[2024-01-24 11:51:24,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c916862-33c4-4320-8ab5-a2e85dff023a/dqc_reference
[2024-01-24 11:51:26,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,158] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,158] [INFO] Running command: gunzip -c /var/lib/cwl/stga65d9eec-ea20-49cc-8e1a-0767a9c62d45/GCF_023008545.1_ASM2300854v1_genomic.fna.gz | prodigal -d GCF_023008545.1_ASM2300854v1_genomic.fna/cds.fna -a GCF_023008545.1_ASM2300854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:48,019] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:48,020] [INFO] Task started: HMMsearch
[2024-01-24 11:51:48,020] [INFO] Running command: hmmsearch --tblout GCF_023008545.1_ASM2300854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c916862-33c4-4320-8ab5-a2e85dff023a/dqc_reference/reference_markers.hmm GCF_023008545.1_ASM2300854v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:48,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:48,284] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga65d9eec-ea20-49cc-8e1a-0767a9c62d45/GCF_023008545.1_ASM2300854v1_genomic.fna.gz]
[2024-01-24 11:51:48,328] [INFO] Query marker FASTA was written to GCF_023008545.1_ASM2300854v1_genomic.fna/markers.fasta
[2024-01-24 11:51:48,329] [INFO] Task started: Blastn
[2024-01-24 11:51:48,329] [INFO] Running command: blastn -query GCF_023008545.1_ASM2300854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c916862-33c4-4320-8ab5-a2e85dff023a/dqc_reference/reference_markers.fasta -out GCF_023008545.1_ASM2300854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:48,855] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:48,859] [INFO] Selected 12 target genomes.
[2024-01-24 11:51:48,859] [INFO] Target genome list was writen to GCF_023008545.1_ASM2300854v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:48,867] [INFO] Task started: fastANI
[2024-01-24 11:51:48,867] [INFO] Running command: fastANI --query /var/lib/cwl/stga65d9eec-ea20-49cc-8e1a-0767a9c62d45/GCF_023008545.1_ASM2300854v1_genomic.fna.gz --refList GCF_023008545.1_ASM2300854v1_genomic.fna/target_genomes.txt --output GCF_023008545.1_ASM2300854v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:00,659] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:00,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c916862-33c4-4320-8ab5-a2e85dff023a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:00,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c916862-33c4-4320-8ab5-a2e85dff023a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:00,671] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:00,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:00,671] [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
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	80.5468	677	1536	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	80.5266	668	1536	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	80.5167	674	1536	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	80.4038	716	1536	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	80.3927	718	1536	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	80.3812	709	1536	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	80.2986	688	1536	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	80.172	679	1536	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	80.1264	642	1536	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	79.9044	622	1536	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	79.83	631	1536	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	79.8013	620	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:00,673] [INFO] DFAST Taxonomy check result was written to GCF_023008545.1_ASM2300854v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:00,673] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:00,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:00,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c916862-33c4-4320-8ab5-a2e85dff023a/dqc_reference/checkm_data
[2024-01-24 11:52:00,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:00,718] [INFO] Task started: CheckM
[2024-01-24 11:52:00,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023008545.1_ASM2300854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023008545.1_ASM2300854v1_genomic.fna/checkm_input GCF_023008545.1_ASM2300854v1_genomic.fna/checkm_result
[2024-01-24 11:53:00,676] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:00,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:00,706] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:00,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:00,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023008545.1_ASM2300854v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:00,708] [INFO] Task started: Blastn
[2024-01-24 11:53:00,708] [INFO] Running command: blastn -query GCF_023008545.1_ASM2300854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c916862-33c4-4320-8ab5-a2e85dff023a/dqc_reference/reference_markers_gtdb.fasta -out GCF_023008545.1_ASM2300854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:01,217] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:01,222] [INFO] Selected 13 target genomes.
[2024-01-24 11:53:01,222] [INFO] Target genome list was writen to GCF_023008545.1_ASM2300854v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:01,231] [INFO] Task started: fastANI
[2024-01-24 11:53:01,231] [INFO] Running command: fastANI --query /var/lib/cwl/stga65d9eec-ea20-49cc-8e1a-0767a9c62d45/GCF_023008545.1_ASM2300854v1_genomic.fna.gz --refList GCF_023008545.1_ASM2300854v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023008545.1_ASM2300854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:13,299] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:13,314] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:13,315] [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_001953745.1	s__Natrinema saccharevitans	80.7014	684	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110455.1	s__Natrinema salifodinae	80.5472	669	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	80.5315	476	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337695.1	s__Natronococcus jeotgali	80.5097	680	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCF_900112205.1	s__Halobiforma haloterrestris	80.3899	709	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	80.3825	726	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_000337115.1	s__Natrinema thermotolerans	80.3117	660	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.7501	97.75	97.75	0.90	0.90	2	-
GCF_005576615.1	s__Natrinema versiforme_A	80.2494	683	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013456555.1	s__Natrinema sp013456555	80.1945	616	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337195.1	s__Natrinema versiforme	80.1282	642	1536	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	80.0829	672	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_002572525.1	s__Natrinema sp002572525	79.9869	664	1536	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	79.8105	620	1536	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 11:53:13,317] [INFO] GTDB search result was written to GCF_023008545.1_ASM2300854v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:13,318] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:13,322] [INFO] DFAST_QC result json was written to GCF_023008545.1_ASM2300854v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:13,322] [INFO] DFAST_QC completed!
[2024-01-24 11:53:13,322] [INFO] Total running time: 0h1m48s