[2024-01-24 12:15:18,863] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,866] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c08b335-ca8b-4387-a327-86586d60c0e4/dqc_reference
[2024-01-24 12:15:20,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,204] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eceea0c-9007-42ba-9825-2c79f24adeef/GCF_023227765.1_ASM2322776v1_genomic.fna.gz | prodigal -d GCF_023227765.1_ASM2322776v1_genomic.fna/cds.fna -a GCF_023227765.1_ASM2322776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:24,267] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:24,268] [INFO] Task started: HMMsearch
[2024-01-24 12:15:24,268] [INFO] Running command: hmmsearch --tblout GCF_023227765.1_ASM2322776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c08b335-ca8b-4387-a327-86586d60c0e4/dqc_reference/reference_markers.hmm GCF_023227765.1_ASM2322776v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:24,523] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:24,524] [INFO] Found 6/6 markers.
[2024-01-24 12:15:24,550] [INFO] Query marker FASTA was written to GCF_023227765.1_ASM2322776v1_genomic.fna/markers.fasta
[2024-01-24 12:15:24,551] [INFO] Task started: Blastn
[2024-01-24 12:15:24,551] [INFO] Running command: blastn -query GCF_023227765.1_ASM2322776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c08b335-ca8b-4387-a327-86586d60c0e4/dqc_reference/reference_markers.fasta -out GCF_023227765.1_ASM2322776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:25,205] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:25,210] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:25,211] [INFO] Target genome list was writen to GCF_023227765.1_ASM2322776v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:25,221] [INFO] Task started: fastANI
[2024-01-24 12:15:25,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eceea0c-9007-42ba-9825-2c79f24adeef/GCF_023227765.1_ASM2322776v1_genomic.fna.gz --refList GCF_023227765.1_ASM2322776v1_genomic.fna/target_genomes.txt --output GCF_023227765.1_ASM2322776v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:36,123] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:36,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c08b335-ca8b-4387-a327-86586d60c0e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:36,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c08b335-ca8b-4387-a327-86586d60c0e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:36,133] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:36,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:36,133] [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
Fuchsiella alkaliacetigena	strain=Z-7100	GCA_023227765.1	957042	957042	type	True	100.0	895	900	95	conclusive
Natroniella sulfidigena	strain=AHT3	GCA_023223645.1	723921	723921	type	True	77.2276	61	900	95	below_threshold
Selenihalanaerobacter shriftii	strain=ATCC BAA-73	GCA_900167185.1	142842	142842	type	True	76.6063	117	900	95	below_threshold
Natroniella acetigena	strain=Z-7937	GCA_023227745.1	52004	52004	type	True	76.5352	69	900	95	below_threshold
Orenia marismortui	strain=DSM 5156	GCA_000379025.1	46469	46469	type	True	75.8401	53	900	95	below_threshold
Halanaerobacter jeridensis	strain=DSM 23230	GCA_016908315.1	706427	706427	type	True	75.2625	54	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:36,134] [INFO] DFAST Taxonomy check result was written to GCF_023227765.1_ASM2322776v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:36,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:36,135] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:36,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c08b335-ca8b-4387-a327-86586d60c0e4/dqc_reference/checkm_data
[2024-01-24 12:15:36,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:36,171] [INFO] Task started: CheckM
[2024-01-24 12:15:36,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023227765.1_ASM2322776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023227765.1_ASM2322776v1_genomic.fna/checkm_input GCF_023227765.1_ASM2322776v1_genomic.fna/checkm_result
[2024-01-24 12:15:55,904] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:55,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:55,933] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:55,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:55,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023227765.1_ASM2322776v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:55,934] [INFO] Task started: Blastn
[2024-01-24 12:15:55,934] [INFO] Running command: blastn -query GCF_023227765.1_ASM2322776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c08b335-ca8b-4387-a327-86586d60c0e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_023227765.1_ASM2322776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:56,978] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:56,982] [INFO] Selected 29 target genomes.
[2024-01-24 12:15:56,982] [INFO] Target genome list was writen to GCF_023227765.1_ASM2322776v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:57,032] [INFO] Task started: fastANI
[2024-01-24 12:15:57,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eceea0c-9007-42ba-9825-2c79f24adeef/GCF_023227765.1_ASM2322776v1_genomic.fna.gz --refList GCF_023227765.1_ASM2322776v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023227765.1_ASM2322776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:09,694] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:09,707] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:09,708] [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_900167185.1	s__Selenihalanaerobacter shriftii	76.6063	117	900	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Acetohalobiaceae;g__Selenihalanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114655.1	s__Frackibacter sp900114655	76.571	124	900	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Acetohalobiaceae;g__Frackibacter	95.0	99.43	98.34	0.95	0.87	4	-
GCF_016908635.1	s__Sporohalobacter salinus	76.3553	96	900	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Acetohalobiaceae;g__Sporohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000144695.1	s__Acetohalobium arabaticum	76.2146	102	900	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Acetohalobiaceae;g__Acetohalobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379025.1	s__Orenia marismortui	75.8671	52	900	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Orenia	95.0	96.95	96.95	0.88	0.88	2	-
GCF_016908315.1	s__Halanaerobacter jeridensis	75.2503	55	900	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Halanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:09,711] [INFO] GTDB search result was written to GCF_023227765.1_ASM2322776v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:09,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:09,714] [INFO] DFAST_QC result json was written to GCF_023227765.1_ASM2322776v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:09,715] [INFO] DFAST_QC completed!
[2024-01-24 12:16:09,715] [INFO] Total running time: 0h0m51s