[2024-01-25 17:34:07,120] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4e6af0f-8558-4f75-a628-c12a0a84d34c/dqc_reference
[2024-01-25 17:34:08,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,952] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,952] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc04cde8-8f90-49ab-969a-7f41955fa910/GCF_023028105.1_ASM2302810v1_genomic.fna.gz | prodigal -d GCF_023028105.1_ASM2302810v1_genomic.fna/cds.fna -a GCF_023028105.1_ASM2302810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:26,638] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:26,638] [INFO] Task started: HMMsearch
[2024-01-25 17:34:26,639] [INFO] Running command: hmmsearch --tblout GCF_023028105.1_ASM2302810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4e6af0f-8558-4f75-a628-c12a0a84d34c/dqc_reference/reference_markers.hmm GCF_023028105.1_ASM2302810v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:26,893] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:26,894] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcc04cde8-8f90-49ab-969a-7f41955fa910/GCF_023028105.1_ASM2302810v1_genomic.fna.gz]
[2024-01-25 17:34:26,930] [INFO] Query marker FASTA was written to GCF_023028105.1_ASM2302810v1_genomic.fna/markers.fasta
[2024-01-25 17:34:26,930] [INFO] Task started: Blastn
[2024-01-25 17:34:26,930] [INFO] Running command: blastn -query GCF_023028105.1_ASM2302810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e6af0f-8558-4f75-a628-c12a0a84d34c/dqc_reference/reference_markers.fasta -out GCF_023028105.1_ASM2302810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:27,444] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:27,447] [INFO] Selected 11 target genomes.
[2024-01-25 17:34:27,447] [INFO] Target genome list was writen to GCF_023028105.1_ASM2302810v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:27,459] [INFO] Task started: fastANI
[2024-01-25 17:34:27,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc04cde8-8f90-49ab-969a-7f41955fa910/GCF_023028105.1_ASM2302810v1_genomic.fna.gz --refList GCF_023028105.1_ASM2302810v1_genomic.fna/target_genomes.txt --output GCF_023028105.1_ASM2302810v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:38,594] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:38,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4e6af0f-8558-4f75-a628-c12a0a84d34c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:38,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4e6af0f-8558-4f75-a628-c12a0a84d34c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:38,602] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:38,603] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:38,603] [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
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	81.5858	834	1584	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	81.5685	828	1584	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	81.3649	818	1584	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	81.3589	810	1584	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	81.2371	870	1584	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	81.2171	824	1584	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	80.9432	796	1584	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	80.8006	804	1584	95	below_threshold
Halopiger djelfimassiliensis	strain=IIH2	GCA_000455365.1	1293047	1293047	type	True	80.7488	738	1584	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	80.6405	692	1584	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	80.5643	717	1584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:38,605] [INFO] DFAST Taxonomy check result was written to GCF_023028105.1_ASM2302810v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:38,605] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:38,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:38,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4e6af0f-8558-4f75-a628-c12a0a84d34c/dqc_reference/checkm_data
[2024-01-25 17:34:38,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:38,652] [INFO] Task started: CheckM
[2024-01-25 17:34:38,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023028105.1_ASM2302810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023028105.1_ASM2302810v1_genomic.fna/checkm_input GCF_023028105.1_ASM2302810v1_genomic.fna/checkm_result
[2024-01-25 17:35:26,164] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:26,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:26,189] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:26,189] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:26,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023028105.1_ASM2302810v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:26,189] [INFO] Task started: Blastn
[2024-01-25 17:35:26,189] [INFO] Running command: blastn -query GCF_023028105.1_ASM2302810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e6af0f-8558-4f75-a628-c12a0a84d34c/dqc_reference/reference_markers_gtdb.fasta -out GCF_023028105.1_ASM2302810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:26,815] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:26,819] [INFO] Selected 13 target genomes.
[2024-01-25 17:35:26,819] [INFO] Target genome list was writen to GCF_023028105.1_ASM2302810v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:26,826] [INFO] Task started: fastANI
[2024-01-25 17:35:26,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc04cde8-8f90-49ab-969a-7f41955fa910/GCF_023028105.1_ASM2302810v1_genomic.fna.gz --refList GCF_023028105.1_ASM2302810v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023028105.1_ASM2302810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:40,383] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:40,392] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:35:40,392] [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_900110455.1	s__Natrinema salifodinae	81.6015	829	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_017352155.1	s__Haloterrigena sp017352155	81.4405	775	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217715.1	s__Halopiger xanaduensis	81.4193	811	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	81.2279	871	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_003610195.1	s__Halopiger aswanensis	81.2237	822	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005576615.1	s__Natrinema versiforme_A	80.9917	784	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000690595.2	s__Natrinema mahii	80.9551	718	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337695.1	s__Natronococcus jeotgali	80.8804	710	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCF_900110865.1	s__Natrinema salaciae	80.8063	802	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455365.1	s__Halopiger_B djelfimassiliensis	80.7613	736	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	80.6646	773	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_000731985.1	s__Natrinema altunense	80.6001	712	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	-
GCF_002494345.1	s__Natrinema ejinorense	80.5611	717	1584	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:40,394] [INFO] GTDB search result was written to GCF_023028105.1_ASM2302810v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:40,394] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:40,397] [INFO] DFAST_QC result json was written to GCF_023028105.1_ASM2302810v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:40,397] [INFO] DFAST_QC completed!
[2024-01-25 17:35:40,397] [INFO] Total running time: 0h1m33s