[2024-01-25 18:53:05,691] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,693] [INFO] DQC Reference Directory: /var/lib/cwl/stge6da8772-c5e2-4649-b6a0-5d04ceed83a4/dqc_reference
[2024-01-25 18:53:06,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:06,817] [INFO] Task started: Prodigal
[2024-01-25 18:53:06,817] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9fe9d6d-390f-4221-8030-1ef14655314e/GCF_000337695.1_ASM33769v1_genomic.fna.gz | prodigal -d GCF_000337695.1_ASM33769v1_genomic.fna/cds.fna -a GCF_000337695.1_ASM33769v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:22,280] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:22,281] [INFO] Task started: HMMsearch
[2024-01-25 18:53:22,281] [INFO] Running command: hmmsearch --tblout GCF_000337695.1_ASM33769v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6da8772-c5e2-4649-b6a0-5d04ceed83a4/dqc_reference/reference_markers.hmm GCF_000337695.1_ASM33769v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:22,585] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:22,586] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc9fe9d6d-390f-4221-8030-1ef14655314e/GCF_000337695.1_ASM33769v1_genomic.fna.gz]
[2024-01-25 18:53:22,684] [INFO] Query marker FASTA was written to GCF_000337695.1_ASM33769v1_genomic.fna/markers.fasta
[2024-01-25 18:53:22,684] [INFO] Task started: Blastn
[2024-01-25 18:53:22,684] [INFO] Running command: blastn -query GCF_000337695.1_ASM33769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6da8772-c5e2-4649-b6a0-5d04ceed83a4/dqc_reference/reference_markers.fasta -out GCF_000337695.1_ASM33769v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:23,215] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:23,218] [INFO] Selected 7 target genomes.
[2024-01-25 18:53:23,219] [INFO] Target genome list was writen to GCF_000337695.1_ASM33769v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:23,225] [INFO] Task started: fastANI
[2024-01-25 18:53:23,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fe9d6d-390f-4221-8030-1ef14655314e/GCF_000337695.1_ASM33769v1_genomic.fna.gz --refList GCF_000337695.1_ASM33769v1_genomic.fna/target_genomes.txt --output GCF_000337695.1_ASM33769v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:31,762] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:31,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6da8772-c5e2-4649-b6a0-5d04ceed83a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:31,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6da8772-c5e2-4649-b6a0-5d04ceed83a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:31,769] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:53:31,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:31,769] [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	100.0	1418	1423	95	conclusive
Natronococcus occultus	strain=SP4	GCA_000328685.1	29288	29288	type	True	87.7087	952	1423	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	86.6257	949	1423	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	82.6846	854	1423	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	81.5833	773	1423	95	below_threshold
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	81.0177	659	1423	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	80.4663	658	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:31,770] [INFO] DFAST Taxonomy check result was written to GCF_000337695.1_ASM33769v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:31,771] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:31,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:31,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6da8772-c5e2-4649-b6a0-5d04ceed83a4/dqc_reference/checkm_data
[2024-01-25 18:53:31,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:31,819] [INFO] Task started: CheckM
[2024-01-25 18:53:31,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337695.1_ASM33769v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337695.1_ASM33769v1_genomic.fna/checkm_input GCF_000337695.1_ASM33769v1_genomic.fna/checkm_result
[2024-01-25 18:54:14,591] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:14,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:14,610] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:14,610] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:14,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337695.1_ASM33769v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:14,611] [INFO] Task started: Blastn
[2024-01-25 18:54:14,612] [INFO] Running command: blastn -query GCF_000337695.1_ASM33769v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6da8772-c5e2-4649-b6a0-5d04ceed83a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337695.1_ASM33769v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:15,115] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:15,118] [INFO] Selected 6 target genomes.
[2024-01-25 18:54:15,118] [INFO] Target genome list was writen to GCF_000337695.1_ASM33769v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:15,125] [INFO] Task started: fastANI
[2024-01-25 18:54:15,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fe9d6d-390f-4221-8030-1ef14655314e/GCF_000337695.1_ASM33769v1_genomic.fna.gz --refList GCF_000337695.1_ASM33769v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337695.1_ASM33769v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:22,416] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:22,421] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:22,421] [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_000337695.1	s__Natronococcus jeotgali	100.0	1418	1423	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	conclusive
GCF_000328685.1	s__Natronococcus occultus	87.6439	957	1423	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003559215.1	s__Natronococcus sp003559215	86.6972	860	1423	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	99.83	99.81	0.98	0.98	4	-
GCF_000337675.1	s__Natronococcus amylolyticus	86.632	948	1423	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122205.1	s__Natronococcus sp008122205	82.6854	853	1423	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	81.595	774	1423	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:22,422] [INFO] GTDB search result was written to GCF_000337695.1_ASM33769v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:22,423] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:22,427] [INFO] DFAST_QC result json was written to GCF_000337695.1_ASM33769v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:22,427] [INFO] DFAST_QC completed!
[2024-01-25 18:54:22,427] [INFO] Total running time: 0h1m17s