[2024-01-24 14:03:02,939] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:02,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:02,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg93b00181-28db-4635-9351-6bb696c2b18c/dqc_reference
[2024-01-24 14:03:04,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:04,221] [INFO] Task started: Prodigal
[2024-01-24 14:03:04,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg197a509e-247f-4e48-a1df-a8430c9613ce/GCF_006965545.2_ASM696554v2_genomic.fna.gz | prodigal -d GCF_006965545.2_ASM696554v2_genomic.fna/cds.fna -a GCF_006965545.2_ASM696554v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:13,132] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:13,132] [INFO] Task started: HMMsearch
[2024-01-24 14:03:13,132] [INFO] Running command: hmmsearch --tblout GCF_006965545.2_ASM696554v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93b00181-28db-4635-9351-6bb696c2b18c/dqc_reference/reference_markers.hmm GCF_006965545.2_ASM696554v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:13,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:13,427] [INFO] Found 6/6 markers.
[2024-01-24 14:03:13,461] [INFO] Query marker FASTA was written to GCF_006965545.2_ASM696554v2_genomic.fna/markers.fasta
[2024-01-24 14:03:13,461] [INFO] Task started: Blastn
[2024-01-24 14:03:13,461] [INFO] Running command: blastn -query GCF_006965545.2_ASM696554v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b00181-28db-4635-9351-6bb696c2b18c/dqc_reference/reference_markers.fasta -out GCF_006965545.2_ASM696554v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:14,082] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:14,085] [INFO] Selected 32 target genomes.
[2024-01-24 14:03:14,086] [INFO] Target genome list was writen to GCF_006965545.2_ASM696554v2_genomic.fna/target_genomes.txt
[2024-01-24 14:03:14,102] [INFO] Task started: fastANI
[2024-01-24 14:03:14,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg197a509e-247f-4e48-a1df-a8430c9613ce/GCF_006965545.2_ASM696554v2_genomic.fna.gz --refList GCF_006965545.2_ASM696554v2_genomic.fna/target_genomes.txt --output GCF_006965545.2_ASM696554v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:35,747] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:35,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93b00181-28db-4635-9351-6bb696c2b18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:35,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93b00181-28db-4635-9351-6bb696c2b18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:35,762] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:35,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:35,762] [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
Paenalkalicoccus suaedae	strain=M4U3P1	GCA_006965545.2	2592382	2592382	type	True	100.0	1341	1345	95	conclusive
Evansella clarkii	strain=DSM 8720	GCA_002019695.1	79879	79879	type	True	81.3739	54	1345	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	79.4597	53	1345	95	below_threshold
Alteribacter populi	strain=FJAT-45347	GCA_002352765.2	2011011	2011011	type	True	79.2757	65	1345	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	78.7802	80	1345	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	78.1058	64	1345	95	below_threshold
Alkalicoccus halolimnae	strain=BZ-SZ-XJ29	GCA_008014775.1	1667239	1667239	type	True	77.439	54	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:35,764] [INFO] DFAST Taxonomy check result was written to GCF_006965545.2_ASM696554v2_genomic.fna/tc_result.tsv
[2024-01-24 14:03:35,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:35,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:35,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93b00181-28db-4635-9351-6bb696c2b18c/dqc_reference/checkm_data
[2024-01-24 14:03:35,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:35,811] [INFO] Task started: CheckM
[2024-01-24 14:03:35,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006965545.2_ASM696554v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006965545.2_ASM696554v2_genomic.fna/checkm_input GCF_006965545.2_ASM696554v2_genomic.fna/checkm_result
[2024-01-24 14:04:07,776] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:07,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:07,801] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:07,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:07,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006965545.2_ASM696554v2_genomic.fna/markers.fasta)
[2024-01-24 14:04:07,803] [INFO] Task started: Blastn
[2024-01-24 14:04:07,803] [INFO] Running command: blastn -query GCF_006965545.2_ASM696554v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg93b00181-28db-4635-9351-6bb696c2b18c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006965545.2_ASM696554v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:08,561] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:08,566] [INFO] Selected 34 target genomes.
[2024-01-24 14:04:08,566] [INFO] Target genome list was writen to GCF_006965545.2_ASM696554v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:08,593] [INFO] Task started: fastANI
[2024-01-24 14:04:08,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg197a509e-247f-4e48-a1df-a8430c9613ce/GCF_006965545.2_ASM696554v2_genomic.fna.gz --refList GCF_006965545.2_ASM696554v2_genomic.fna/target_genomes_gtdb.txt --output GCF_006965545.2_ASM696554v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:33,978] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:33,990] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:33,990] [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_006965545.2	s__Alkalicoccus sp006965545	100.0	1344	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002019695.1	s__Evansella clarkii	81.4722	55	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	98.30	98.30	0.93	0.93	2	-
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	80.7059	59	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	97.46	97.46	0.83	0.83	2	-
GCF_002352765.1	s__Alteribacter populi	79.2757	65	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	99.66	99.66	0.95	0.95	2	-
GCF_000429705.1	s__Alteribacter aurantiacus	78.0891	65	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014775.1	s__Alkalicoccus halolimnae	77.439	54	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:33,992] [INFO] GTDB search result was written to GCF_006965545.2_ASM696554v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:33,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:33,995] [INFO] DFAST_QC result json was written to GCF_006965545.2_ASM696554v2_genomic.fna/dqc_result.json
[2024-01-24 14:04:33,996] [INFO] DFAST_QC completed!
[2024-01-24 14:04:33,996] [INFO] Total running time: 0h1m31s