[2024-01-24 13:36:45,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg16edd292-6656-4384-9ab8-459305b1b417/dqc_reference
[2024-01-24 13:36:47,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,018] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg3577766b-83ae-4615-b63d-9411f4a95197/GCF_006861655.1_ASM686165v1_genomic.fna.gz | prodigal -d GCF_006861655.1_ASM686165v1_genomic.fna/cds.fna -a GCF_006861655.1_ASM686165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:01,302] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:01,302] [INFO] Task started: HMMsearch
[2024-01-24 13:37:01,302] [INFO] Running command: hmmsearch --tblout GCF_006861655.1_ASM686165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16edd292-6656-4384-9ab8-459305b1b417/dqc_reference/reference_markers.hmm GCF_006861655.1_ASM686165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:01,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:01,492] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3577766b-83ae-4615-b63d-9411f4a95197/GCF_006861655.1_ASM686165v1_genomic.fna.gz]
[2024-01-24 13:37:01,515] [INFO] Query marker FASTA was written to GCF_006861655.1_ASM686165v1_genomic.fna/markers.fasta
[2024-01-24 13:37:01,516] [INFO] Task started: Blastn
[2024-01-24 13:37:01,516] [INFO] Running command: blastn -query GCF_006861655.1_ASM686165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16edd292-6656-4384-9ab8-459305b1b417/dqc_reference/reference_markers.fasta -out GCF_006861655.1_ASM686165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:02,032] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:02,035] [INFO] Selected 5 target genomes.
[2024-01-24 13:37:02,036] [INFO] Target genome list was writen to GCF_006861655.1_ASM686165v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:02,039] [INFO] Task started: fastANI
[2024-01-24 13:37:02,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg3577766b-83ae-4615-b63d-9411f4a95197/GCF_006861655.1_ASM686165v1_genomic.fna.gz --refList GCF_006861655.1_ASM686165v1_genomic.fna/target_genomes.txt --output GCF_006861655.1_ASM686165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:05,638] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:05,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16edd292-6656-4384-9ab8-459305b1b417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:05,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16edd292-6656-4384-9ab8-459305b1b417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:05,645] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:05,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:05,645] [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
Halonotius roseus	strain=F9-27	GCA_006861655.1	2511997	2511997	type	True	100.0	852	852	95	conclusive
Halonotius aquaticus	strain=F13-13	GCA_003605575.1	2216978	2216978	type	True	87.4338	637	852	95	below_threshold
Halonotius pteroides	strain=CECT 7525	GCA_003605635.1	268735	268735	type	True	85.7557	606	852	95	below_threshold
Halonotius terrestris	strain=F15B	GCA_006861665.1	2487750	2487750	type	True	84.143	589	852	95	below_threshold
Halohasta litchfieldiae	strain=tADL	GCA_002788215.1	1073996	1073996	type	True	78.8043	381	852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:05,664] [INFO] DFAST Taxonomy check result was written to GCF_006861655.1_ASM686165v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:05,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:05,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:05,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16edd292-6656-4384-9ab8-459305b1b417/dqc_reference/checkm_data
[2024-01-24 13:37:05,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:05,695] [INFO] Task started: CheckM
[2024-01-24 13:37:05,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006861655.1_ASM686165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006861655.1_ASM686165v1_genomic.fna/checkm_input GCF_006861655.1_ASM686165v1_genomic.fna/checkm_result
[2024-01-24 13:37:47,236] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:47,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:47,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:47,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:47,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006861655.1_ASM686165v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:47,256] [INFO] Task started: Blastn
[2024-01-24 13:37:47,256] [INFO] Running command: blastn -query GCF_006861655.1_ASM686165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16edd292-6656-4384-9ab8-459305b1b417/dqc_reference/reference_markers_gtdb.fasta -out GCF_006861655.1_ASM686165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:47,729] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:47,732] [INFO] Selected 6 target genomes.
[2024-01-24 13:37:47,732] [INFO] Target genome list was writen to GCF_006861655.1_ASM686165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:47,739] [INFO] Task started: fastANI
[2024-01-24 13:37:47,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg3577766b-83ae-4615-b63d-9411f4a95197/GCF_006861655.1_ASM686165v1_genomic.fna.gz --refList GCF_006861655.1_ASM686165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006861655.1_ASM686165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:51,957] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:51,963] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:51,964] [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_006861655.1	s__Halonotius roseus	100.0	852	852	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003605575.1	s__Halonotius sp003605575	87.4338	637	852	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605635.1	s__Halonotius pteroides	85.7276	608	852	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861665.1	s__Halonotius terrestris	84.1098	591	852	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000496215.1	s__Halonotius sp000496215	82.4574	468	852	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	96.16	96.16	0.87	0.87	2	-
GCF_900109065.1	s__Halohasta litchfieldiae	78.8096	380	852	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halohasta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:51,965] [INFO] GTDB search result was written to GCF_006861655.1_ASM686165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:51,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:51,968] [INFO] DFAST_QC result json was written to GCF_006861655.1_ASM686165v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:51,968] [INFO] DFAST_QC completed!
[2024-01-24 13:37:51,968] [INFO] Total running time: 0h1m6s