[2023-06-08 12:26:29,268] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:29,271] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:29,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg61e2c120-6bd4-4b80-ab4e-faa3c7082789/dqc_reference
[2023-06-08 12:26:30,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:30,564] [INFO] Task started: Prodigal
[2023-06-08 12:26:30,565] [INFO] Running command: gunzip -c /var/lib/cwl/stg029d9fba-1fe6-45f2-a5a0-b2a5e7da4488/GCA_000416005.1_HQX_031812_genomic.fna.gz | prodigal -d GCA_000416005.1_HQX_031812_genomic.fna/cds.fna -a GCA_000416005.1_HQX_031812_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:44,631] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:44,631] [INFO] Task started: HMMsearch
[2023-06-08 12:26:44,632] [INFO] Running command: hmmsearch --tblout GCA_000416005.1_HQX_031812_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61e2c120-6bd4-4b80-ab4e-faa3c7082789/dqc_reference/reference_markers.hmm GCA_000416005.1_HQX_031812_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:44,909] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:44,910] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg029d9fba-1fe6-45f2-a5a0-b2a5e7da4488/GCA_000416005.1_HQX_031812_genomic.fna.gz]
[2023-06-08 12:26:44,943] [INFO] Query marker FASTA was written to GCA_000416005.1_HQX_031812_genomic.fna/markers.fasta
[2023-06-08 12:26:44,944] [INFO] Task started: Blastn
[2023-06-08 12:26:44,944] [INFO] Running command: blastn -query GCA_000416005.1_HQX_031812_genomic.fna/markers.fasta -db /var/lib/cwl/stg61e2c120-6bd4-4b80-ab4e-faa3c7082789/dqc_reference/reference_markers.fasta -out GCA_000416005.1_HQX_031812_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:45,467] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:45,472] [INFO] Selected 5 target genomes.
[2023-06-08 12:26:45,473] [INFO] Target genome list was writen to GCA_000416005.1_HQX_031812_genomic.fna/target_genomes.txt
[2023-06-08 12:26:45,476] [INFO] Task started: fastANI
[2023-06-08 12:26:45,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg029d9fba-1fe6-45f2-a5a0-b2a5e7da4488/GCA_000416005.1_HQX_031812_genomic.fna.gz --refList GCA_000416005.1_HQX_031812_genomic.fna/target_genomes.txt --output GCA_000416005.1_HQX_031812_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:26:49,483] [INFO] Task succeeded: fastANI
[2023-06-08 12:26:49,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61e2c120-6bd4-4b80-ab4e-faa3c7082789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:26:49,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61e2c120-6bd4-4b80-ab4e-faa3c7082789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:26:49,490] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:26:49,490] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:26:49,491] [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
Halosegnis rubeus	strain=F17-44	GCA_009184545.1	2212850	2212850	type	True	77.3347	50	1006	95	below_threshold
Haloquadratum walsbyi	strain=DSM 16854 = C23	GCA_000237865.1	293091	293091	type	True	76.7518	105	1006	95	below_threshold
Haloprofundus marisrubri	strain=SB9	GCA_001469955.1	1514971	1514971	type	True	75.7477	56	1006	95	below_threshold
Halogranum salarium	strain=B-1	GCA_000283335.1	693851	693851	type	True	75.6913	60	1006	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:26:49,495] [INFO] DFAST Taxonomy check result was written to GCA_000416005.1_HQX_031812_genomic.fna/tc_result.tsv
[2023-06-08 12:26:49,496] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:26:49,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:26:49,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61e2c120-6bd4-4b80-ab4e-faa3c7082789/dqc_reference/checkm_data
[2023-06-08 12:26:49,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:26:49,540] [INFO] Task started: CheckM
[2023-06-08 12:26:49,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_000416005.1_HQX_031812_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_000416005.1_HQX_031812_genomic.fna/checkm_input GCA_000416005.1_HQX_031812_genomic.fna/checkm_result
[2023-06-08 12:27:34,757] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:34,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.53%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:34,782] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:34,782] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:34,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_000416005.1_HQX_031812_genomic.fna/markers.fasta)
[2023-06-08 12:27:34,783] [INFO] Task started: Blastn
[2023-06-08 12:27:34,783] [INFO] Running command: blastn -query GCA_000416005.1_HQX_031812_genomic.fna/markers.fasta -db /var/lib/cwl/stg61e2c120-6bd4-4b80-ab4e-faa3c7082789/dqc_reference/reference_markers_gtdb.fasta -out GCA_000416005.1_HQX_031812_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:35,206] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:35,210] [INFO] Selected 5 target genomes.
[2023-06-08 12:27:35,210] [INFO] Target genome list was writen to GCA_000416005.1_HQX_031812_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:35,318] [INFO] Task started: fastANI
[2023-06-08 12:27:35,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg029d9fba-1fe6-45f2-a5a0-b2a5e7da4488/GCA_000416005.1_HQX_031812_genomic.fna.gz --refList GCA_000416005.1_HQX_031812_genomic.fna/target_genomes_gtdb.txt --output GCA_000416005.1_HQX_031812_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:38,603] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:38,610] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:27:38,611] [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_000416005.1	s__Haloquadratum sp000416005	99.9236	909	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloquadratum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000237865.1	s__Haloquadratum walsbyi	76.7518	105	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloquadratum	95.0	98.21	97.91	0.91	0.82	6	-
GCF_001469955.1	s__Haloprofundus marisrubri	75.7628	55	1006	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:38,614] [INFO] GTDB search result was written to GCA_000416005.1_HQX_031812_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:38,615] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:38,618] [INFO] DFAST_QC result json was written to GCA_000416005.1_HQX_031812_genomic.fna/dqc_result.json
[2023-06-08 12:27:38,618] [INFO] DFAST_QC completed!
[2023-06-08 12:27:38,618] [INFO] Total running time: 0h1m9s