[2024-01-25 19:43:20,725] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:20,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:20,727] [INFO] DQC Reference Directory: /var/lib/cwl/stgd73cb765-e0db-4901-9256-8fdc785f7b92/dqc_reference
[2024-01-25 19:43:21,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:21,875] [INFO] Task started: Prodigal
[2024-01-25 19:43:21,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a08375f-f2aa-460a-8495-1160fcacc5dd/GCF_030813635.1_ASM3081363v1_genomic.fna.gz | prodigal -d GCF_030813635.1_ASM3081363v1_genomic.fna/cds.fna -a GCF_030813635.1_ASM3081363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:28,758] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:28,759] [INFO] Task started: HMMsearch
[2024-01-25 19:43:28,759] [INFO] Running command: hmmsearch --tblout GCF_030813635.1_ASM3081363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd73cb765-e0db-4901-9256-8fdc785f7b92/dqc_reference/reference_markers.hmm GCF_030813635.1_ASM3081363v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:28,989] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:28,990] [INFO] Found 6/6 markers.
[2024-01-25 19:43:29,017] [INFO] Query marker FASTA was written to GCF_030813635.1_ASM3081363v1_genomic.fna/markers.fasta
[2024-01-25 19:43:29,017] [INFO] Task started: Blastn
[2024-01-25 19:43:29,017] [INFO] Running command: blastn -query GCF_030813635.1_ASM3081363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd73cb765-e0db-4901-9256-8fdc785f7b92/dqc_reference/reference_markers.fasta -out GCF_030813635.1_ASM3081363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:29,566] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:29,569] [INFO] Selected 28 target genomes.
[2024-01-25 19:43:29,569] [INFO] Target genome list was writen to GCF_030813635.1_ASM3081363v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:29,581] [INFO] Task started: fastANI
[2024-01-25 19:43:29,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a08375f-f2aa-460a-8495-1160fcacc5dd/GCF_030813635.1_ASM3081363v1_genomic.fna.gz --refList GCF_030813635.1_ASM3081363v1_genomic.fna/target_genomes.txt --output GCF_030813635.1_ASM3081363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:45,135] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:45,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd73cb765-e0db-4901-9256-8fdc785f7b92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:45,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd73cb765-e0db-4901-9256-8fdc785f7b92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:45,141] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:43:45,141] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:43:45,141] [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 qingdaonense	strain=CGMCC 1.6134	GCA_900114715.1	266892	266892	type	True	77.8416	169	1125	95	below_threshold
Salibacterium halotolerans	strain=S7	GCA_900115625.1	1884432	1884432	type	True	77.6778	150	1125	95	below_threshold
Alteribacillus iranensis	strain=DSM 23995	GCA_900113025.1	930128	930128	type	True	76.9739	64	1125	95	below_threshold
Alteribacillus persepolensis	strain=DSM 21632	GCA_900099605.1	568899	568899	type	True	76.9155	132	1125	95	below_threshold
Sinobaca qinghaiensis	strain=DSM 17008	GCA_003610495.1	342944	342944	type	True	76.7492	54	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:45,142] [INFO] DFAST Taxonomy check result was written to GCF_030813635.1_ASM3081363v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:45,143] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:45,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:45,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd73cb765-e0db-4901-9256-8fdc785f7b92/dqc_reference/checkm_data
[2024-01-25 19:43:45,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:45,178] [INFO] Task started: CheckM
[2024-01-25 19:43:45,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813635.1_ASM3081363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813635.1_ASM3081363v1_genomic.fna/checkm_input GCF_030813635.1_ASM3081363v1_genomic.fna/checkm_result
[2024-01-25 19:44:09,883] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:09,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:09,930] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:09,930] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:09,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813635.1_ASM3081363v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:09,932] [INFO] Task started: Blastn
[2024-01-25 19:44:09,932] [INFO] Running command: blastn -query GCF_030813635.1_ASM3081363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd73cb765-e0db-4901-9256-8fdc785f7b92/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813635.1_ASM3081363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:10,663] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:10,671] [INFO] Selected 29 target genomes.
[2024-01-25 19:44:10,671] [INFO] Target genome list was writen to GCF_030813635.1_ASM3081363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:10,686] [INFO] Task started: fastANI
[2024-01-25 19:44:10,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a08375f-f2aa-460a-8495-1160fcacc5dd/GCF_030813635.1_ASM3081363v1_genomic.fna.gz --refList GCF_030813635.1_ASM3081363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813635.1_ASM3081363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:30,746] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:30,751] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:44:30,751] [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_900114715.1	s__Salibacterium qingdaonense	77.8416	169	1125	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_900115625.1	s__Salibacterium halotolerans	77.6413	151	1125	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	77.1426	195	1125	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_900113025.1	s__Alteribacillus_A iranensis	76.9691	65	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Alteribacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099605.1	s__Alteribacillus persepolensis	76.9155	132	1125	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_003610495.1	s__Sinobaca qinghaiensis	76.7492	54	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Sinobaca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:30,752] [INFO] GTDB search result was written to GCF_030813635.1_ASM3081363v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:30,753] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:30,755] [INFO] DFAST_QC result json was written to GCF_030813635.1_ASM3081363v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:30,755] [INFO] DFAST_QC completed!
[2024-01-25 19:44:30,755] [INFO] Total running time: 0h1m10s