[2024-01-25 18:07:35,576] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:35,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:35,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d73e359-dfef-4ebc-a552-f6d5c8f82943/dqc_reference
[2024-01-25 18:07:36,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:36,745] [INFO] Task started: Prodigal
[2024-01-25 18:07:36,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b7ae96b-29ce-45a3-86ca-1d701d1cc943/GCF_000337235.1_ASM33723v1_genomic.fna.gz | prodigal -d GCF_000337235.1_ASM33723v1_genomic.fna/cds.fna -a GCF_000337235.1_ASM33723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:55,970] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:55,970] [INFO] Task started: HMMsearch
[2024-01-25 18:07:55,970] [INFO] Running command: hmmsearch --tblout GCF_000337235.1_ASM33723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d73e359-dfef-4ebc-a552-f6d5c8f82943/dqc_reference/reference_markers.hmm GCF_000337235.1_ASM33723v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:56,215] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:56,216] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6b7ae96b-29ce-45a3-86ca-1d701d1cc943/GCF_000337235.1_ASM33723v1_genomic.fna.gz]
[2024-01-25 18:07:56,258] [INFO] Query marker FASTA was written to GCF_000337235.1_ASM33723v1_genomic.fna/markers.fasta
[2024-01-25 18:07:56,258] [INFO] Task started: Blastn
[2024-01-25 18:07:56,258] [INFO] Running command: blastn -query GCF_000337235.1_ASM33723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d73e359-dfef-4ebc-a552-f6d5c8f82943/dqc_reference/reference_markers.fasta -out GCF_000337235.1_ASM33723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:56,763] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:56,766] [INFO] Selected 7 target genomes.
[2024-01-25 18:07:56,766] [INFO] Target genome list was writen to GCF_000337235.1_ASM33723v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:56,773] [INFO] Task started: fastANI
[2024-01-25 18:07:56,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b7ae96b-29ce-45a3-86ca-1d701d1cc943/GCF_000337235.1_ASM33723v1_genomic.fna.gz --refList GCF_000337235.1_ASM33723v1_genomic.fna/target_genomes.txt --output GCF_000337235.1_ASM33723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:04,997] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:04,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d73e359-dfef-4ebc-a552-f6d5c8f82943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:04,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d73e359-dfef-4ebc-a552-f6d5c8f82943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:05,008] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:08:05,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:05,008] [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
Natronorubrum tibetense	strain=GA33	GCA_000337235.1	63128	63128	type	True	100.0	1606	1611	95	conclusive
Natronorubrum tibetense	strain=GA33	GCA_000383975.1	63128	63128	type	True	99.992	1606	1611	95	conclusive
Natronorubrum halophilum	strain=SHR37	GCA_003670115.1	1702106	1702106	type	True	82.954	925	1611	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	82.7982	978	1611	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	82.4277	895	1611	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	82.1986	881	1611	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	81.8903	894	1611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:05,012] [INFO] DFAST Taxonomy check result was written to GCF_000337235.1_ASM33723v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:05,012] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:05,013] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:05,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d73e359-dfef-4ebc-a552-f6d5c8f82943/dqc_reference/checkm_data
[2024-01-25 18:08:05,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:05,075] [INFO] Task started: CheckM
[2024-01-25 18:08:05,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337235.1_ASM33723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337235.1_ASM33723v1_genomic.fna/checkm_input GCF_000337235.1_ASM33723v1_genomic.fna/checkm_result
[2024-01-25 18:08:56,846] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:56,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:56,865] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:56,866] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:56,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337235.1_ASM33723v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:56,866] [INFO] Task started: Blastn
[2024-01-25 18:08:56,866] [INFO] Running command: blastn -query GCF_000337235.1_ASM33723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d73e359-dfef-4ebc-a552-f6d5c8f82943/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337235.1_ASM33723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:57,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:57,382] [INFO] Selected 8 target genomes.
[2024-01-25 18:08:57,382] [INFO] Target genome list was writen to GCF_000337235.1_ASM33723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:57,389] [INFO] Task started: fastANI
[2024-01-25 18:08:57,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b7ae96b-29ce-45a3-86ca-1d701d1cc943/GCF_000337235.1_ASM33723v1_genomic.fna.gz --refList GCF_000337235.1_ASM33723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337235.1_ASM33723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:07,119] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:07,126] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:07,126] [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_000383975.1	s__Natronorubrum tibetense	99.992	1606	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900100335.1	s__Natronorubrum texcoconense	90.9298	1217	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670115.1	s__Natronorubrum sp003670115	82.957	924	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.42	97.42	0.91	0.91	2	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	82.8105	977	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	82.5121	841	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337495.1	s__Haloterrigena salina	82.2051	879	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	82.1852	912	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_003977755.1	s__Haloterrigena salifodinae	81.8937	893	1611	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:07,128] [INFO] GTDB search result was written to GCF_000337235.1_ASM33723v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:07,130] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:07,132] [INFO] DFAST_QC result json was written to GCF_000337235.1_ASM33723v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:07,132] [INFO] DFAST_QC completed!
[2024-01-25 18:09:07,132] [INFO] Total running time: 0h1m32s