[2024-01-24 13:18:45,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:45,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:45,886] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2f56fc9-22aa-40b7-a941-b06bc031a7b5/dqc_reference
[2024-01-24 13:18:47,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,281] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc2414c-6da8-4a83-a814-3e0726e53e5b/GCF_000246895.1_ASM24689v2_genomic.fna.gz | prodigal -d GCF_000246895.1_ASM24689v2_genomic.fna/cds.fna -a GCF_000246895.1_ASM24689v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:53,026] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:53,027] [INFO] Task started: HMMsearch
[2024-01-24 13:18:53,027] [INFO] Running command: hmmsearch --tblout GCF_000246895.1_ASM24689v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2f56fc9-22aa-40b7-a941-b06bc031a7b5/dqc_reference/reference_markers.hmm GCF_000246895.1_ASM24689v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:53,336] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:53,338] [INFO] Found 6/6 markers.
[2024-01-24 13:18:53,367] [INFO] Query marker FASTA was written to GCF_000246895.1_ASM24689v2_genomic.fna/markers.fasta
[2024-01-24 13:18:53,367] [INFO] Task started: Blastn
[2024-01-24 13:18:53,367] [INFO] Running command: blastn -query GCF_000246895.1_ASM24689v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2f56fc9-22aa-40b7-a941-b06bc031a7b5/dqc_reference/reference_markers.fasta -out GCF_000246895.1_ASM24689v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:53,928] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:53,931] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:53,931] [INFO] Target genome list was writen to GCF_000246895.1_ASM24689v2_genomic.fna/target_genomes.txt
[2024-01-24 13:18:53,981] [INFO] Task started: fastANI
[2024-01-24 13:18:53,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc2414c-6da8-4a83-a814-3e0726e53e5b/GCF_000246895.1_ASM24689v2_genomic.fna.gz --refList GCF_000246895.1_ASM24689v2_genomic.fna/target_genomes.txt --output GCF_000246895.1_ASM24689v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:12,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:12,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2f56fc9-22aa-40b7-a941-b06bc031a7b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:12,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2f56fc9-22aa-40b7-a941-b06bc031a7b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:12,735] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:12,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:12,735] [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 arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	100.0	1209	1219	95	conclusive
Clostridium pasteurianum	strain=DSM 525	GCA_000330945.1	1501	1501	type	True	81.7774	753	1219	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_000724205.3	1501	1501	type	True	81.7102	763	1219	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	81.7097	762	1219	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_001856645.1	1501	1501	type	True	81.6981	754	1219	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.5106	184	1219	95	below_threshold
Clostridium combesii	strain=DSM 20696	GCA_002749945.1	39481	39481	type	True	76.5005	164	1219	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.4969	178	1219	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.4361	180	1219	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	76.3502	167	1219	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.3479	135	1219	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	76.3311	170	1219	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	76.0249	147	1219	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.003	140	1219	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	75.992	148	1219	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	75.9711	114	1219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:12,737] [INFO] DFAST Taxonomy check result was written to GCF_000246895.1_ASM24689v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:12,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:12,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:12,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2f56fc9-22aa-40b7-a941-b06bc031a7b5/dqc_reference/checkm_data
[2024-01-24 13:19:12,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:12,779] [INFO] Task started: CheckM
[2024-01-24 13:19:12,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000246895.1_ASM24689v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000246895.1_ASM24689v2_genomic.fna/checkm_input GCF_000246895.1_ASM24689v2_genomic.fna/checkm_result
[2024-01-24 13:19:37,053] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:37,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:37,074] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:37,074] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:37,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000246895.1_ASM24689v2_genomic.fna/markers.fasta)
[2024-01-24 13:19:37,075] [INFO] Task started: Blastn
[2024-01-24 13:19:37,075] [INFO] Running command: blastn -query GCF_000246895.1_ASM24689v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2f56fc9-22aa-40b7-a941-b06bc031a7b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000246895.1_ASM24689v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:37,917] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:37,920] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:37,921] [INFO] Target genome list was writen to GCF_000246895.1_ASM24689v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:37,938] [INFO] Task started: fastANI
[2024-01-24 13:19:37,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc2414c-6da8-4a83-a814-3e0726e53e5b/GCF_000246895.1_ASM24689v2_genomic.fna.gz --refList GCF_000246895.1_ASM24689v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000246895.1_ASM24689v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:53,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:53,186] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:53,186] [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_000246895.1	s__Clostridium_I arbusti	100.0	1209	1219	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	conclusive
GCF_000389635.1	s__Clostridium_I pasteurianum_A	83.3718	887	1219	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_000807255.1	s__Clostridium_I pasteurianum	81.6935	766	1219	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	-
GCF_900176305.1	s__Clostridium_I acidisoli	78.2205	311	1219	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	77.5017	280	1219	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_000968375.1	s__Clostridium_AM scatologenes	76.8136	208	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_012926525.1	s__Clostridium_AM sp012926525	76.5743	205	1219	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	76.5295	142	1219	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_002008345.1	s__Clostridium_F tepidum	76.3342	136	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_001276985.1	s__Clostridium_F botulinum	76.3311	170	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_000498355.1	s__Clostridium sp000498355	76.2385	131	1219	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_014836835.1	s__Clostridium_J sp900547625	76.1847	124	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	-
GCF_002934235.1	s__Clostridium_L algidicarnis	76.1506	93	1219	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	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.1373	151	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_900141845.1	s__Clostridium_AG cavendishii	76.003	140	1219	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_018917145.1	s__Clostridium_AN bornimense_A	75.9578	112	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002050515.1	s__Clostridium thermobutyricum	75.9444	116	1219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
GCA_002455975.1	s__Clostridium_J sp002455975	75.8631	119	1219	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:53,187] [INFO] GTDB search result was written to GCF_000246895.1_ASM24689v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:53,188] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:53,192] [INFO] DFAST_QC result json was written to GCF_000246895.1_ASM24689v2_genomic.fna/dqc_result.json
[2024-01-24 13:19:53,192] [INFO] DFAST_QC completed!
[2024-01-24 13:19:53,192] [INFO] Total running time: 0h1m7s