[2024-01-24 14:06:45,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:45,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:45,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg23ff7bcd-8ae6-4201-95d2-97d529fedb41/dqc_reference
[2024-01-24 14:06:46,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:46,755] [INFO] Task started: Prodigal
[2024-01-24 14:06:46,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg55a25e74-3299-460d-b407-b4b1b0cb0813/GCF_000311865.1_ASM31186v1_genomic.fna.gz | prodigal -d GCF_000311865.1_ASM31186v1_genomic.fna/cds.fna -a GCF_000311865.1_ASM31186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:49,975] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:49,975] [INFO] Task started: HMMsearch
[2024-01-24 14:06:49,975] [INFO] Running command: hmmsearch --tblout GCF_000311865.1_ASM31186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23ff7bcd-8ae6-4201-95d2-97d529fedb41/dqc_reference/reference_markers.hmm GCF_000311865.1_ASM31186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:50,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:50,207] [INFO] Found 6/6 markers.
[2024-01-24 14:06:50,232] [INFO] Query marker FASTA was written to GCF_000311865.1_ASM31186v1_genomic.fna/markers.fasta
[2024-01-24 14:06:50,232] [INFO] Task started: Blastn
[2024-01-24 14:06:50,232] [INFO] Running command: blastn -query GCF_000311865.1_ASM31186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23ff7bcd-8ae6-4201-95d2-97d529fedb41/dqc_reference/reference_markers.fasta -out GCF_000311865.1_ASM31186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:50,890] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:50,897] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:50,898] [INFO] Target genome list was writen to GCF_000311865.1_ASM31186v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:50,905] [INFO] Task started: fastANI
[2024-01-24 14:06:50,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a25e74-3299-460d-b407-b4b1b0cb0813/GCF_000311865.1_ASM31186v1_genomic.fna.gz --refList GCF_000311865.1_ASM31186v1_genomic.fna/target_genomes.txt --output GCF_000311865.1_ASM31186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:56,664] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:56,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23ff7bcd-8ae6-4201-95d2-97d529fedb41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:56,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23ff7bcd-8ae6-4201-95d2-97d529fedb41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:56,675] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:56,675] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:56,675] [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
Peptoniphilus obesi	strain=ph1	GCA_000311865.1	1472765	1472765	type	True	99.9998	587	589	95	conclusive
Peptoniphilus harei	strain=FDAARGOS_1136	GCA_016726485.1	54005	54005	suspected-type	True	83.5731	116	589	95	below_threshold
Peptoniphilus harei	strain=NCTC13076	GCA_900454685.1	54005	54005	suspected-type	True	83.5056	113	589	95	below_threshold
Peptoniphilus phoceensis	strain=SIT15	GCA_001517665.2	1720298	1720298	type	True	80.6139	90	589	95	below_threshold
Anaerosphaera aminiphila	strain=DSM 21120	GCA_900129925.1	1120994	1120994	type	True	78.6025	87	589	95	below_threshold
Peptoniphilus indolicus	strain=NCTC11088	GCA_900454665.1	33030	33030	type	True	77.3367	91	589	95	below_threshold
Peptoniphilus mikwangii	strain=ChDC B134	GCA_000468535.1	1354300	1354300	type	True	77.2248	75	589	95	below_threshold
Peptoniphilus indolicus	strain=ATCC 29427	GCA_000227315.1	33030	33030	type	True	77.102	88	589	95	below_threshold
Peptoniphilus stercorisuis	strain=DSM 27563	GCA_017874395.1	1436965	1436965	type	True	76.8339	102	589	95	below_threshold
Anaerosphaera massiliensis	strain=Marseille-P4592	GCA_902167235.1	2040296	2040296	type	True	76.7171	84	589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:56,678] [INFO] DFAST Taxonomy check result was written to GCF_000311865.1_ASM31186v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:56,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:56,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:56,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23ff7bcd-8ae6-4201-95d2-97d529fedb41/dqc_reference/checkm_data
[2024-01-24 14:06:56,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:56,706] [INFO] Task started: CheckM
[2024-01-24 14:06:56,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000311865.1_ASM31186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000311865.1_ASM31186v1_genomic.fna/checkm_input GCF_000311865.1_ASM31186v1_genomic.fna/checkm_result
[2024-01-24 14:07:13,513] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:13,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:13,534] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:13,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:13,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000311865.1_ASM31186v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:13,536] [INFO] Task started: Blastn
[2024-01-24 14:07:13,536] [INFO] Running command: blastn -query GCF_000311865.1_ASM31186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23ff7bcd-8ae6-4201-95d2-97d529fedb41/dqc_reference/reference_markers_gtdb.fasta -out GCF_000311865.1_ASM31186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:14,316] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:14,514] [INFO] Selected 18 target genomes.
[2024-01-24 14:07:14,515] [INFO] Target genome list was writen to GCF_000311865.1_ASM31186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:14,531] [INFO] Task started: fastANI
[2024-01-24 14:07:14,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a25e74-3299-460d-b407-b4b1b0cb0813/GCF_000311865.1_ASM31186v1_genomic.fna.gz --refList GCF_000311865.1_ASM31186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000311865.1_ASM31186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:21,236] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:21,250] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:21,250] [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_000311865.1	s__Peptoniphilus_E obesi	99.9998	587	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000146345.1	s__Peptoniphilus_B duerdenii	85.2651	111	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_B	95.0	96.19	96.19	0.86	0.86	2	-
GCF_900454685.1	s__Peptoniphilus_A harei	83.4977	114	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.43	96.58	0.91	0.87	7	-
GCF_901447155.2	s__Peptoniphilus_E catoniae	80.6066	156	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312025.1	s__Peptoniphilus_A timonensis	79.428	88	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	N/A	N/A	N/A	N/A	1	-
GCF_900129925.1	s__Anaerosphaera aminiphila	78.6504	86	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000468535.1	s__Anaerosphaera mikwangii	77.3161	75	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	99.03	99.03	0.96	0.96	2	-
GCF_000227315.1	s__Peptoniphilus indolicus	77.102	88	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus	95.0	99.65	99.65	0.96	0.96	2	-
GCA_000952975.1	s__Peptoniphilus_E sp000952975	77.0743	92	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874395.1	s__Anaerosphaera stercorisuis	76.8555	101	589	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:21,252] [INFO] GTDB search result was written to GCF_000311865.1_ASM31186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:21,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:21,255] [INFO] DFAST_QC result json was written to GCF_000311865.1_ASM31186v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:21,256] [INFO] DFAST_QC completed!
[2024-01-24 14:07:21,256] [INFO] Total running time: 0h0m36s