[2024-01-24 13:57:15,946] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:15,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:15,953] [INFO] DQC Reference Directory: /var/lib/cwl/stg632ae4f9-8805-4616-899e-c7a2a42b27d8/dqc_reference
[2024-01-24 13:57:17,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,379] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,380] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9f4279a-52cf-4f64-bb53-adab2d00229a/GCF_017352155.2_ASM1735215v2_genomic.fna.gz | prodigal -d GCF_017352155.2_ASM1735215v2_genomic.fna/cds.fna -a GCF_017352155.2_ASM1735215v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:37,011] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:37,011] [INFO] Task started: HMMsearch
[2024-01-24 13:57:37,011] [INFO] Running command: hmmsearch --tblout GCF_017352155.2_ASM1735215v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg632ae4f9-8805-4616-899e-c7a2a42b27d8/dqc_reference/reference_markers.hmm GCF_017352155.2_ASM1735215v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:37,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:37,280] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf9f4279a-52cf-4f64-bb53-adab2d00229a/GCF_017352155.2_ASM1735215v2_genomic.fna.gz]
[2024-01-24 13:57:37,316] [INFO] Query marker FASTA was written to GCF_017352155.2_ASM1735215v2_genomic.fna/markers.fasta
[2024-01-24 13:57:37,316] [INFO] Task started: Blastn
[2024-01-24 13:57:37,316] [INFO] Running command: blastn -query GCF_017352155.2_ASM1735215v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg632ae4f9-8805-4616-899e-c7a2a42b27d8/dqc_reference/reference_markers.fasta -out GCF_017352155.2_ASM1735215v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:37,900] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:37,903] [INFO] Selected 7 target genomes.
[2024-01-24 13:57:37,903] [INFO] Target genome list was writen to GCF_017352155.2_ASM1735215v2_genomic.fna/target_genomes.txt
[2024-01-24 13:57:37,911] [INFO] Task started: fastANI
[2024-01-24 13:57:37,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f4279a-52cf-4f64-bb53-adab2d00229a/GCF_017352155.2_ASM1735215v2_genomic.fna.gz --refList GCF_017352155.2_ASM1735215v2_genomic.fna/target_genomes.txt --output GCF_017352155.2_ASM1735215v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:47,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:47,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg632ae4f9-8805-4616-899e-c7a2a42b27d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:47,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg632ae4f9-8805-4616-899e-c7a2a42b27d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:47,397] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:47,397] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:47,397] [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 alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	100.0	1421	1422	95	conclusive
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	85.9044	999	1422	95	below_threshold
Haloterrigena turkmenica	strain=DSM 5511	GCA_000025325.1	62320	62320	type	True	85.9013	1029	1422	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	85.5126	983	1422	95	below_threshold
Natronorubrum halophilum	strain=SHR37	GCA_003670115.1	1702106	1702106	type	True	82.6929	874	1422	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	82.65	839	1422	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	82.3349	856	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:47,399] [INFO] DFAST Taxonomy check result was written to GCF_017352155.2_ASM1735215v2_genomic.fna/tc_result.tsv
[2024-01-24 13:57:47,399] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:47,399] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:47,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg632ae4f9-8805-4616-899e-c7a2a42b27d8/dqc_reference/checkm_data
[2024-01-24 13:57:47,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:47,447] [INFO] Task started: CheckM
[2024-01-24 13:57:47,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017352155.2_ASM1735215v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017352155.2_ASM1735215v2_genomic.fna/checkm_input GCF_017352155.2_ASM1735215v2_genomic.fna/checkm_result
[2024-01-24 13:58:41,381] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:41,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,405] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:41,405] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:41,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017352155.2_ASM1735215v2_genomic.fna/markers.fasta)
[2024-01-24 13:58:41,406] [INFO] Task started: Blastn
[2024-01-24 13:58:41,406] [INFO] Running command: blastn -query GCF_017352155.2_ASM1735215v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg632ae4f9-8805-4616-899e-c7a2a42b27d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017352155.2_ASM1735215v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:41,934] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:41,938] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:41,938] [INFO] Target genome list was writen to GCF_017352155.2_ASM1735215v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:41,945] [INFO] Task started: fastANI
[2024-01-24 13:58:41,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f4279a-52cf-4f64-bb53-adab2d00229a/GCF_017352155.2_ASM1735215v2_genomic.fna.gz --refList GCF_017352155.2_ASM1735215v2_genomic.fna/target_genomes_gtdb.txt --output GCF_017352155.2_ASM1735215v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:50,558] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:50,569] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:50,569] [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_017352155.1	s__Haloterrigena sp017352155	100.0	1273	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013342135.1	s__Haloterrigena sp013342135	86.0781	1016	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000337495.1	s__Haloterrigena salina	85.9032	1000	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025325.1	s__Haloterrigena turkmenica	85.8955	1030	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	85.4894	985	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_900100335.1	s__Natronorubrum texcoconense	82.9416	916	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	82.335	856	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:50,571] [INFO] GTDB search result was written to GCF_017352155.2_ASM1735215v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:50,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:50,574] [INFO] DFAST_QC result json was written to GCF_017352155.2_ASM1735215v2_genomic.fna/dqc_result.json
[2024-01-24 13:58:50,574] [INFO] DFAST_QC completed!
[2024-01-24 13:58:50,574] [INFO] Total running time: 0h1m35s