[2024-01-24 14:14:44,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:44,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:44,608] [INFO] DQC Reference Directory: /var/lib/cwl/stgdebc9064-7407-4199-8058-1615ab617f3c/dqc_reference
[2024-01-24 14:14:45,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:45,863] [INFO] Task started: Prodigal
[2024-01-24 14:14:45,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8529097-4347-490a-98ad-9a1de7f4a432/GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna.gz | prodigal -d GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/cds.fna -a GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:54,061] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:54,062] [INFO] Task started: HMMsearch
[2024-01-24 14:14:54,062] [INFO] Running command: hmmsearch --tblout GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdebc9064-7407-4199-8058-1615ab617f3c/dqc_reference/reference_markers.hmm GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:54,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:54,323] [INFO] Found 6/6 markers.
[2024-01-24 14:14:54,359] [INFO] Query marker FASTA was written to GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/markers.fasta
[2024-01-24 14:14:54,360] [INFO] Task started: Blastn
[2024-01-24 14:14:54,360] [INFO] Running command: blastn -query GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/markers.fasta -db /var/lib/cwl/stgdebc9064-7407-4199-8058-1615ab617f3c/dqc_reference/reference_markers.fasta -out GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:55,535] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:55,541] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:55,542] [INFO] Target genome list was writen to GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/target_genomes.txt
[2024-01-24 14:14:55,554] [INFO] Task started: fastANI
[2024-01-24 14:14:55,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8529097-4347-490a-98ad-9a1de7f4a432/GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna.gz --refList GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/target_genomes.txt --output GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:07,559] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:07,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdebc9064-7407-4199-8058-1615ab617f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:07,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdebc9064-7407-4199-8058-1615ab617f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:07,578] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:07,578] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:07,579] [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
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	79.8785	451	977	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	79.728	439	977	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	79.0935	421	977	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	79.0491	369	977	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_004324765.1	433330	433330	type	True	79.0238	373	977	95	below_threshold
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	78.3526	272	977	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	78.2573	276	977	95	below_threshold
Micropruina glycogenica		GCA_900289045.1	75385	75385	type	True	78.1552	325	977	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	78.0971	289	977	95	below_threshold
Raineyella antarctica	strain=LZ-22	GCA_900092135.1	1577474	1577474	type	True	77.9764	288	977	95	below_threshold
Propioniciclava flava	strain=VG341	GCA_004126535.1	2072026	2072026	type	True	77.862	268	977	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.8345	291	977	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.7812	337	977	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.7327	313	977	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	77.6001	335	977	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	77.5351	244	977	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.3825	254	977	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	77.1655	261	977	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	76.7653	217	977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:07,580] [INFO] DFAST Taxonomy check result was written to GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/tc_result.tsv
[2024-01-24 14:15:07,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:07,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:07,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdebc9064-7407-4199-8058-1615ab617f3c/dqc_reference/checkm_data
[2024-01-24 14:15:07,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:07,616] [INFO] Task started: CheckM
[2024-01-24 14:15:07,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/checkm_input GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/checkm_result
[2024-01-24 14:15:37,877] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:37,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:37,900] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:37,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:37,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/markers.fasta)
[2024-01-24 14:15:37,901] [INFO] Task started: Blastn
[2024-01-24 14:15:37,901] [INFO] Running command: blastn -query GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/markers.fasta -db /var/lib/cwl/stgdebc9064-7407-4199-8058-1615ab617f3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:39,716] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:39,721] [INFO] Selected 18 target genomes.
[2024-01-24 14:15:39,721] [INFO] Target genome list was writen to GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:39,737] [INFO] Task started: fastANI
[2024-01-24 14:15:39,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8529097-4347-490a-98ad-9a1de7f4a432/GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna.gz --refList GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/target_genomes_gtdb.txt --output GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:51,332] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:51,353] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:51,354] [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_000826085.1	s__Nigerium massiliense	100.0	976	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017569205.1	s__Brevilactibacter sp014164685	79.9443	457	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	99.00	98.00	0.92	0.83	3	-
GCF_011393335.1	s__Brevilactibacter coleopterorum	79.838	454	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004324755.1	s__Brevilactibacter sinopodophylli	79.6874	442	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838755.1	s__Brevilactibacter sp012838755	79.6788	399	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711325.1	s__Brevilactibacter sp016711325	79.6201	358	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517965.1	s__Propioniciclava sp012517965	79.1303	400	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014858005.1	s__Brevilactibacter sp014858005	79.0927	421	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182665.1	s__Propioniciclava tarda	79.0502	370	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013693855.1	s__Micropruina sp013693855	78.688	334	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	78.5201	303	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306015.1	s__Propionicimonas sp017306015	78.4438	345	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900289045.1	s__Micropruina glycogenica	78.1338	327	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	78.0509	326	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004126535.1	s__Brevilactibacter flavus	77.862	268	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.7993	294	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_009742705.1	s__Auraticoccus cholistanensis	77.7105	316	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105065.1	s__Friedmanniella luteola	77.6438	330	977	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:51,356] [INFO] GTDB search result was written to GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:51,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:51,361] [INFO] DFAST_QC result json was written to GCF_000826085.1_Nigerium_massiliensis_SIT7_genomic.fna/dqc_result.json
[2024-01-24 14:15:51,361] [INFO] DFAST_QC completed!
[2024-01-24 14:15:51,361] [INFO] Total running time: 0h1m7s