[2024-01-24 12:29:20,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:20,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:20,532] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdb47449-b6e9-42c8-9a40-0904a2880e1a/dqc_reference
[2024-01-24 12:29:21,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:21,768] [INFO] Task started: Prodigal
[2024-01-24 12:29:21,768] [INFO] Running command: gunzip -c /var/lib/cwl/stga7cef9c0-1284-4ade-b83b-9a8b554ef468/GCF_000724205.2_ASM72420v3_genomic.fna.gz | prodigal -d GCF_000724205.2_ASM72420v3_genomic.fna/cds.fna -a GCF_000724205.2_ASM72420v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:28,934] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:28,934] [INFO] Task started: HMMsearch
[2024-01-24 12:29:28,934] [INFO] Running command: hmmsearch --tblout GCF_000724205.2_ASM72420v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdb47449-b6e9-42c8-9a40-0904a2880e1a/dqc_reference/reference_markers.hmm GCF_000724205.2_ASM72420v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:29,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:29,210] [INFO] Found 6/6 markers.
[2024-01-24 12:29:29,247] [INFO] Query marker FASTA was written to GCF_000724205.2_ASM72420v3_genomic.fna/markers.fasta
[2024-01-24 12:29:29,247] [INFO] Task started: Blastn
[2024-01-24 12:29:29,247] [INFO] Running command: blastn -query GCF_000724205.2_ASM72420v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdb47449-b6e9-42c8-9a40-0904a2880e1a/dqc_reference/reference_markers.fasta -out GCF_000724205.2_ASM72420v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:29,829] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:29,832] [INFO] Selected 10 target genomes.
[2024-01-24 12:29:29,833] [INFO] Target genome list was writen to GCF_000724205.2_ASM72420v3_genomic.fna/target_genomes.txt
[2024-01-24 12:29:29,844] [INFO] Task started: fastANI
[2024-01-24 12:29:29,844] [INFO] Running command: fastANI --query /var/lib/cwl/stga7cef9c0-1284-4ade-b83b-9a8b554ef468/GCF_000724205.2_ASM72420v3_genomic.fna.gz --refList GCF_000724205.2_ASM72420v3_genomic.fna/target_genomes.txt --output GCF_000724205.2_ASM72420v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:43,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:43,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdb47449-b6e9-42c8-9a40-0904a2880e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:43,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdb47449-b6e9-42c8-9a40-0904a2880e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:43,169] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:29:43,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:43,170] [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 pasteurianum	strain=ATCC 6013	GCA_000724205.3	1501	1501	type	True	100.0	1456	1461	95	conclusive
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	99.9993	1449	1461	95	conclusive
Clostridium pasteurianum	strain=ATCC 6013	GCA_000807175.1	1501	1501	type	True	99.9993	1449	1461	95	conclusive
Clostridium pasteurianum	strain=ATCC 6013	GCA_001856645.1	1501	1501	type	True	99.9993	1448	1461	95	conclusive
Clostridium pasteurianum	strain=DSM 525	GCA_000330945.1	1501	1501	type	True	99.9735	1402	1461	95	conclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	77.9855	177	1461	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	77.9492	202	1461	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	77.7672	198	1461	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	77.7596	207	1461	95	below_threshold
Defluviitalea phaphyphila	strain=Alg1	GCA_001466305.1	1473580	1473580	type	True	75.2495	95	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:43,171] [INFO] DFAST Taxonomy check result was written to GCF_000724205.2_ASM72420v3_genomic.fna/tc_result.tsv
[2024-01-24 12:29:43,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:43,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:43,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdb47449-b6e9-42c8-9a40-0904a2880e1a/dqc_reference/checkm_data
[2024-01-24 12:29:43,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:43,223] [INFO] Task started: CheckM
[2024-01-24 12:29:43,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000724205.2_ASM72420v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000724205.2_ASM72420v3_genomic.fna/checkm_input GCF_000724205.2_ASM72420v3_genomic.fna/checkm_result
[2024-01-24 12:30:10,421] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:10,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:10,448] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:10,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:10,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000724205.2_ASM72420v3_genomic.fna/markers.fasta)
[2024-01-24 12:30:10,449] [INFO] Task started: Blastn
[2024-01-24 12:30:10,450] [INFO] Running command: blastn -query GCF_000724205.2_ASM72420v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdb47449-b6e9-42c8-9a40-0904a2880e1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000724205.2_ASM72420v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:11,222] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:11,228] [INFO] Selected 13 target genomes.
[2024-01-24 12:30:11,228] [INFO] Target genome list was writen to GCF_000724205.2_ASM72420v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:11,238] [INFO] Task started: fastANI
[2024-01-24 12:30:11,239] [INFO] Running command: fastANI --query /var/lib/cwl/stga7cef9c0-1284-4ade-b83b-9a8b554ef468/GCF_000724205.2_ASM72420v3_genomic.fna.gz --refList GCF_000724205.2_ASM72420v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000724205.2_ASM72420v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:22,790] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:22,806] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:22,806] [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_000807255.1	s__Clostridium_I pasteurianum	99.9993	1450	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	99.98	99.90	1.00	0.99	7	conclusive
GCF_000389635.1	s__Clostridium_I pasteurianum_A	82.6008	897	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246895.1	s__Clostridium_I arbusti	81.4896	780	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176305.1	s__Clostridium_I acidisoli	78.0549	318	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686725.1	s__Clostridium_I akagii	77.5377	268	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038625.1	s__Clostridium_AM carboxidivorans	77.496	253	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_001705235.1	s__Clostridium_S pasteurianum_A	77.4177	204	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012926525.1	s__Clostridium_AM sp012926525	76.9568	230	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758365.1	s__Clostridium_C acetireducens	76.4848	163	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873215.1	s__Clostridium_AO tetanomorphum	76.4022	181	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	99.85	99.71	0.98	0.97	5	-
GCF_007115085.1	s__Clostridium sp007115085	76.2046	119	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.42	99.42	0.90	0.90	2	-
GCF_001243045.1	s__Clostridium_F niameyense	76.1994	154	1461	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	-
GCA_015058405.1	s__Clostridium sp015058405	75.2818	105	1461	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 12:30:22,809] [INFO] GTDB search result was written to GCF_000724205.2_ASM72420v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:22,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:22,814] [INFO] DFAST_QC result json was written to GCF_000724205.2_ASM72420v3_genomic.fna/dqc_result.json
[2024-01-24 12:30:22,814] [INFO] DFAST_QC completed!
[2024-01-24 12:30:22,815] [INFO] Total running time: 0h1m2s