[2024-01-24 13:01:12,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg0952cb6a-dac7-4b81-8d68-3822e30a17df/dqc_reference
[2024-01-24 13:01:13,571] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,572] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,573] [INFO] Running command: gunzip -c /var/lib/cwl/stgc411a30b-83fb-4cd4-ad3e-e429d888ea64/GCF_001643775.1_ASM164377v1_genomic.fna.gz | prodigal -d GCF_001643775.1_ASM164377v1_genomic.fna/cds.fna -a GCF_001643775.1_ASM164377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:26,053] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:26,054] [INFO] Task started: HMMsearch
[2024-01-24 13:01:26,054] [INFO] Running command: hmmsearch --tblout GCF_001643775.1_ASM164377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0952cb6a-dac7-4b81-8d68-3822e30a17df/dqc_reference/reference_markers.hmm GCF_001643775.1_ASM164377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:26,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:26,338] [INFO] Found 6/6 markers.
[2024-01-24 13:01:26,370] [INFO] Query marker FASTA was written to GCF_001643775.1_ASM164377v1_genomic.fna/markers.fasta
[2024-01-24 13:01:26,370] [INFO] Task started: Blastn
[2024-01-24 13:01:26,371] [INFO] Running command: blastn -query GCF_001643775.1_ASM164377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0952cb6a-dac7-4b81-8d68-3822e30a17df/dqc_reference/reference_markers.fasta -out GCF_001643775.1_ASM164377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:26,999] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:27,015] [INFO] Selected 17 target genomes.
[2024-01-24 13:01:27,015] [INFO] Target genome list was writen to GCF_001643775.1_ASM164377v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:27,021] [INFO] Task started: fastANI
[2024-01-24 13:01:27,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgc411a30b-83fb-4cd4-ad3e-e429d888ea64/GCF_001643775.1_ASM164377v1_genomic.fna.gz --refList GCF_001643775.1_ASM164377v1_genomic.fna/target_genomes.txt --output GCF_001643775.1_ASM164377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:36,298] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:36,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0952cb6a-dac7-4b81-8d68-3822e30a17df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:36,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0952cb6a-dac7-4b81-8d68-3822e30a17df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:36,309] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:36,309] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:36,309] [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
Denitrobacterium detoxificans	strain=NPOH1	GCA_001643775.1	79604	79604	type	True	100.0	813	815	95	conclusive
Denitrobacterium detoxificans	strain=DSM 21843	GCA_900110565.1	79604	79604	type	True	99.9605	777	815	95	conclusive
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	78.4092	110	815	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	78.0205	163	815	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	77.9377	162	815	95	below_threshold
Slackia piriformis	strain=YIT 12062	GCA_000296445.1	626934	626934	type	True	77.9188	86	815	95	below_threshold
Raoultibacter timonensis	strain=Marseille-P3277	GCA_900240215.1	1907662	1907662	type	True	77.8473	106	815	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	77.821	161	815	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.7604	150	815	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	77.752	50	815	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.6846	153	815	95	below_threshold
Raoultibacter massiliensis	strain=Marseille-P2849	GCA_900199545.1	1852371	1852371	type	True	77.5264	101	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:36,311] [INFO] DFAST Taxonomy check result was written to GCF_001643775.1_ASM164377v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:36,311] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:36,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:36,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0952cb6a-dac7-4b81-8d68-3822e30a17df/dqc_reference/checkm_data
[2024-01-24 13:01:36,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:36,338] [INFO] Task started: CheckM
[2024-01-24 13:01:36,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001643775.1_ASM164377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001643775.1_ASM164377v1_genomic.fna/checkm_input GCF_001643775.1_ASM164377v1_genomic.fna/checkm_result
[2024-01-24 13:02:12,609] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:12,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:12,631] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:12,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:12,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001643775.1_ASM164377v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:12,632] [INFO] Task started: Blastn
[2024-01-24 13:02:12,632] [INFO] Running command: blastn -query GCF_001643775.1_ASM164377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0952cb6a-dac7-4b81-8d68-3822e30a17df/dqc_reference/reference_markers_gtdb.fasta -out GCF_001643775.1_ASM164377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:13,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:13,562] [INFO] Selected 17 target genomes.
[2024-01-24 13:02:13,562] [INFO] Target genome list was writen to GCF_001643775.1_ASM164377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:13,592] [INFO] Task started: fastANI
[2024-01-24 13:02:13,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgc411a30b-83fb-4cd4-ad3e-e429d888ea64/GCF_001643775.1_ASM164377v1_genomic.fna.gz --refList GCF_001643775.1_ASM164377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001643775.1_ASM164377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:20,914] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:20,926] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:20,926] [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_001643775.1	s__Denitrobacterium detoxificans	100.0	813	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_015062615.1	s__Denitrobacterium detoxificans_A	94.4638	692	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001486445.1	s__RUG013 sp001486445	79.2003	172	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RUG013	95.0	98.36	97.63	0.92	0.89	7	-
GCA_905236045.1	s__Denitrobacterium sp905236045	78.2099	150	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215325.1	s__Senegalimassilia sp905215325	78.0814	135	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339815.1	s__Eggerthella sinensis	77.9786	160	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCA_900170005.1	s__Gordonibacter massiliensis	77.9264	163	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCA_017459925.1	s__UBA9715 sp017459925	77.8718	133	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234785.1	s__UBA9715 sp905234785	77.7692	128	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555335.1	s__W1P20-047 sp004555335	77.4185	91	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__W1P20-047	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767025.1	s__CACXMZ01 sp902767025	77.0027	98	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CACXMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420575.1	s__CAJFUR01 sp904420575	76.9464	104	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAJFUR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585575.1	s__Adlercreutzia sp910585575	76.8953	127	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589125.1	s__MGBC163016 sp910589125	76.554	74	815	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__MGBC163016	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,928] [INFO] GTDB search result was written to GCF_001643775.1_ASM164377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:20,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:20,932] [INFO] DFAST_QC result json was written to GCF_001643775.1_ASM164377v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:20,933] [INFO] DFAST_QC completed!
[2024-01-24 13:02:20,933] [INFO] Total running time: 0h1m9s