93	2	-
GCF_901411515.1	s__Raoultibacter sp901411515	80.939	649	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	78.8345	328	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCF_000024265.1	s__Eggerthella lenta	78.7879	334	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCA_900170005.1	s__Gordonibacter massiliensis	78.5026	313	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCF_902386925.1	s__Arabia massiliensis	78.3983	300	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900184265.1	s__Eggerthella timonensis	78.3891	329	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339845.1	s__Gordonibacter sp003339845	78.3518	324	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003340345.1	s__Paraeggerthella hongkongensis_A	77.8961	262	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Paraeggerthella	95.0	98.75	98.26	0.95	0.89	5	-
GCA_900550385.1	s__Aphodovivens sp900550385	77.6941	135	1214	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	99.66	99.66	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:31,119] [INFO] GTDB search result was written to GCF_900199545.1_PRJEB21863_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:31,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:31,124] [INFO] DFAST_QC result json was written to GCF_900199545.1_PRJEB21863_genomic.fna/dqc_result.json
[2024-01-24 12:37:31,124] [INFO] DFAST_QC completed!
[2024-01-24 12:37:31,124] [INFO] Total running time: 0h1m6s