[2024-01-24 11:59:35,252] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,254] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,254] [INFO] DQC Reference Directory: /var/lib/cwl/stga34a8dc1-3220-4a37-b58e-6a3ed46729ce/dqc_reference
[2024-01-24 11:59:36,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,489] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb5e26f4-903f-4770-b3ef-8007e962a2de/GCF_002114285.1_ASM211428v1_genomic.fna.gz | prodigal -d GCF_002114285.1_ASM211428v1_genomic.fna/cds.fna -a GCF_002114285.1_ASM211428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:51,996] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:51,996] [INFO] Task started: HMMsearch
[2024-01-24 11:59:51,996] [INFO] Running command: hmmsearch --tblout GCF_002114285.1_ASM211428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga34a8dc1-3220-4a37-b58e-6a3ed46729ce/dqc_reference/reference_markers.hmm GCF_002114285.1_ASM211428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:52,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:52,273] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgeb5e26f4-903f-4770-b3ef-8007e962a2de/GCF_002114285.1_ASM211428v1_genomic.fna.gz]
[2024-01-24 11:59:52,306] [INFO] Query marker FASTA was written to GCF_002114285.1_ASM211428v1_genomic.fna/markers.fasta
[2024-01-24 11:59:52,306] [INFO] Task started: Blastn
[2024-01-24 11:59:52,306] [INFO] Running command: blastn -query GCF_002114285.1_ASM211428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga34a8dc1-3220-4a37-b58e-6a3ed46729ce/dqc_reference/reference_markers.fasta -out GCF_002114285.1_ASM211428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:52,831] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:52,836] [INFO] Selected 7 target genomes.
[2024-01-24 11:59:52,836] [INFO] Target genome list was writen to GCF_002114285.1_ASM211428v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:52,867] [INFO] Task started: fastANI
[2024-01-24 11:59:52,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5e26f4-903f-4770-b3ef-8007e962a2de/GCF_002114285.1_ASM211428v1_genomic.fna.gz --refList GCF_002114285.1_ASM211428v1_genomic.fna/target_genomes.txt --output GCF_002114285.1_ASM211428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:59,910] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:59,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga34a8dc1-3220-4a37-b58e-6a3ed46729ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:59,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga34a8dc1-3220-4a37-b58e-6a3ed46729ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:59,922] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:59,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:59,923] [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 ezzemoulense	strain=DSM 17463	GCA_002114285.1	337243	337243	type	True	100.0	1110	1119	95	conclusive
Halorubrum ezzemoulense	strain=DSM 17463	GCA_000421805.1	337243	337243	type	True	99.9203	1090	1119	95	conclusive
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	90.0744	797	1119	95	below_threshold
Halorubrum distributum	strain=JCM 10118	GCA_000337335.1	29283	29283	suspected-type	True	89.9047	805	1119	95	below_threshold
Halorubrum distributum	strain=JCM 9100	GCA_000337055.1	29283	29283	suspected-type	True	89.8341	806	1119	95	below_threshold
Halorubrum arcis	strain=JCM 13916	GCA_000337015.1	368454	368454	type	True	89.6469	802	1119	95	below_threshold
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	85.2213	679	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:59,924] [INFO] DFAST Taxonomy check result was written to GCF_002114285.1_ASM211428v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:59,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:59,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:59,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga34a8dc1-3220-4a37-b58e-6a3ed46729ce/dqc_reference/checkm_data
[2024-01-24 11:59:59,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:59,966] [INFO] Task started: CheckM
[2024-01-24 11:59:59,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002114285.1_ASM211428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002114285.1_ASM211428v1_genomic.fna/checkm_input GCF_002114285.1_ASM211428v1_genomic.fna/checkm_result
[2024-01-24 12:00:44,963] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:44,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:44,991] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:44,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:44,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002114285.1_ASM211428v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:44,992] [INFO] Task started: Blastn
[2024-01-24 12:00:44,992] [INFO] Running command: blastn -query GCF_002114285.1_ASM211428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga34a8dc1-3220-4a37-b58e-6a3ed46729ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_002114285.1_ASM211428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:45,494] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:45,534] [INFO] Selected 8 target genomes.
[2024-01-24 12:00:45,534] [INFO] Target genome list was writen to GCF_002114285.1_ASM211428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:45,555] [INFO] Task started: fastANI
[2024-01-24 12:00:45,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5e26f4-903f-4770-b3ef-8007e962a2de/GCF_002114285.1_ASM211428v1_genomic.fna.gz --refList GCF_002114285.1_ASM211428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002114285.1_ASM211428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:54,350] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:54,362] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:54,363] [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_002114285.1	s__Halorubrum ezzemoulense	100.0	1110	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.69	98.29	0.85	0.81	17	conclusive
GCF_000337035.1	s__Halorubrum coriense	90.0358	799	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337335.1	s__Halorubrum distributum	89.9212	804	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.52	97.80	0.88	0.83	7	-
GCF_000336875.1	s__Halorubrum californiense	89.6051	807	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.69	99.69	0.88	0.88	2	-
GCF_002355655.1	s__Halorubrum trapanicum_A	89.5851	772	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666015.1	s__Halorubrum sp003666015	89.5559	808	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228765.1	s__Halorubrum sp000296615	89.4715	792	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.09	99.09	0.95	0.95	2	-
GCF_001280455.1	s__Halorubrum tropicale	89.0486	853	1119	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	97.18	95.21	0.82	0.77	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:54,364] [INFO] GTDB search result was written to GCF_002114285.1_ASM211428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:54,365] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:54,367] [INFO] DFAST_QC result json was written to GCF_002114285.1_ASM211428v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:54,368] [INFO] DFAST_QC completed!
[2024-01-24 12:00:54,368] [INFO] Total running time: 0h1m19s