[2024-01-24 11:30:49,519] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,521] [INFO] DQC Reference Directory: /var/lib/cwl/stga6541925-9889-40de-b98a-7f4c5d86f767/dqc_reference
[2024-01-24 11:30:50,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,767] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,767] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3cff65b-70b5-4eaa-a1b0-0c6fb844f3a9/GCF_024623255.1_ASM2462325v1_genomic.fna.gz | prodigal -d GCF_024623255.1_ASM2462325v1_genomic.fna/cds.fna -a GCF_024623255.1_ASM2462325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:05,233] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:05,233] [INFO] Task started: HMMsearch
[2024-01-24 11:31:05,234] [INFO] Running command: hmmsearch --tblout GCF_024623255.1_ASM2462325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6541925-9889-40de-b98a-7f4c5d86f767/dqc_reference/reference_markers.hmm GCF_024623255.1_ASM2462325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:05,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:05,453] [INFO] Found 6/6 markers.
[2024-01-24 11:31:05,481] [INFO] Query marker FASTA was written to GCF_024623255.1_ASM2462325v1_genomic.fna/markers.fasta
[2024-01-24 11:31:05,482] [INFO] Task started: Blastn
[2024-01-24 11:31:05,482] [INFO] Running command: blastn -query GCF_024623255.1_ASM2462325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6541925-9889-40de-b98a-7f4c5d86f767/dqc_reference/reference_markers.fasta -out GCF_024623255.1_ASM2462325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:06,199] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:06,203] [INFO] Selected 10 target genomes.
[2024-01-24 11:31:06,203] [INFO] Target genome list was writen to GCF_024623255.1_ASM2462325v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:06,209] [INFO] Task started: fastANI
[2024-01-24 11:31:06,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3cff65b-70b5-4eaa-a1b0-0c6fb844f3a9/GCF_024623255.1_ASM2462325v1_genomic.fna.gz --refList GCF_024623255.1_ASM2462325v1_genomic.fna/target_genomes.txt --output GCF_024623255.1_ASM2462325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:12,143] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:12,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6541925-9889-40de-b98a-7f4c5d86f767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:12,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6541925-9889-40de-b98a-7f4c5d86f767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:12,155] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:31:12,155] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:12,156] [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
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	99.9999	911	920	95	conclusive
Adlercreutzia mucosicola	strain=DSM 19490	GCA_000422625.1	580026	580026	type	True	99.9882	915	920	95	conclusive
Adlercreutzia muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	89.0996	571	920	95	below_threshold
Adlercreutzia muris	strain=DSM 29508	GCA_024623245.1	1796610	1796610	type	True	88.996	586	920	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	88.1683	557	920	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	88.1212	562	920	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	83.817	521	920	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	79.4774	334	920	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	79.3262	334	920	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	79.2896	334	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:12,157] [INFO] DFAST Taxonomy check result was written to GCF_024623255.1_ASM2462325v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:12,158] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:12,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:12,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6541925-9889-40de-b98a-7f4c5d86f767/dqc_reference/checkm_data
[2024-01-24 11:31:12,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:12,188] [INFO] Task started: CheckM
[2024-01-24 11:31:12,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024623255.1_ASM2462325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024623255.1_ASM2462325v1_genomic.fna/checkm_input GCF_024623255.1_ASM2462325v1_genomic.fna/checkm_result
[2024-01-24 11:31:53,299] [INFO] Task succeeded: CheckM
[2024-01-24 11:31:53,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:31:53,322] [INFO] ===== Completeness check finished =====
[2024-01-24 11:31:53,322] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:31:53,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024623255.1_ASM2462325v1_genomic.fna/markers.fasta)
[2024-01-24 11:31:53,323] [INFO] Task started: Blastn
[2024-01-24 11:31:53,323] [INFO] Running command: blastn -query GCF_024623255.1_ASM2462325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6541925-9889-40de-b98a-7f4c5d86f767/dqc_reference/reference_markers_gtdb.fasta -out GCF_024623255.1_ASM2462325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:54,473] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:54,507] [INFO] Selected 11 target genomes.
[2024-01-24 11:31:54,507] [INFO] Target genome list was writen to GCF_024623255.1_ASM2462325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:31:54,519] [INFO] Task started: fastANI
[2024-01-24 11:31:54,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3cff65b-70b5-4eaa-a1b0-0c6fb844f3a9/GCF_024623255.1_ASM2462325v1_genomic.fna.gz --refList GCF_024623255.1_ASM2462325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024623255.1_ASM2462325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:00,794] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:00,810] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:00,810] [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_000422625.1	s__Adlercreutzia mucosicola	99.9882	915	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	conclusive
GCF_008831045.1	s__Adlercreutzia muris	89.1149	570	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
GCF_000403355.2	s__Adlercreutzia caecimuris	88.1393	558	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.41	97.35	0.86	0.85	5	-
GCF_011405655.1	s__Adlercreutzia celatus_A	84.1509	510	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	96.32	95.52	0.87	0.80	16	-
GCF_000478885.1	s__Adlercreutzia equolifaciens	83.9154	519	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.05	95.56	0.84	0.79	7	-
GCA_910589165.1	s__Adlercreutzia sp910589165	83.2186	483	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911695.1	s__QWKK01 sp009911695	81.4594	354	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	98.01	97.98	0.92	0.92	3	-
GCF_013185065.1	s__CAAEEV01 sp013185065	81.0705	301	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCA_910589695.1	s__QWKK01 sp910589695	81.0049	316	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900170005.1	s__Gordonibacter massiliensis	79.7805	313	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCA_017440565.1	s__RGIG3135 sp017440565	78.4588	174	920	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RGIG3135	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:00,812] [INFO] GTDB search result was written to GCF_024623255.1_ASM2462325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:00,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:00,816] [INFO] DFAST_QC result json was written to GCF_024623255.1_ASM2462325v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:00,816] [INFO] DFAST_QC completed!
[2024-01-24 11:32:00,816] [INFO] Total running time: 0h1m11s