[2024-01-24 14:05:36,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgb61dcc44-4431-42f5-9d4c-7d8418dacd1a/dqc_reference
[2024-01-24 14:05:38,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:38,059] [INFO] Task started: Prodigal
[2024-01-24 14:05:38,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e579f76-7aa3-4a72-ac1b-81bce4ca9c1d/GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/cds.fna -a GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:41,703] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:41,703] [INFO] Task started: HMMsearch
[2024-01-24 14:05:41,703] [INFO] Running command: hmmsearch --tblout GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb61dcc44-4431-42f5-9d4c-7d8418dacd1a/dqc_reference/reference_markers.hmm GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:41,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:41,996] [INFO] Found 6/6 markers.
[2024-01-24 14:05:42,026] [INFO] Query marker FASTA was written to GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:42,026] [INFO] Task started: Blastn
[2024-01-24 14:05:42,027] [INFO] Running command: blastn -query GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61dcc44-4431-42f5-9d4c-7d8418dacd1a/dqc_reference/reference_markers.fasta -out GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:42,705] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:42,708] [INFO] Selected 15 target genomes.
[2024-01-24 14:05:42,709] [INFO] Target genome list was writen to GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:42,742] [INFO] Task started: fastANI
[2024-01-24 14:05:42,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e579f76-7aa3-4a72-ac1b-81bce4ca9c1d/GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna.gz --refList GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:51,972] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:51,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb61dcc44-4431-42f5-9d4c-7d8418dacd1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:51,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb61dcc44-4431-42f5-9d4c-7d8418dacd1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:51,989] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:51,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:51,989] [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
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	100.0	798	807	95	conclusive
Tepidibacter thalassicus	strain=DSM 15285	GCA_900129915.1	214905	214905	type	True	87.0038	561	807	95	below_threshold
Tepidibacter mesophilus	strain=JCM 16806	GCA_002724055.1	655607	655607	type	True	79.7281	452	807	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	76.7392	180	807	95	below_threshold
Clostridioides difficile	strain=ATCC 9689	GCA_000376285.1	1496	1496	type	True	76.55	153	807	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	76.5454	169	807	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	76.5225	189	807	95	below_threshold
Clostridioides difficile	strain=DSM 1296	GCA_000438845.1	1496	1496	type	True	76.5002	156	807	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	76.4771	174	807	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	76.3642	136	807	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	76.3087	136	807	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	76.2723	137	807	95	below_threshold
Peptacetobacter hominis	strain=ZHW00191	GCA_006861675.1	2743610	2743610	type	True	75.951	70	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:51,993] [INFO] DFAST Taxonomy check result was written to GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:05:51,994] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:51,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:51,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb61dcc44-4431-42f5-9d4c-7d8418dacd1a/dqc_reference/checkm_data
[2024-01-24 14:05:51,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:52,028] [INFO] Task started: CheckM
[2024-01-24 14:05:52,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/checkm_input GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:06:11,300] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:11,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:11,319] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:11,319] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:11,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:06:11,320] [INFO] Task started: Blastn
[2024-01-24 14:06:11,320] [INFO] Running command: blastn -query GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61dcc44-4431-42f5-9d4c-7d8418dacd1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:12,368] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:12,371] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:12,371] [INFO] Target genome list was writen to GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:12,399] [INFO] Task started: fastANI
[2024-01-24 14:06:12,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e579f76-7aa3-4a72-ac1b-81bce4ca9c1d/GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna.gz --refList GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:23,039] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:23,054] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:23,054] [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_900142235.1	s__Tepidibacter formicigenes	100.0	798	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129915.1	s__Tepidibacter thalassicus	86.9674	562	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002724055.1	s__Tepidibacter_A mesophilus	79.7559	450	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001584565.1	s__Clostridium_Y paradoxum	78.2872	241	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridium_Y	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002029295.1	s__Clostridium_Y thermoalcaliphilum	78.1679	241	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridium_Y	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015668515.1	s__Paraclostridium tenue	76.8948	196	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	-
GCF_002251085.2	s__Romboutsia_B maritimum	76.6207	184	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001077535.1	s__Clostridioides difficile	76.5896	157	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	98.86	95.94	0.94	0.86	2225	-
GCF_000953675.1	s__Paraclostridium sordellii	76.5335	190	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
GCF_012317385.1	s__GCA-900066495 sp900545985	76.5057	174	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	98.78	98.75	0.89	0.89	3	-
GCF_000439105.1	s__Terrisporobacter glycolicus	76.3223	135	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
GCA_902363255.1	s__Terrisporobacter sp902363255	76.3056	139	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873185.1	s__Clostridioides_A mangenotii	76.178	78	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A	95.0	96.86	96.86	0.88	0.88	2	-
GCA_014385225.1	s__JACRTK01 sp014385225	75.7905	54	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__JACRTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557165.1	s__Terrisporobacter sp900557165	75.7517	102	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.06	99.06	0.78	0.78	2	-
GCA_900553685.1	s__Scatovivens faecipullorum	74.9662	58	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	98.76	98.76	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:23,056] [INFO] GTDB search result was written to GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:23,056] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:23,100] [INFO] DFAST_QC result json was written to GCF_900142235.1_IMG-taxon_2585428175_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:23,100] [INFO] DFAST_QC completed!
[2024-01-24 14:06:23,101] [INFO] Total running time: 0h0m46s