[2024-01-24 12:13:28,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg89a1276e-07ec-46e3-9320-02d678d8aef3/dqc_reference
[2024-01-24 12:13:30,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,157] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e4d60ce-e4e0-40be-8c6f-84115ee28d92/GCF_000337355.1_ASM33735v1_genomic.fna.gz | prodigal -d GCF_000337355.1_ASM33735v1_genomic.fna/cds.fna -a GCF_000337355.1_ASM33735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:46,289] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:46,289] [INFO] Task started: HMMsearch
[2024-01-24 12:13:46,289] [INFO] Running command: hmmsearch --tblout GCF_000337355.1_ASM33735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89a1276e-07ec-46e3-9320-02d678d8aef3/dqc_reference/reference_markers.hmm GCF_000337355.1_ASM33735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:46,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:46,572] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7e4d60ce-e4e0-40be-8c6f-84115ee28d92/GCF_000337355.1_ASM33735v1_genomic.fna.gz]
[2024-01-24 12:13:46,606] [INFO] Query marker FASTA was written to GCF_000337355.1_ASM33735v1_genomic.fna/markers.fasta
[2024-01-24 12:13:46,606] [INFO] Task started: Blastn
[2024-01-24 12:13:46,607] [INFO] Running command: blastn -query GCF_000337355.1_ASM33735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89a1276e-07ec-46e3-9320-02d678d8aef3/dqc_reference/reference_markers.fasta -out GCF_000337355.1_ASM33735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:47,148] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:47,152] [INFO] Selected 8 target genomes.
[2024-01-24 12:13:47,152] [INFO] Target genome list was writen to GCF_000337355.1_ASM33735v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:47,167] [INFO] Task started: fastANI
[2024-01-24 12:13:47,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4d60ce-e4e0-40be-8c6f-84115ee28d92/GCF_000337355.1_ASM33735v1_genomic.fna.gz --refList GCF_000337355.1_ASM33735v1_genomic.fna/target_genomes.txt --output GCF_000337355.1_ASM33735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:55,557] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:55,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89a1276e-07ec-46e3-9320-02d678d8aef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:55,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89a1276e-07ec-46e3-9320-02d678d8aef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:55,565] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:55,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:55,566] [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
Halorubrum kocurii	strain=JCM 14978	GCA_000337355.1	478441	478441	type	True	100.0	1150	1156	95	conclusive
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	91.3244	810	1156	95	below_threshold
Halorubrum salsamenti	strain=Y69	GCA_007671685.1	2583990	2583990	type	True	90.0167	786	1156	95	below_threshold
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	89.6148	736	1156	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	89.4667	783	1156	95	below_threshold
Halorubrum halophilum	strain=B8	GCA_000739595.1	413816	413816	type	True	89.4551	792	1156	95	below_threshold
Halorubrum amylolyticum	strain=ZC67	GCA_004114995.1	2508724	2508724	type	True	89.3199	756	1156	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	89.0352	731	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:55,568] [INFO] DFAST Taxonomy check result was written to GCF_000337355.1_ASM33735v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:55,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:55,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:55,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89a1276e-07ec-46e3-9320-02d678d8aef3/dqc_reference/checkm_data
[2024-01-24 12:13:55,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:55,620] [INFO] Task started: CheckM
[2024-01-24 12:13:55,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337355.1_ASM33735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337355.1_ASM33735v1_genomic.fna/checkm_input GCF_000337355.1_ASM33735v1_genomic.fna/checkm_result
[2024-01-24 12:14:42,716] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:42,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:42,746] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:42,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:42,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337355.1_ASM33735v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:42,747] [INFO] Task started: Blastn
[2024-01-24 12:14:42,747] [INFO] Running command: blastn -query GCF_000337355.1_ASM33735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89a1276e-07ec-46e3-9320-02d678d8aef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337355.1_ASM33735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:43,292] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:43,295] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:43,295] [INFO] Target genome list was writen to GCF_000337355.1_ASM33735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:43,302] [INFO] Task started: fastANI
[2024-01-24 12:14:43,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4d60ce-e4e0-40be-8c6f-84115ee28d92/GCF_000337355.1_ASM33735v1_genomic.fna.gz --refList GCF_000337355.1_ASM33735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337355.1_ASM33735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:54,157] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:54,166] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:54,166] [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_000337355.1	s__Halorubrum kocurii	100.0	1150	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000337375.1	s__Halorubrum lipolyticum	91.325	809	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007671685.1	s__Halorubrum salsamenti	90.013	786	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337915.1	s__Halorubrum saccharovorum	89.6178	737	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286985.1	s__Halorubrum sp002286985	89.4932	781	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.74	98.74	0.87	0.87	2	-
GCF_003781945.1	s__Halorubrum sp003781945	89.4413	801	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739595.1	s__Halorubrum halophilum	89.4362	793	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.11	98.11	0.88	0.88	2	-
GCF_002727125.1	s__Halorubrum persicum	89.0748	729	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022205.1	s__Halorubrum lacusprofundi	88.7667	768	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.55	99.24	0.92	0.87	3	-
GCF_003721435.2	s__Halorubrum sp003721435	87.5635	784	1156	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:54,167] [INFO] GTDB search result was written to GCF_000337355.1_ASM33735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:54,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:54,171] [INFO] DFAST_QC result json was written to GCF_000337355.1_ASM33735v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:54,171] [INFO] DFAST_QC completed!
[2024-01-24 12:14:54,171] [INFO] Total running time: 0h1m25s