[2024-01-24 13:57:16,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,452] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ccfa8f7-48c8-45ff-8c8a-fd5a836a00d8/dqc_reference
[2024-01-24 13:57:17,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,886] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,886] [INFO] Running command: gunzip -c /var/lib/cwl/stge019d297-dcee-4bb1-be1c-385dcf808927/GCF_000429685.1_ASM42968v1_genomic.fna.gz | prodigal -d GCF_000429685.1_ASM42968v1_genomic.fna/cds.fna -a GCF_000429685.1_ASM42968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:28,703] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:28,703] [INFO] Task started: HMMsearch
[2024-01-24 13:57:28,703] [INFO] Running command: hmmsearch --tblout GCF_000429685.1_ASM42968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ccfa8f7-48c8-45ff-8c8a-fd5a836a00d8/dqc_reference/reference_markers.hmm GCF_000429685.1_ASM42968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:29,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:29,011] [INFO] Found 6/6 markers.
[2024-01-24 13:57:29,050] [INFO] Query marker FASTA was written to GCF_000429685.1_ASM42968v1_genomic.fna/markers.fasta
[2024-01-24 13:57:29,050] [INFO] Task started: Blastn
[2024-01-24 13:57:29,050] [INFO] Running command: blastn -query GCF_000429685.1_ASM42968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ccfa8f7-48c8-45ff-8c8a-fd5a836a00d8/dqc_reference/reference_markers.fasta -out GCF_000429685.1_ASM42968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:29,612] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:29,616] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:29,616] [INFO] Target genome list was writen to GCF_000429685.1_ASM42968v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:29,623] [INFO] Task started: fastANI
[2024-01-24 13:57:29,623] [INFO] Running command: fastANI --query /var/lib/cwl/stge019d297-dcee-4bb1-be1c-385dcf808927/GCF_000429685.1_ASM42968v1_genomic.fna.gz --refList GCF_000429685.1_ASM42968v1_genomic.fna/target_genomes.txt --output GCF_000429685.1_ASM42968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:42,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:42,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ccfa8f7-48c8-45ff-8c8a-fd5a836a00d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:42,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ccfa8f7-48c8-45ff-8c8a-fd5a836a00d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:42,186] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:42,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:42,187] [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
Salibacterium aidingense	strain=DSM 18341	GCA_000429685.1	384933	384933	type	True	100.0	1444	1448	95	conclusive
Salibacterium halotolerans	strain=S7	GCA_900115625.1	1884432	1884432	type	True	78.5494	333	1448	95	below_threshold
Salibacterium qingdaonense	strain=CGMCC 1.6134	GCA_900114715.1	266892	266892	type	True	78.132	298	1448	95	below_threshold
Marinococcus halophilus	strain=KCTC 2843	GCA_002265875.1	1371	1371	type	True	75.9561	50	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:42,188] [INFO] DFAST Taxonomy check result was written to GCF_000429685.1_ASM42968v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:42,189] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:42,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:42,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ccfa8f7-48c8-45ff-8c8a-fd5a836a00d8/dqc_reference/checkm_data
[2024-01-24 13:57:42,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:42,238] [INFO] Task started: CheckM
[2024-01-24 13:57:42,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429685.1_ASM42968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429685.1_ASM42968v1_genomic.fna/checkm_input GCF_000429685.1_ASM42968v1_genomic.fna/checkm_result
[2024-01-24 13:58:19,249] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:19,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:19,267] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:19,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:19,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429685.1_ASM42968v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:19,268] [INFO] Task started: Blastn
[2024-01-24 13:58:19,268] [INFO] Running command: blastn -query GCF_000429685.1_ASM42968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ccfa8f7-48c8-45ff-8c8a-fd5a836a00d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429685.1_ASM42968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:20,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:20,131] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:20,132] [INFO] Target genome list was writen to GCF_000429685.1_ASM42968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:20,148] [INFO] Task started: fastANI
[2024-01-24 13:58:20,148] [INFO] Running command: fastANI --query /var/lib/cwl/stge019d297-dcee-4bb1-be1c-385dcf808927/GCF_000429685.1_ASM42968v1_genomic.fna.gz --refList GCF_000429685.1_ASM42968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429685.1_ASM42968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:35,861] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:35,872] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:35,873] [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_000429685.1	s__Bacillus_AP aidingensis	100.0	1444	1448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Bacillus_AP	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115625.1	s__Salibacterium halotolerans	78.5255	335	1448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114715.1	s__Salibacterium qingdaonense	78.1407	299	1448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765375.1	s__Alteribacillus sp009765375	76.9734	160	1448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Alteribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002265875.1	s__Marinococcus halophilus	75.9561	50	1448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Marinococcus	95.0	99.35	98.70	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:35,875] [INFO] GTDB search result was written to GCF_000429685.1_ASM42968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:35,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:35,877] [INFO] DFAST_QC result json was written to GCF_000429685.1_ASM42968v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:35,878] [INFO] DFAST_QC completed!
[2024-01-24 13:58:35,878] [INFO] Total running time: 0h1m19s