[2024-01-24 14:06:44,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg056c8622-cd92-41f7-bbaf-0b6e98ee2577/dqc_reference
[2024-01-24 14:06:45,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:45,463] [INFO] Task started: Prodigal
[2024-01-24 14:06:45,463] [INFO] Running command: gunzip -c /var/lib/cwl/stga0cd9c71-23a0-45f3-859c-7b61f69cdb14/GCF_002934235.1_ASM293423v1_genomic.fna.gz | prodigal -d GCF_002934235.1_ASM293423v1_genomic.fna/cds.fna -a GCF_002934235.1_ASM293423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:49,910] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:49,910] [INFO] Task started: HMMsearch
[2024-01-24 14:06:49,910] [INFO] Running command: hmmsearch --tblout GCF_002934235.1_ASM293423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg056c8622-cd92-41f7-bbaf-0b6e98ee2577/dqc_reference/reference_markers.hmm GCF_002934235.1_ASM293423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:50,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:50,210] [INFO] Found 6/6 markers.
[2024-01-24 14:06:50,237] [INFO] Query marker FASTA was written to GCF_002934235.1_ASM293423v1_genomic.fna/markers.fasta
[2024-01-24 14:06:50,238] [INFO] Task started: Blastn
[2024-01-24 14:06:50,238] [INFO] Running command: blastn -query GCF_002934235.1_ASM293423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056c8622-cd92-41f7-bbaf-0b6e98ee2577/dqc_reference/reference_markers.fasta -out GCF_002934235.1_ASM293423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:50,845] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:50,850] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:50,850] [INFO] Target genome list was writen to GCF_002934235.1_ASM293423v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:50,861] [INFO] Task started: fastANI
[2024-01-24 14:06:50,862] [INFO] Running command: fastANI --query /var/lib/cwl/stga0cd9c71-23a0-45f3-859c-7b61f69cdb14/GCF_002934235.1_ASM293423v1_genomic.fna.gz --refList GCF_002934235.1_ASM293423v1_genomic.fna/target_genomes.txt --output GCF_002934235.1_ASM293423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:01,952] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:01,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg056c8622-cd92-41f7-bbaf-0b6e98ee2577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:01,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg056c8622-cd92-41f7-bbaf-0b6e98ee2577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:01,964] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:01,964] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:01,964] [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 algidicarnis	strain=DSM 15099	GCA_002934235.1	37659	37659	type	True	100.0	922	925	95	conclusive
Clostridium putrefaciens	strain=NCTC9836	GCA_900461105.1	99675	99675	type	True	91.8186	748	925	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	79.8942	492	925	95	below_threshold
Desnuesiella massiliensis	strain=mt10	GCA_001403615.1	1650662	1650662	type	True	76.9173	187	925	95	below_threshold
Clostridium polynesiense	strain=MS1	GCA_000820705.1	1325933	1325933	type	True	76.471	70	925	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.4275	159	925	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	76.4131	132	925	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	76.3381	114	925	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.2918	151	925	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.1907	138	925	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	76.1874	135	925	95	below_threshold
Clostridium psychrophilum	strain=DSM 14207	GCA_018861705.1	132926	132926	type	True	75.9645	87	925	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	75.9172	123	925	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	75.8822	92	925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,966] [INFO] DFAST Taxonomy check result was written to GCF_002934235.1_ASM293423v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:01,967] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:01,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:01,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg056c8622-cd92-41f7-bbaf-0b6e98ee2577/dqc_reference/checkm_data
[2024-01-24 14:07:01,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:01,997] [INFO] Task started: CheckM
[2024-01-24 14:07:01,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934235.1_ASM293423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934235.1_ASM293423v1_genomic.fna/checkm_input GCF_002934235.1_ASM293423v1_genomic.fna/checkm_result
[2024-01-24 14:07:23,252] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:23,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:23,274] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:23,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:23,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934235.1_ASM293423v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:23,275] [INFO] Task started: Blastn
[2024-01-24 14:07:23,275] [INFO] Running command: blastn -query GCF_002934235.1_ASM293423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg056c8622-cd92-41f7-bbaf-0b6e98ee2577/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934235.1_ASM293423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:24,019] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:24,023] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:24,024] [INFO] Target genome list was writen to GCF_002934235.1_ASM293423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:24,042] [INFO] Task started: fastANI
[2024-01-24 14:07:24,042] [INFO] Running command: fastANI --query /var/lib/cwl/stga0cd9c71-23a0-45f3-859c-7b61f69cdb14/GCF_002934235.1_ASM293423v1_genomic.fna.gz --refList GCF_002934235.1_ASM293423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934235.1_ASM293423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:34,742] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:34,756] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:34,756] [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_002934235.1	s__Clostridium_L algidicarnis	100.0	922	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	97.66	96.15	0.89	0.86	14	conclusive
GCF_900461105.1	s__Clostridium_L putrefaciens	91.8187	748	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	79.6846	503	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	99.33	97.98	0.97	0.93	4	-
GCF_900184255.1	s__Haloimpatiens massiliensis	76.7962	167	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129365.1	s__Clostridium_AH fallax	76.365	158	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000285575.1	s__Clostridium_J senegalense	76.3572	147	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.19	95.52	0.93	0.91	5	-
GCF_014836325.1	s__Clostridium sp014836325	76.2041	137	925	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_900548455.1	s__Clostridium_J sp900548455	76.2029	105	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873245.1	s__Clostridium tertium	76.1817	134	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_018918055.1	s__Clostridium sp018918055	76.1792	83	925	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_900141845.1	s__Clostridium_AG cavendishii	76.1579	142	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498355.1	s__Clostridium sp000498355	76.0467	122	925	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_900167505.1	s__F0540 sp900167505	76.0357	125	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCA_900759995.1	s__Clostridium sp900759995	76.0105	118	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
GCA_910588715.1	s__Clostridium sp910588715	76.0007	97	925	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_018861705.1	s__Clostridium_AD psychrophilum	75.9645	87	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000320405.1	s__Clostridium celatum	75.8822	92	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:34,758] [INFO] GTDB search result was written to GCF_002934235.1_ASM293423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:34,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:34,763] [INFO] DFAST_QC result json was written to GCF_002934235.1_ASM293423v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:34,763] [INFO] DFAST_QC completed!
[2024-01-24 14:07:34,763] [INFO] Total running time: 0h0m51s