[2024-01-24 11:26:28,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,031] [INFO] DQC Reference Directory: /var/lib/cwl/stge7d2cd63-c979-4886-9fe4-512d2cd5fe52/dqc_reference
[2024-01-24 11:26:29,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,529] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg208d7992-958b-4e32-91cc-cfd6ff69a90f/GCF_004343035.1_ASM434303v1_genomic.fna.gz | prodigal -d GCF_004343035.1_ASM434303v1_genomic.fna/cds.fna -a GCF_004343035.1_ASM434303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:35,355] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:35,355] [INFO] Task started: HMMsearch
[2024-01-24 11:26:35,355] [INFO] Running command: hmmsearch --tblout GCF_004343035.1_ASM434303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7d2cd63-c979-4886-9fe4-512d2cd5fe52/dqc_reference/reference_markers.hmm GCF_004343035.1_ASM434303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:35,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:35,689] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg208d7992-958b-4e32-91cc-cfd6ff69a90f/GCF_004343035.1_ASM434303v1_genomic.fna.gz]
[2024-01-24 11:26:35,719] [INFO] Query marker FASTA was written to GCF_004343035.1_ASM434303v1_genomic.fna/markers.fasta
[2024-01-24 11:26:35,720] [INFO] Task started: Blastn
[2024-01-24 11:26:35,720] [INFO] Running command: blastn -query GCF_004343035.1_ASM434303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7d2cd63-c979-4886-9fe4-512d2cd5fe52/dqc_reference/reference_markers.fasta -out GCF_004343035.1_ASM434303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:36,330] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:36,333] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:36,334] [INFO] Target genome list was writen to GCF_004343035.1_ASM434303v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:36,339] [INFO] Task started: fastANI
[2024-01-24 11:26:36,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg208d7992-958b-4e32-91cc-cfd6ff69a90f/GCF_004343035.1_ASM434303v1_genomic.fna.gz --refList GCF_004343035.1_ASM434303v1_genomic.fna/target_genomes.txt --output GCF_004343035.1_ASM434303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:45,155] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:45,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7d2cd63-c979-4886-9fe4-512d2cd5fe52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:45,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7d2cd63-c979-4886-9fe4-512d2cd5fe52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:45,166] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:45,166] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:45,166] [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
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	100.0	1027	1029	95	conclusive
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	99.9885	1015	1029	95	conclusive
Coprobacillus cateniformis	strain=JCM 10604	GCA_001312445.1	100884	100884	type	True	80.6971	517	1029	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	80.6882	525	1029	95	below_threshold
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	78.7905	213	1029	95	below_threshold
Faecalibacillus intestinalis	strain=SNUG30099	GCA_003024685.1	1982626	1982626	type	True	78.5307	230	1029	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.2799	182	1029	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	77.8838	227	1029	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	77.7716	156	1029	95	below_threshold
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	77.268	115	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:45,168] [INFO] DFAST Taxonomy check result was written to GCF_004343035.1_ASM434303v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:45,169] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:45,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:45,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7d2cd63-c979-4886-9fe4-512d2cd5fe52/dqc_reference/checkm_data
[2024-01-24 11:26:45,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:45,206] [INFO] Task started: CheckM
[2024-01-24 11:26:45,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004343035.1_ASM434303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004343035.1_ASM434303v1_genomic.fna/checkm_input GCF_004343035.1_ASM434303v1_genomic.fna/checkm_result
[2024-01-24 11:27:10,568] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:10,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:10,594] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:10,594] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:10,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004343035.1_ASM434303v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:10,595] [INFO] Task started: Blastn
[2024-01-24 11:27:10,595] [INFO] Running command: blastn -query GCF_004343035.1_ASM434303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7d2cd63-c979-4886-9fe4-512d2cd5fe52/dqc_reference/reference_markers_gtdb.fasta -out GCF_004343035.1_ASM434303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:11,544] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:11,547] [INFO] Selected 11 target genomes.
[2024-01-24 11:27:11,547] [INFO] Target genome list was writen to GCF_004343035.1_ASM434303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:11,557] [INFO] Task started: fastANI
[2024-01-24 11:27:11,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg208d7992-958b-4e32-91cc-cfd6ff69a90f/GCF_004343035.1_ASM434303v1_genomic.fna.gz --refList GCF_004343035.1_ASM434303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004343035.1_ASM434303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:19,174] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:19,183] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:19,183] [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_004343035.1	s__Longibaculum muris	100.0	1027	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	98.90	96.51	0.88	0.82	7	conclusive
GCA_900538465.1	s__Longibaculum sp900538465	85.9652	574	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244545.1	s__Stoquefichus sp001244545	81.7692	595	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	98.22	98.22	0.87	0.87	2	-
GCF_000455285.1	s__Stoquefichus massiliensis	81.5611	555	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009767585.1	s__Coprobacillus cateniformis	80.6867	524	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Coprobacillus	95.0	99.28	99.05	0.92	0.87	12	-
GCF_002160815.1	s__Massiliomicrobiota merdigallinarum	80.3312	393	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Massiliomicrobiota	95.0	98.05	97.64	0.81	0.77	12	-
GCF_002160865.1	s__Massiliomicrobiota sp002160865	80.1916	424	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Massiliomicrobiota	95.0	97.99	97.96	0.87	0.83	4	-
GCA_002359025.1	s__UBA3379 sp002359025	79.9475	268	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__UBA3379	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586805.1	s__MGBC140090 sp910586805	79.7533	293	1029	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC140090	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:19,185] [INFO] GTDB search result was written to GCF_004343035.1_ASM434303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:19,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:19,188] [INFO] DFAST_QC result json was written to GCF_004343035.1_ASM434303v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:19,188] [INFO] DFAST_QC completed!
[2024-01-24 11:27:19,189] [INFO] Total running time: 0h0m51s