[2024-01-24 11:43:25,078] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,082] [INFO] DQC Reference Directory: /var/lib/cwl/stgf087ef82-1395-45e1-87ec-607e49e5c340/dqc_reference
[2024-01-24 11:43:30,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,060] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,060] [INFO] Running command: gunzip -c /var/lib/cwl/stga43096b0-ceb8-4ef4-a6ab-f2dba0728045/GCF_017873235.1_ASM1787323v1_genomic.fna.gz | prodigal -d GCF_017873235.1_ASM1787323v1_genomic.fna/cds.fna -a GCF_017873235.1_ASM1787323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:33,782] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:33,783] [INFO] Task started: HMMsearch
[2024-01-24 11:43:33,783] [INFO] Running command: hmmsearch --tblout GCF_017873235.1_ASM1787323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf087ef82-1395-45e1-87ec-607e49e5c340/dqc_reference/reference_markers.hmm GCF_017873235.1_ASM1787323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:34,064] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:34,065] [INFO] Found 6/6 markers.
[2024-01-24 11:43:34,092] [INFO] Query marker FASTA was written to GCF_017873235.1_ASM1787323v1_genomic.fna/markers.fasta
[2024-01-24 11:43:34,092] [INFO] Task started: Blastn
[2024-01-24 11:43:34,093] [INFO] Running command: blastn -query GCF_017873235.1_ASM1787323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf087ef82-1395-45e1-87ec-607e49e5c340/dqc_reference/reference_markers.fasta -out GCF_017873235.1_ASM1787323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:35,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:35,028] [INFO] Selected 19 target genomes.
[2024-01-24 11:43:35,028] [INFO] Target genome list was writen to GCF_017873235.1_ASM1787323v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:35,046] [INFO] Task started: fastANI
[2024-01-24 11:43:35,047] [INFO] Running command: fastANI --query /var/lib/cwl/stga43096b0-ceb8-4ef4-a6ab-f2dba0728045/GCF_017873235.1_ASM1787323v1_genomic.fna.gz --refList GCF_017873235.1_ASM1787323v1_genomic.fna/target_genomes.txt --output GCF_017873235.1_ASM1787323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:48,226] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:48,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf087ef82-1395-45e1-87ec-607e49e5c340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:48,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf087ef82-1395-45e1-87ec-607e49e5c340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:48,242] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:48,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:48,242] [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
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	100.0	856	857	95	conclusive
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	82.768	606	857	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	79.0545	370	857	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	78.6323	358	857	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	78.2673	242	857	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.261	300	857	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	78.0542	279	857	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.9222	319	857	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.9076	258	857	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.9045	285	857	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.8864	236	857	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.818	281	857	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.6977	294	857	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.4878	224	857	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	77.4361	262	857	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	77.335	211	857	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	77.2795	223	857	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	77.0335	241	857	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:48,244] [INFO] DFAST Taxonomy check result was written to GCF_017873235.1_ASM1787323v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:48,245] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:48,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:48,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf087ef82-1395-45e1-87ec-607e49e5c340/dqc_reference/checkm_data
[2024-01-24 11:43:48,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:48,276] [INFO] Task started: CheckM
[2024-01-24 11:43:48,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873235.1_ASM1787323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873235.1_ASM1787323v1_genomic.fna/checkm_input GCF_017873235.1_ASM1787323v1_genomic.fna/checkm_result
[2024-01-24 11:44:06,990] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:06,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:07,010] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:07,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:07,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873235.1_ASM1787323v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:07,011] [INFO] Task started: Blastn
[2024-01-24 11:44:07,011] [INFO] Running command: blastn -query GCF_017873235.1_ASM1787323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf087ef82-1395-45e1-87ec-607e49e5c340/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873235.1_ASM1787323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:07,819] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:07,822] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:07,823] [INFO] Target genome list was writen to GCF_017873235.1_ASM1787323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:07,830] [INFO] Task started: fastANI
[2024-01-24 11:44:07,831] [INFO] Running command: fastANI --query /var/lib/cwl/stga43096b0-ceb8-4ef4-a6ab-f2dba0728045/GCF_017873235.1_ASM1787323v1_genomic.fna.gz --refList GCF_017873235.1_ASM1787323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873235.1_ASM1787323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:14,072] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:14,089] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:14,090] [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_017873235.1	s__Clostridium moniliforme	100.0	856	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907995.1	s__Clostridium sardiniense	82.7505	608	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498355.1	s__Clostridium sp000498355	81.9128	558	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789395.1	s__Clostridium baratii	81.3731	533	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCF_002050515.1	s__Clostridium thermobutyricum	79.0784	368	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
GCF_015234215.1	s__Clostridium sp015234215	78.6565	356	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290265.1	s__Clostridium cagae	77.8999	286	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_014836325.1	s__Clostridium sp014836325	77.7838	284	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540255.1	s__Clostridium sp900540255	77.5053	242	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
GCA_015058375.1	s__Clostridium sp015058375	77.301	186	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:14,094] [INFO] GTDB search result was written to GCF_017873235.1_ASM1787323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:14,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:14,102] [INFO] DFAST_QC result json was written to GCF_017873235.1_ASM1787323v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:14,102] [INFO] DFAST_QC completed!
[2024-01-24 11:44:14,102] [INFO] Total running time: 0h0m49s