[2024-01-24 11:26:11,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,388] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg80abf462-0255-43a7-9788-cb1c521608a1/dqc_reference
[2024-01-24 11:26:12,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:12,709] [INFO] Task started: Prodigal
[2024-01-24 11:26:12,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg3413b98a-962c-4fc7-a957-a143ec575402/GCF_016908115.1_ASM1690811v1_genomic.fna.gz | prodigal -d GCF_016908115.1_ASM1690811v1_genomic.fna/cds.fna -a GCF_016908115.1_ASM1690811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:15,997] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:15,997] [INFO] Task started: HMMsearch
[2024-01-24 11:26:15,998] [INFO] Running command: hmmsearch --tblout GCF_016908115.1_ASM1690811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80abf462-0255-43a7-9788-cb1c521608a1/dqc_reference/reference_markers.hmm GCF_016908115.1_ASM1690811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:16,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:16,255] [INFO] Found 6/6 markers.
[2024-01-24 11:26:16,274] [INFO] Query marker FASTA was written to GCF_016908115.1_ASM1690811v1_genomic.fna/markers.fasta
[2024-01-24 11:26:16,276] [INFO] Task started: Blastn
[2024-01-24 11:26:16,276] [INFO] Running command: blastn -query GCF_016908115.1_ASM1690811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80abf462-0255-43a7-9788-cb1c521608a1/dqc_reference/reference_markers.fasta -out GCF_016908115.1_ASM1690811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:16,897] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:16,901] [INFO] Selected 7 target genomes.
[2024-01-24 11:26:16,901] [INFO] Target genome list was writen to GCF_016908115.1_ASM1690811v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:16,945] [INFO] Task started: fastANI
[2024-01-24 11:26:16,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg3413b98a-962c-4fc7-a957-a143ec575402/GCF_016908115.1_ASM1690811v1_genomic.fna.gz --refList GCF_016908115.1_ASM1690811v1_genomic.fna/target_genomes.txt --output GCF_016908115.1_ASM1690811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:20,378] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:20,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80abf462-0255-43a7-9788-cb1c521608a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:20,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80abf462-0255-43a7-9788-cb1c521608a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:20,456] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:20,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:20,457] [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 gorbachii	strain=DSM 21461	GCA_016908115.1	411567	411567	type	True	100.0	612	613	95	conclusive
Peptoniphilus grossensis	strain=ph5	GCA_000311825.1	1465756	1465756	type	True	89.2092	500	613	95	below_threshold
Peptoniphilus senegalensis	strain=type strain: JC140	GCA_000321025.1	1465757	1465757	type	True	87.6448	461	613	95	below_threshold
Peptoniphilus phoceensis	strain=SIT15	GCA_001517665.2	1720298	1720298	type	True	83.7818	435	613	95	below_threshold
Peptoniphilus timonensis	strain=JC401	GCA_000312025.1	1268254	1268254	type	True	83.6625	414	613	95	below_threshold
Peptoniphilus harei	strain=NCTC13076	GCA_900454685.1	54005	54005	suspected-type	True	83.6348	420	613	95	below_threshold
Peptoniphilus harei	strain=FDAARGOS_1136	GCA_016726485.1	54005	54005	suspected-type	True	83.5454	422	613	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:20,458] [INFO] DFAST Taxonomy check result was written to GCF_016908115.1_ASM1690811v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:20,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:20,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:20,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80abf462-0255-43a7-9788-cb1c521608a1/dqc_reference/checkm_data
[2024-01-24 11:26:20,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:20,487] [INFO] Task started: CheckM
[2024-01-24 11:26:20,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908115.1_ASM1690811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908115.1_ASM1690811v1_genomic.fna/checkm_input GCF_016908115.1_ASM1690811v1_genomic.fna/checkm_result
[2024-01-24 11:26:41,391] [INFO] Task succeeded: CheckM
[2024-01-24 11:26:41,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:26:41,441] [INFO] ===== Completeness check finished =====
[2024-01-24 11:26:41,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:26:41,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908115.1_ASM1690811v1_genomic.fna/markers.fasta)
[2024-01-24 11:26:41,442] [INFO] Task started: Blastn
[2024-01-24 11:26:41,442] [INFO] Running command: blastn -query GCF_016908115.1_ASM1690811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80abf462-0255-43a7-9788-cb1c521608a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908115.1_ASM1690811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:42,832] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:42,835] [INFO] Selected 7 target genomes.
[2024-01-24 11:26:42,835] [INFO] Target genome list was writen to GCF_016908115.1_ASM1690811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:26:42,865] [INFO] Task started: fastANI
[2024-01-24 11:26:42,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg3413b98a-962c-4fc7-a957-a143ec575402/GCF_016908115.1_ASM1690811v1_genomic.fna.gz --refList GCF_016908115.1_ASM1690811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908115.1_ASM1690811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:26:46,640] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:46,659] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:26:46,659] [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_016908115.1	s__Peptoniphilus_A gorbachii	100.0	612	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	96.70	96.17	0.85	0.82	5	conclusive
GCF_000311825.1	s__Peptoniphilus_A grossensis	89.2092	500	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.39	95.38	0.93	0.87	4	-
GCF_000321025.1	s__Peptoniphilus_A senegalensis	87.6448	461	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	98.73	97.46	0.94	0.88	3	-
GCF_012976305.1	s__Peptoniphilus_A faecalis	84.7454	426	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	98.47	98.47	0.83	0.83	2	-
GCF_001517665.2	s__Peptoniphilus_A phoceensis	83.7754	437	613	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	100.00	100.00	1.00	1.00	2	-
GCF_000312025.1	s__Peptoniphilus_A timonensis	83.6625	414	613	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_900454685.1	s__Peptoniphilus_A harei	83.6106	422	613	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:26:46,661] [INFO] GTDB search result was written to GCF_016908115.1_ASM1690811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:26:46,662] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:26:46,665] [INFO] DFAST_QC result json was written to GCF_016908115.1_ASM1690811v1_genomic.fna/dqc_result.json
[2024-01-24 11:26:46,665] [INFO] DFAST_QC completed!
[2024-01-24 11:26:46,665] [INFO] Total running time: 0h0m35s