[2024-01-24 13:51:11,631] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:11,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:11,634] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc5ab41c-da04-47ed-bfcd-12b223b65bb0/dqc_reference
[2024-01-24 13:51:12,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:12,971] [INFO] Task started: Prodigal
[2024-01-24 13:51:12,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg814f7b9d-f99e-439b-b03c-7f7aa7e2f830/GCF_014384745.1_ASM1438474v1_genomic.fna.gz | prodigal -d GCF_014384745.1_ASM1438474v1_genomic.fna/cds.fna -a GCF_014384745.1_ASM1438474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:20,764] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:20,764] [INFO] Task started: HMMsearch
[2024-01-24 13:51:20,765] [INFO] Running command: hmmsearch --tblout GCF_014384745.1_ASM1438474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc5ab41c-da04-47ed-bfcd-12b223b65bb0/dqc_reference/reference_markers.hmm GCF_014384745.1_ASM1438474v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:21,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:21,039] [INFO] Found 6/6 markers.
[2024-01-24 13:51:21,067] [INFO] Query marker FASTA was written to GCF_014384745.1_ASM1438474v1_genomic.fna/markers.fasta
[2024-01-24 13:51:21,068] [INFO] Task started: Blastn
[2024-01-24 13:51:21,068] [INFO] Running command: blastn -query GCF_014384745.1_ASM1438474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc5ab41c-da04-47ed-bfcd-12b223b65bb0/dqc_reference/reference_markers.fasta -out GCF_014384745.1_ASM1438474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:21,700] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:21,704] [INFO] Selected 25 target genomes.
[2024-01-24 13:51:21,704] [INFO] Target genome list was writen to GCF_014384745.1_ASM1438474v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:21,718] [INFO] Task started: fastANI
[2024-01-24 13:51:21,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg814f7b9d-f99e-439b-b03c-7f7aa7e2f830/GCF_014384745.1_ASM1438474v1_genomic.fna.gz --refList GCF_014384745.1_ASM1438474v1_genomic.fna/target_genomes.txt --output GCF_014384745.1_ASM1438474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:35,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:35,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc5ab41c-da04-47ed-bfcd-12b223b65bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:35,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc5ab41c-da04-47ed-bfcd-12b223b65bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:35,573] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:51:35,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:35,573] [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
Luoshenia tenuis	strain=NSJ-44	GCA_014384745.1	2763654	2763654	type	True	100.0	880	880	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:51:35,575] [INFO] DFAST Taxonomy check result was written to GCF_014384745.1_ASM1438474v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:35,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:35,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:35,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc5ab41c-da04-47ed-bfcd-12b223b65bb0/dqc_reference/checkm_data
[2024-01-24 13:51:35,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:35,609] [INFO] Task started: CheckM
[2024-01-24 13:51:35,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384745.1_ASM1438474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384745.1_ASM1438474v1_genomic.fna/checkm_input GCF_014384745.1_ASM1438474v1_genomic.fna/checkm_result
[2024-01-24 13:52:03,306] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:03,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:03,334] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:03,334] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:03,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384745.1_ASM1438474v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:03,335] [INFO] Task started: Blastn
[2024-01-24 13:52:03,335] [INFO] Running command: blastn -query GCF_014384745.1_ASM1438474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc5ab41c-da04-47ed-bfcd-12b223b65bb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384745.1_ASM1438474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:04,238] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:04,242] [INFO] Selected 29 target genomes.
[2024-01-24 13:52:04,242] [INFO] Target genome list was writen to GCF_014384745.1_ASM1438474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:04,267] [INFO] Task started: fastANI
[2024-01-24 13:52:04,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg814f7b9d-f99e-439b-b03c-7f7aa7e2f830/GCF_014384745.1_ASM1438474v1_genomic.fna.gz --refList GCF_014384745.1_ASM1438474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384745.1_ASM1438474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:17,109] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:17,119] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:17,120] [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_005845105.1	s__GCA-900066905 sp900066905	95.6629	805	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__GCA-900066905;g__GCA-900066905	95.0	97.17	95.66	0.94	0.91	5	conclusive
GCA_018710985.1	s__Limiplasma pullicola	76.5301	67	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540045.1	s__Limiplasma merdipullorum	76.4772	53	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Limiplasma	95.0	97.42	97.19	0.80	0.74	6	-
GCA_017937505.1	s__Ventricola sp017937505	76.278	53	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Ventricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542005.1	s__Parachristensenella sp900542005	76.0304	67	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UMGS416;g__Parachristensenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716755.1	s__Alectryocaccomicrobium excrementavium	75.8193	52	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__Alectryocaccomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:17,121] [INFO] GTDB search result was written to GCF_014384745.1_ASM1438474v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:17,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:17,124] [INFO] DFAST_QC result json was written to GCF_014384745.1_ASM1438474v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:17,124] [INFO] DFAST_QC completed!
[2024-01-24 13:52:17,125] [INFO] Total running time: 0h1m5s