[2024-01-24 11:34:41,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg550bfb65-ca7b-44ef-9a07-594480d9c029/dqc_reference
[2024-01-24 11:34:42,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,666] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg4918b3b4-3aae-4238-a8db-9f5d8beda9a1/GCF_024204665.1_ASM2420466v1_genomic.fna.gz | prodigal -d GCF_024204665.1_ASM2420466v1_genomic.fna/cds.fna -a GCF_024204665.1_ASM2420466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:03,939] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:03,940] [INFO] Task started: HMMsearch
[2024-01-24 11:35:03,940] [INFO] Running command: hmmsearch --tblout GCF_024204665.1_ASM2420466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg550bfb65-ca7b-44ef-9a07-594480d9c029/dqc_reference/reference_markers.hmm GCF_024204665.1_ASM2420466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:04,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:04,244] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4918b3b4-3aae-4238-a8db-9f5d8beda9a1/GCF_024204665.1_ASM2420466v1_genomic.fna.gz]
[2024-01-24 11:35:04,290] [INFO] Query marker FASTA was written to GCF_024204665.1_ASM2420466v1_genomic.fna/markers.fasta
[2024-01-24 11:35:04,290] [INFO] Task started: Blastn
[2024-01-24 11:35:04,290] [INFO] Running command: blastn -query GCF_024204665.1_ASM2420466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg550bfb65-ca7b-44ef-9a07-594480d9c029/dqc_reference/reference_markers.fasta -out GCF_024204665.1_ASM2420466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:04,942] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:04,945] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:04,946] [INFO] Target genome list was writen to GCF_024204665.1_ASM2420466v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:04,951] [INFO] Task started: fastANI
[2024-01-24 11:35:04,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg4918b3b4-3aae-4238-a8db-9f5d8beda9a1/GCF_024204665.1_ASM2420466v1_genomic.fna.gz --refList GCF_024204665.1_ASM2420466v1_genomic.fna/target_genomes.txt --output GCF_024204665.1_ASM2420466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:18,928] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:18,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg550bfb65-ca7b-44ef-9a07-594480d9c029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:18,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg550bfb65-ca7b-44ef-9a07-594480d9c029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:18,940] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:18,940] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:18,940] [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	79.4441	597	1436	95	below_threshold
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	79.3611	566	1436	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	79.2831	600	1436	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	79.2444	585	1436	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.1856	541	1436	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.1581	550	1436	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.0982	553	1436	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	79.0613	569	1436	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	78.9989	575	1436	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	78.8577	493	1436	95	below_threshold
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	78.8007	467	1436	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	78.7895	491	1436	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	78.7797	475	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:18,942] [INFO] DFAST Taxonomy check result was written to GCF_024204665.1_ASM2420466v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:18,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:18,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:18,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg550bfb65-ca7b-44ef-9a07-594480d9c029/dqc_reference/checkm_data
[2024-01-24 11:35:18,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:18,998] [INFO] Task started: CheckM
[2024-01-24 11:35:18,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024204665.1_ASM2420466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024204665.1_ASM2420466v1_genomic.fna/checkm_input GCF_024204665.1_ASM2420466v1_genomic.fna/checkm_result
[2024-01-24 11:36:13,767] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:13,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,787] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:13,787] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:13,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024204665.1_ASM2420466v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:13,788] [INFO] Task started: Blastn
[2024-01-24 11:36:13,788] [INFO] Running command: blastn -query GCF_024204665.1_ASM2420466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg550bfb65-ca7b-44ef-9a07-594480d9c029/dqc_reference/reference_markers_gtdb.fasta -out GCF_024204665.1_ASM2420466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:14,322] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:14,326] [INFO] Selected 11 target genomes.
[2024-01-24 11:36:14,326] [INFO] Target genome list was writen to GCF_024204665.1_ASM2420466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:14,333] [INFO] Task started: fastANI
[2024-01-24 11:36:14,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg4918b3b4-3aae-4238-a8db-9f5d8beda9a1/GCF_024204665.1_ASM2420466v1_genomic.fna.gz --refList GCF_024204665.1_ASM2420466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024204665.1_ASM2420466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:23,870] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:23,880] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:36:23,880] [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
GCA_017357105.1	s__Tc-Br11 sp017357105	92.1848	1084	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337695.1	s__Natronococcus jeotgali	79.3665	566	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCA_001564275.1	s__Tc-Br11 sp001564275	79.3124	513	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	99.79	99.79	0.91	0.91	2	-
GCF_008122205.1	s__Natronococcus sp008122205	79.2979	598	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	79.2252	587	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110455.1	s__Natrinema salifodinae	79.2041	546	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000337675.1	s__Natronococcus amylolyticus	79.0778	565	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	79.0364	412	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	79.0179	573	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731985.1	s__Natrinema altunense	78.8434	494	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	-
GCF_000337615.1	s__Natrinema pallidum	78.8061	472	1436	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:23,882] [INFO] GTDB search result was written to GCF_024204665.1_ASM2420466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:23,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:23,887] [INFO] DFAST_QC result json was written to GCF_024204665.1_ASM2420466v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:23,887] [INFO] DFAST_QC completed!
[2024-01-24 11:36:23,887] [INFO] Total running time: 0h1m42s