[2024-01-24 12:39:35,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgea26f914-a951-4444-987e-27370568b76a/dqc_reference
[2024-01-24 12:39:36,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,661] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,661] [INFO] Running command: gunzip -c /var/lib/cwl/stgb77a7937-806d-4416-865a-191cfe1c7ca7/GCF_002265875.1_ASM226587v1_genomic.fna.gz | prodigal -d GCF_002265875.1_ASM226587v1_genomic.fna/cds.fna -a GCF_002265875.1_ASM226587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:44,637] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:44,637] [INFO] Task started: HMMsearch
[2024-01-24 12:39:44,638] [INFO] Running command: hmmsearch --tblout GCF_002265875.1_ASM226587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea26f914-a951-4444-987e-27370568b76a/dqc_reference/reference_markers.hmm GCF_002265875.1_ASM226587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:44,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:44,903] [INFO] Found 6/6 markers.
[2024-01-24 12:39:44,939] [INFO] Query marker FASTA was written to GCF_002265875.1_ASM226587v1_genomic.fna/markers.fasta
[2024-01-24 12:39:44,939] [INFO] Task started: Blastn
[2024-01-24 12:39:44,939] [INFO] Running command: blastn -query GCF_002265875.1_ASM226587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea26f914-a951-4444-987e-27370568b76a/dqc_reference/reference_markers.fasta -out GCF_002265875.1_ASM226587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:45,532] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:45,537] [INFO] Selected 12 target genomes.
[2024-01-24 12:39:45,537] [INFO] Target genome list was writen to GCF_002265875.1_ASM226587v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:45,543] [INFO] Task started: fastANI
[2024-01-24 12:39:45,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77a7937-806d-4416-865a-191cfe1c7ca7/GCF_002265875.1_ASM226587v1_genomic.fna.gz --refList GCF_002265875.1_ASM226587v1_genomic.fna/target_genomes.txt --output GCF_002265875.1_ASM226587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:53,961] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:53,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea26f914-a951-4444-987e-27370568b76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:53,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea26f914-a951-4444-987e-27370568b76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:53,969] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:39:53,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:53,969] [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
Marinococcus halophilus	strain=KCTC 2843	GCA_002265875.1	1371	1371	type	True	100.0	1058	1060	95	conclusive
Marinococcus halophilus	strain=NBRC 102359	GCA_007989565.1	1371	1371	type	True	99.9734	1035	1060	95	conclusive
Marinococcus halotolerans	strain=DSM 16375	GCA_000420725.1	301092	301092	type	True	86.7798	825	1060	95	below_threshold
Marinococcus luteus	strain=DSM 23126	GCA_900106595.1	1122204	1122204	type	True	86.3493	815	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:53,971] [INFO] DFAST Taxonomy check result was written to GCF_002265875.1_ASM226587v1_genomic.fna/tc_result.tsv
[2024-01-24 12:39:53,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:53,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:53,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea26f914-a951-4444-987e-27370568b76a/dqc_reference/checkm_data
[2024-01-24 12:39:53,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:54,011] [INFO] Task started: CheckM
[2024-01-24 12:39:54,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002265875.1_ASM226587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002265875.1_ASM226587v1_genomic.fna/checkm_input GCF_002265875.1_ASM226587v1_genomic.fna/checkm_result
[2024-01-24 12:40:23,455] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:23,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:23,483] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:23,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:23,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002265875.1_ASM226587v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:23,484] [INFO] Task started: Blastn
[2024-01-24 12:40:23,484] [INFO] Running command: blastn -query GCF_002265875.1_ASM226587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea26f914-a951-4444-987e-27370568b76a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002265875.1_ASM226587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:24,324] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:24,329] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:24,329] [INFO] Target genome list was writen to GCF_002265875.1_ASM226587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:24,342] [INFO] Task started: fastANI
[2024-01-24 12:40:24,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77a7937-806d-4416-865a-191cfe1c7ca7/GCF_002265875.1_ASM226587v1_genomic.fna.gz --refList GCF_002265875.1_ASM226587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002265875.1_ASM226587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:35,762] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:35,770] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:35,770] [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_002265875.1	s__Marinococcus halophilus	100.0	1058	1060	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Marinococcus	95.0	99.35	98.70	0.96	0.92	3	conclusive
GCF_000420725.1	s__Marinococcus halotolerans	86.7737	826	1060	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Marinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106595.1	s__Marinococcus luteus	86.3493	815	1060	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Marinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:35,775] [INFO] GTDB search result was written to GCF_002265875.1_ASM226587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:35,776] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:35,779] [INFO] DFAST_QC result json was written to GCF_002265875.1_ASM226587v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:35,779] [INFO] DFAST_QC completed!
[2024-01-24 12:40:35,779] [INFO] Total running time: 0h1m0s