[2024-01-24 13:31:42,663] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:42,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:42,665] [INFO] DQC Reference Directory: /var/lib/cwl/stge4f04a8b-1aa8-4299-b184-2a6c3303a86f/dqc_reference
[2024-01-24 13:31:43,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:43,917] [INFO] Task started: Prodigal
[2024-01-24 13:31:43,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg9eb11bc4-50f0-4c73-baa1-431c4a5defff/GCF_001312445.1_ASM131244v1_genomic.fna.gz | prodigal -d GCF_001312445.1_ASM131244v1_genomic.fna/cds.fna -a GCF_001312445.1_ASM131244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:50,680] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:50,680] [INFO] Task started: HMMsearch
[2024-01-24 13:31:50,680] [INFO] Running command: hmmsearch --tblout GCF_001312445.1_ASM131244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4f04a8b-1aa8-4299-b184-2a6c3303a86f/dqc_reference/reference_markers.hmm GCF_001312445.1_ASM131244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:50,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:50,959] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9eb11bc4-50f0-4c73-baa1-431c4a5defff/GCF_001312445.1_ASM131244v1_genomic.fna.gz]
[2024-01-24 13:31:51,006] [INFO] Query marker FASTA was written to GCF_001312445.1_ASM131244v1_genomic.fna/markers.fasta
[2024-01-24 13:31:51,007] [INFO] Task started: Blastn
[2024-01-24 13:31:51,007] [INFO] Running command: blastn -query GCF_001312445.1_ASM131244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4f04a8b-1aa8-4299-b184-2a6c3303a86f/dqc_reference/reference_markers.fasta -out GCF_001312445.1_ASM131244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:51,605] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:51,608] [INFO] Selected 10 target genomes.
[2024-01-24 13:31:51,608] [INFO] Target genome list was writen to GCF_001312445.1_ASM131244v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:51,610] [INFO] Task started: fastANI
[2024-01-24 13:31:51,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb11bc4-50f0-4c73-baa1-431c4a5defff/GCF_001312445.1_ASM131244v1_genomic.fna.gz --refList GCF_001312445.1_ASM131244v1_genomic.fna/target_genomes.txt --output GCF_001312445.1_ASM131244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:57,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:57,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4f04a8b-1aa8-4299-b184-2a6c3303a86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:57,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4f04a8b-1aa8-4299-b184-2a6c3303a86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:57,258] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:57,259] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:57,259] [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
Coprobacillus cateniformis	strain=JCM 10604	GCA_001312445.1	100884	100884	type	True	100.0	1147	1149	95	conclusive
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	99.888	1149	1149	95	conclusive
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	80.6913	516	1149	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	80.5092	530	1149	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	77.9467	155	1149	95	below_threshold
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	77.9164	175	1149	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_024622895.1	69824	69824	type	True	77.8359	146	1149	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	77.6522	114	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:57,260] [INFO] DFAST Taxonomy check result was written to GCF_001312445.1_ASM131244v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:57,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:57,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:57,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4f04a8b-1aa8-4299-b184-2a6c3303a86f/dqc_reference/checkm_data
[2024-01-24 13:31:57,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:57,303] [INFO] Task started: CheckM
[2024-01-24 13:31:57,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001312445.1_ASM131244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001312445.1_ASM131244v1_genomic.fna/checkm_input GCF_001312445.1_ASM131244v1_genomic.fna/checkm_result
[2024-01-24 13:32:25,117] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:25,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,141] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:25,142] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:25,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001312445.1_ASM131244v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:25,143] [INFO] Task started: Blastn
[2024-01-24 13:32:25,143] [INFO] Running command: blastn -query GCF_001312445.1_ASM131244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4f04a8b-1aa8-4299-b184-2a6c3303a86f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001312445.1_ASM131244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:26,069] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:26,073] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:26,074] [INFO] Target genome list was writen to GCF_001312445.1_ASM131244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:26,115] [INFO] Task started: fastANI
[2024-01-24 13:32:26,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb11bc4-50f0-4c73-baa1-431c4a5defff/GCF_001312445.1_ASM131244v1_genomic.fna.gz --refList GCF_001312445.1_ASM131244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001312445.1_ASM131244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:33,975] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:33,991] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:33,991] [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_009767585.1	s__Coprobacillus cateniformis	99.888	1149	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Coprobacillus	95.0	99.28	99.05	0.92	0.87	12	conclusive
GCF_001244545.1	s__Stoquefichus sp001244545	81.7319	592	1149	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	81.5948	584	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900538465.1	s__Longibaculum sp900538465	81.1061	485	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343035.1	s__Longibaculum muris	80.672	518	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	98.90	96.51	0.88	0.82	7	-
GCA_910588075.1	s__MGBC163490 sp910588075	79.716	342	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160815.1	s__Massiliomicrobiota merdigallinarum	79.5347	343	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Massiliomicrobiota	95.0	98.05	97.64	0.81	0.77	12	-
GCA_002359025.1	s__UBA3379 sp002359025	79.2261	227	1149	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	79.225	274	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC140090	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160495.1	s__Erysipelatoclostridium merdavium	77.9699	175	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCF_900102365.1	s__Erysipelatoclostridium cocleatum	77.8092	152	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.07	98.04	0.92	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:33,994] [INFO] GTDB search result was written to GCF_001312445.1_ASM131244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:33,994] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:33,999] [INFO] DFAST_QC result json was written to GCF_001312445.1_ASM131244v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:33,999] [INFO] DFAST_QC completed!
[2024-01-24 13:32:34,000] [INFO] Total running time: 0h0m51s