[2024-01-24 13:49:27,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgae933eee-3d5c-4ce6-b463-c3810c1b6fc3/dqc_reference
[2024-01-24 13:49:28,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,858] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,858] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a253581-8a23-4062-b383-ddc2c0966905/GCF_030815085.1_ASM3081508v1_genomic.fna.gz | prodigal -d GCF_030815085.1_ASM3081508v1_genomic.fna/cds.fna -a GCF_030815085.1_ASM3081508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:33,990] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:33,991] [INFO] Task started: HMMsearch
[2024-01-24 13:49:33,991] [INFO] Running command: hmmsearch --tblout GCF_030815085.1_ASM3081508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae933eee-3d5c-4ce6-b463-c3810c1b6fc3/dqc_reference/reference_markers.hmm GCF_030815085.1_ASM3081508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,284] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,317] [INFO] Query marker FASTA was written to GCF_030815085.1_ASM3081508v1_genomic.fna/markers.fasta
[2024-01-24 13:49:34,318] [INFO] Task started: Blastn
[2024-01-24 13:49:34,318] [INFO] Running command: blastn -query GCF_030815085.1_ASM3081508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae933eee-3d5c-4ce6-b463-c3810c1b6fc3/dqc_reference/reference_markers.fasta -out GCF_030815085.1_ASM3081508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,909] [INFO] Selected 6 target genomes.
[2024-01-24 13:49:34,910] [INFO] Target genome list was writen to GCF_030815085.1_ASM3081508v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:34,915] [INFO] Task started: fastANI
[2024-01-24 13:49:34,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a253581-8a23-4062-b383-ddc2c0966905/GCF_030815085.1_ASM3081508v1_genomic.fna.gz --refList GCF_030815085.1_ASM3081508v1_genomic.fna/target_genomes.txt --output GCF_030815085.1_ASM3081508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:40,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:40,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae933eee-3d5c-4ce6-b463-c3810c1b6fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:40,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae933eee-3d5c-4ce6-b463-c3810c1b6fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:40,106] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:40,107] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:40,107] [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
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	87.532	829	1142	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	87.4815	831	1142	95	below_threshold
Paraclostridium bifermentans subsp. muricolitidis	strain=PAGU 1678	GCA_019650315.1	2663173	1490	type	True	87.4762	807	1142	95	below_threshold
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	87.4592	760	1142	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	87.4297	841	1142	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	87.3702	825	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:40,108] [INFO] DFAST Taxonomy check result was written to GCF_030815085.1_ASM3081508v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:40,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:40,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:40,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae933eee-3d5c-4ce6-b463-c3810c1b6fc3/dqc_reference/checkm_data
[2024-01-24 13:49:40,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:40,158] [INFO] Task started: CheckM
[2024-01-24 13:49:40,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030815085.1_ASM3081508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030815085.1_ASM3081508v1_genomic.fna/checkm_input GCF_030815085.1_ASM3081508v1_genomic.fna/checkm_result
[2024-01-24 13:50:03,722] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:03,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:03,748] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:03,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:03,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030815085.1_ASM3081508v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:03,750] [INFO] Task started: Blastn
[2024-01-24 13:50:03,750] [INFO] Running command: blastn -query GCF_030815085.1_ASM3081508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae933eee-3d5c-4ce6-b463-c3810c1b6fc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030815085.1_ASM3081508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:04,565] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:04,568] [INFO] Selected 5 target genomes.
[2024-01-24 13:50:04,568] [INFO] Target genome list was writen to GCF_030815085.1_ASM3081508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:04,577] [INFO] Task started: fastANI
[2024-01-24 13:50:04,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a253581-8a23-4062-b383-ddc2c0966905/GCF_030815085.1_ASM3081508v1_genomic.fna.gz --refList GCF_030815085.1_ASM3081508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030815085.1_ASM3081508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:08,670] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,679] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:08,679] [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_006802875.1	s__Paraclostridium bifermentans	87.51	830	1142	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_001006285.1	s__Paraclostridium benzoelyticum	87.458	759	1142	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_000452245.2	s__Paraclostridium bifermentans_A	87.419	842	1142	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_015668515.1	s__Paraclostridium tenue	83.4015	644	1142	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_000953675.1	s__Paraclostridium sordellii	82.6003	667	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,681] [INFO] GTDB search result was written to GCF_030815085.1_ASM3081508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:08,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:08,684] [INFO] DFAST_QC result json was written to GCF_030815085.1_ASM3081508v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:08,684] [INFO] DFAST_QC completed!
[2024-01-24 13:50:08,684] [INFO] Total running time: 0h0m41s