[2024-01-25 18:28:35,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:35,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:35,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d71179-bb29-4816-8d69-0c19ddb94400/dqc_reference
[2024-01-25 18:28:36,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:36,644] [INFO] Task started: Prodigal
[2024-01-25 18:28:36,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgc76bbd49-4074-44ff-bcfc-9e3499c71dde/GCF_002270055.1_ASM227005v1_genomic.fna.gz | prodigal -d GCF_002270055.1_ASM227005v1_genomic.fna/cds.fna -a GCF_002270055.1_ASM227005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:43,554] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:43,555] [INFO] Task started: HMMsearch
[2024-01-25 18:28:43,555] [INFO] Running command: hmmsearch --tblout GCF_002270055.1_ASM227005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d71179-bb29-4816-8d69-0c19ddb94400/dqc_reference/reference_markers.hmm GCF_002270055.1_ASM227005v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:43,785] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:43,786] [INFO] Found 6/6 markers.
[2024-01-25 18:28:43,825] [INFO] Query marker FASTA was written to GCF_002270055.1_ASM227005v1_genomic.fna/markers.fasta
[2024-01-25 18:28:43,825] [INFO] Task started: Blastn
[2024-01-25 18:28:43,825] [INFO] Running command: blastn -query GCF_002270055.1_ASM227005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d71179-bb29-4816-8d69-0c19ddb94400/dqc_reference/reference_markers.fasta -out GCF_002270055.1_ASM227005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:44,385] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:44,388] [INFO] Selected 21 target genomes.
[2024-01-25 18:28:44,388] [INFO] Target genome list was writen to GCF_002270055.1_ASM227005v1_genomic.fna/target_genomes.txt
[2024-01-25 18:28:44,417] [INFO] Task started: fastANI
[2024-01-25 18:28:44,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgc76bbd49-4074-44ff-bcfc-9e3499c71dde/GCF_002270055.1_ASM227005v1_genomic.fna.gz --refList GCF_002270055.1_ASM227005v1_genomic.fna/target_genomes.txt --output GCF_002270055.1_ASM227005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:28:57,261] [INFO] Task succeeded: fastANI
[2024-01-25 18:28:57,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d71179-bb29-4816-8d69-0c19ddb94400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:28:57,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d71179-bb29-4816-8d69-0c19ddb94400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:28:57,273] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:28:57,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:28:57,273] [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
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	100.0	1535	1540	95	conclusive
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	77.5569	229	1540	95	below_threshold
Crassaminicella thermophila	strain=SY095	GCA_008152325.1	2599308	2599308	type	True	76.6959	200	1540	95	below_threshold
Geosporobacter ferrireducens	strain=IRF9	GCA_001750685.1	1424294	1424294	type	True	76.1144	61	1540	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	75.6695	105	1540	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	75.6294	103	1540	95	below_threshold
Gottschalkia acidurici	strain=9a	GCA_000299355.1	1556	1556	type	True	75.5875	70	1540	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	75.4432	104	1540	95	below_threshold
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	75.4173	95	1540	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	75.3616	85	1540	95	below_threshold
Paraclostridium bifermentans subsp. muricolitidis	strain=PAGU 1678	GCA_019650315.1	2663173	1490	type	True	75.3561	92	1540	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	75.3387	99	1540	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	75.3143	75	1540	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	75.3109	66	1540	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.2295	65	1540	95	below_threshold
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	75.1973	89	1540	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	74.9981	55	1540	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	74.9295	92	1540	95	below_threshold
Defluviitalea phaphyphila	strain=Alg1	GCA_001466305.1	1473580	1473580	type	True	74.8642	61	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:28:57,275] [INFO] DFAST Taxonomy check result was written to GCF_002270055.1_ASM227005v1_genomic.fna/tc_result.tsv
[2024-01-25 18:28:57,275] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:28:57,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:28:57,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d71179-bb29-4816-8d69-0c19ddb94400/dqc_reference/checkm_data
[2024-01-25 18:28:57,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:28:57,321] [INFO] Task started: CheckM
[2024-01-25 18:28:57,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002270055.1_ASM227005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002270055.1_ASM227005v1_genomic.fna/checkm_input GCF_002270055.1_ASM227005v1_genomic.fna/checkm_result
[2024-01-25 18:29:22,071] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:22,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:22,091] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:22,091] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:22,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002270055.1_ASM227005v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:22,092] [INFO] Task started: Blastn
[2024-01-25 18:29:22,092] [INFO] Running command: blastn -query GCF_002270055.1_ASM227005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d71179-bb29-4816-8d69-0c19ddb94400/dqc_reference/reference_markers_gtdb.fasta -out GCF_002270055.1_ASM227005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:22,969] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:22,972] [INFO] Selected 23 target genomes.
[2024-01-25 18:29:22,972] [INFO] Target genome list was writen to GCF_002270055.1_ASM227005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:22,989] [INFO] Task started: fastANI
[2024-01-25 18:29:22,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgc76bbd49-4074-44ff-bcfc-9e3499c71dde/GCF_002270055.1_ASM227005v1_genomic.fna.gz --refList GCF_002270055.1_ASM227005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002270055.1_ASM227005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:35,687] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:35,701] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:35,701] [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_002270055.1	s__Anaeromicrobium sediminis	100.0	1535	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Anaeromicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004345705.1	s__Marinisporobacter balticus	76.9915	169	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Marinisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203185.1	s__143-21 sp019203185	76.8445	160	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__143-21	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008152325.1	s__SY095 sp008152325	76.7161	202	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__SY095	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138215.1	s__Inediibacterium nitritogenes	76.2161	155	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614235.1	s__Clostridium_H haemolyticum	75.5953	60	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.44	97.38	0.90	0.84	13	-
GCF_000299355.1	s__Gottschalkia acidurici	75.5563	72	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006285.1	s__Paraclostridium benzoelyticum	75.4173	95	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.4733	N/A	N/A	N/A	N/A	1	-
GCF_001190785.1	s__Gottschalkia_A purinilytica	75.3807	83	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006802875.1	s__Paraclostridium bifermentans	75.3387	99	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCF_000452245.2	s__Paraclostridium bifermentans_A	75.3203	104	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.39	96.64	0.88	0.81	7	-
GCF_017590215.1	s__CCUG-7971 sp017590215	75.2801	84	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001316435.1	s__Caloranaerobacter sp001316435	75.2763	72	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900002575.1	s__Romboutsia_C hominis	75.2627	100	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
GCF_001730685.1	s__Caloranaerobacter ferrireducens	75.2295	65	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001243045.1	s__Clostridium_F niameyense	75.1476	61	1540	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	-
GCF_001405015.1	s__Clostridium disporicum	75.1432	69	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCF_900142075.1	s__Clostridium_AA amylolyticum	74.9876	56	1540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:29:35,703] [INFO] GTDB search result was written to GCF_002270055.1_ASM227005v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:35,703] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:35,707] [INFO] DFAST_QC result json was written to GCF_002270055.1_ASM227005v1_genomic.fna/dqc_result.json
[2024-01-25 18:29:35,708] [INFO] DFAST_QC completed!
[2024-01-25 18:29:35,708] [INFO] Total running time: 0h1m0s