[2024-01-24 15:18:05,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,095] [INFO] DQC Reference Directory: /var/lib/cwl/stgde2da10c-c7d1-4a5a-ad92-806377269b00/dqc_reference
[2024-01-24 15:18:07,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,532] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg40f96965-efee-4ea3-84e7-072ab2fd64c3/GCF_004217335.1_ASM421733v1_genomic.fna.gz | prodigal -d GCF_004217335.1_ASM421733v1_genomic.fna/cds.fna -a GCF_004217335.1_ASM421733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:29,206] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:29,206] [INFO] Task started: HMMsearch
[2024-01-24 15:18:29,206] [INFO] Running command: hmmsearch --tblout GCF_004217335.1_ASM421733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde2da10c-c7d1-4a5a-ad92-806377269b00/dqc_reference/reference_markers.hmm GCF_004217335.1_ASM421733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:29,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:29,503] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg40f96965-efee-4ea3-84e7-072ab2fd64c3/GCF_004217335.1_ASM421733v1_genomic.fna.gz]
[2024-01-24 15:18:29,542] [INFO] Query marker FASTA was written to GCF_004217335.1_ASM421733v1_genomic.fna/markers.fasta
[2024-01-24 15:18:29,543] [INFO] Task started: Blastn
[2024-01-24 15:18:29,543] [INFO] Running command: blastn -query GCF_004217335.1_ASM421733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2da10c-c7d1-4a5a-ad92-806377269b00/dqc_reference/reference_markers.fasta -out GCF_004217335.1_ASM421733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:30,092] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:30,096] [INFO] Selected 9 target genomes.
[2024-01-24 15:18:30,097] [INFO] Target genome list was writen to GCF_004217335.1_ASM421733v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:30,102] [INFO] Task started: fastANI
[2024-01-24 15:18:30,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f96965-efee-4ea3-84e7-072ab2fd64c3/GCF_004217335.1_ASM421733v1_genomic.fna.gz --refList GCF_004217335.1_ASM421733v1_genomic.fna/target_genomes.txt --output GCF_004217335.1_ASM421733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:39,781] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:39,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde2da10c-c7d1-4a5a-ad92-806377269b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:39,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde2da10c-c7d1-4a5a-ad92-806377269b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:39,795] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:39,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:39,795] [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
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	100.0	1407	1413	95	conclusive
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	94.2215	1019	1413	95	below_threshold
Natrinema pellirubrum	strain=DSM 15624	GCA_000230735.3	69525	69525	type	True	83.2558	807	1413	95	below_threshold
Natrinema pellirubrum	strain=DSM 15624	GCA_000337635.1	69525	69525	type	True	83.1846	778	1413	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	82.8698	786	1413	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	82.7359	783	1413	95	below_threshold
Natrinema gari	strain=JCM 14663	GCA_000337175.1	419186	419186	type	True	82.4518	752	1413	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	82.3442	733	1413	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	81.4293	693	1413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:39,797] [INFO] DFAST Taxonomy check result was written to GCF_004217335.1_ASM421733v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:39,797] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:39,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:39,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde2da10c-c7d1-4a5a-ad92-806377269b00/dqc_reference/checkm_data
[2024-01-24 15:18:39,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:39,846] [INFO] Task started: CheckM
[2024-01-24 15:18:39,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217335.1_ASM421733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217335.1_ASM421733v1_genomic.fna/checkm_input GCF_004217335.1_ASM421733v1_genomic.fna/checkm_result
[2024-01-24 15:19:39,956] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:39,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:39,982] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:39,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:39,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217335.1_ASM421733v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:39,983] [INFO] Task started: Blastn
[2024-01-24 15:19:39,984] [INFO] Running command: blastn -query GCF_004217335.1_ASM421733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde2da10c-c7d1-4a5a-ad92-806377269b00/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217335.1_ASM421733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:40,494] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:40,498] [INFO] Selected 7 target genomes.
[2024-01-24 15:19:40,498] [INFO] Target genome list was writen to GCF_004217335.1_ASM421733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:40,504] [INFO] Task started: fastANI
[2024-01-24 15:19:40,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f96965-efee-4ea3-84e7-072ab2fd64c3/GCF_004217335.1_ASM421733v1_genomic.fna.gz --refList GCF_004217335.1_ASM421733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217335.1_ASM421733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:48,927] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:48,934] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:48,935] [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_004217335.1	s__Natrinema hispanicum	100.0	1407	1413	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000337475.1	s__Natrinema limicola	94.2143	1020	1413	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111485.1	s__Natrinema hispanicum_A	94.152	1117	1413	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	99.65	99.65	0.93	0.93	2	-
GCF_005938085.1	s__Natrinema sp005938085	90.0659	1077	1413	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005576615.1	s__Natrinema versiforme_A	83.0078	801	1413	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	82.7609	787	1413	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_013342135.1	s__Haloterrigena sp013342135	81.5678	705	1413	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:48,936] [INFO] GTDB search result was written to GCF_004217335.1_ASM421733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:48,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:48,941] [INFO] DFAST_QC result json was written to GCF_004217335.1_ASM421733v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:48,941] [INFO] DFAST_QC completed!
[2024-01-24 15:19:48,941] [INFO] Total running time: 0h1m44s