[2024-01-24 12:52:51,115] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg75a9b45a-cfcc-4454-91df-7b6cdf3ae578/dqc_reference
[2024-01-24 12:52:53,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,751] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg45a5986d-d2dc-48a3-918d-f3fde15a6345/GCF_000466485.1_ASM46648v1_genomic.fna.gz | prodigal -d GCF_000466485.1_ASM46648v1_genomic.fna/cds.fna -a GCF_000466485.1_ASM46648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:04,309] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:04,310] [INFO] Task started: HMMsearch
[2024-01-24 12:53:04,310] [INFO] Running command: hmmsearch --tblout GCF_000466485.1_ASM46648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75a9b45a-cfcc-4454-91df-7b6cdf3ae578/dqc_reference/reference_markers.hmm GCF_000466485.1_ASM46648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:04,608] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:04,610] [INFO] Found 6/6 markers.
[2024-01-24 12:53:04,653] [INFO] Query marker FASTA was written to GCF_000466485.1_ASM46648v1_genomic.fna/markers.fasta
[2024-01-24 12:53:04,654] [INFO] Task started: Blastn
[2024-01-24 12:53:04,654] [INFO] Running command: blastn -query GCF_000466485.1_ASM46648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75a9b45a-cfcc-4454-91df-7b6cdf3ae578/dqc_reference/reference_markers.fasta -out GCF_000466485.1_ASM46648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:05,300] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:05,304] [INFO] Selected 22 target genomes.
[2024-01-24 12:53:05,304] [INFO] Target genome list was writen to GCF_000466485.1_ASM46648v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:05,346] [INFO] Task started: fastANI
[2024-01-24 12:53:05,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg45a5986d-d2dc-48a3-918d-f3fde15a6345/GCF_000466485.1_ASM46648v1_genomic.fna.gz --refList GCF_000466485.1_ASM46648v1_genomic.fna/target_genomes.txt --output GCF_000466485.1_ASM46648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:18,719] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:18,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75a9b45a-cfcc-4454-91df-7b6cdf3ae578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:18,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75a9b45a-cfcc-4454-91df-7b6cdf3ae578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:18,737] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:53:18,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:53:18,738] [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 porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	78.5005	86	1468	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	78.041	166	1468	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.9187	101	1468	95	below_threshold
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	77.777	196	1468	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	77.6302	98	1468	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	77.0488	93	1468	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.0405	52	1468	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.0346	52	1468	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	76.9176	79	1468	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.855	101	1468	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.7985	97	1468	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.6632	54	1468	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.5179	57	1468	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_002915525.1	341220	341220	suspected-type	True	76.4936	55	1468	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.2015	67	1468	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.1467	53	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:18,741] [INFO] DFAST Taxonomy check result was written to GCF_000466485.1_ASM46648v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:18,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:18,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:18,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75a9b45a-cfcc-4454-91df-7b6cdf3ae578/dqc_reference/checkm_data
[2024-01-24 12:53:18,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:18,801] [INFO] Task started: CheckM
[2024-01-24 12:53:18,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000466485.1_ASM46648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000466485.1_ASM46648v1_genomic.fna/checkm_input GCF_000466485.1_ASM46648v1_genomic.fna/checkm_result
[2024-01-24 12:53:54,529] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:54,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:54,555] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:54,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:54,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000466485.1_ASM46648v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:54,557] [INFO] Task started: Blastn
[2024-01-24 12:53:54,557] [INFO] Running command: blastn -query GCF_000466485.1_ASM46648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75a9b45a-cfcc-4454-91df-7b6cdf3ae578/dqc_reference/reference_markers_gtdb.fasta -out GCF_000466485.1_ASM46648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:55,624] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:55,629] [INFO] Selected 18 target genomes.
[2024-01-24 12:53:55,629] [INFO] Target genome list was writen to GCF_000466485.1_ASM46648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:55,662] [INFO] Task started: fastANI
[2024-01-24 12:53:55,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg45a5986d-d2dc-48a3-918d-f3fde15a6345/GCF_000466485.1_ASM46648v1_genomic.fna.gz --refList GCF_000466485.1_ASM46648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000466485.1_ASM46648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:09,445] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:09,475] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:09,475] [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_000466485.1	s__Clostridium_Q symbiosum	100.0	1454	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.57	0.86	0.81	32	conclusive
GCA_900547735.1	s__Clostridium_Q sp900547735	81.2843	803	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	81.1854	798	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302185.1	s__Clostridium_Q sp016302185	78.2514	149	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223375.1	s__Clostridium_Q sp000435655	78.1219	172	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.36	96.90	0.90	0.85	8	-
GCF_003201875.1	s__Hungatella effluvii	78.0691	164	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	95.81	95.49	0.78	0.75	20	-
GCF_003024715.1	s__Clostridium_Q fessum	77.7944	195	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.33	97.70	0.88	0.81	31	-
GCA_910575795.1	s__Clostridium_Q sp910575795	77.7582	202	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	99.66	99.05	0.95	0.91	4	-
GCA_018378255.1	s__CHH4-2 sp018378255	77.6623	111	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018377235.1	s__Clostridium_Q sp018377235	77.6578	173	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240245.1	s__Lachnoclostridium_A edouardi	77.6302	98	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017482945.1	s__Copromonas sp017482945	77.3779	58	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526575.1	s__Lacrimispora sp000526575	77.3701	82	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	98.63	98.56	0.93	0.92	3	-
GCF_003480315.1	s__Ventrimonas sp003480315	77.238	84	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCF_000235505.1	s__Hungatella_A hathewayi_A	77.204	133	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella_A	95.0	99.27	96.59	0.97	0.86	6	-
GCF_000687555.1	s__Lacrimispora aerotolerans	76.8886	80	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389905.1	s__Lacrimispora sp002389905	76.7898	90	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551225.1	s__Enterocloster sp900551225	76.0298	99	1468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:09,477] [INFO] GTDB search result was written to GCF_000466485.1_ASM46648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:09,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:09,484] [INFO] DFAST_QC result json was written to GCF_000466485.1_ASM46648v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:09,484] [INFO] DFAST_QC completed!
[2024-01-24 12:54:09,484] [INFO] Total running time: 0h1m18s