[2024-01-24 12:54:21,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:21,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:21,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c3134ee-d1a6-4e4d-a695-d508c226ce71/dqc_reference
[2024-01-24 12:54:23,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:23,879] [INFO] Task started: Prodigal
[2024-01-24 12:54:23,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg9acead8e-6fc2-4a64-9bbd-0930c6216613/GCF_000429705.1_ASM42970v1_genomic.fna.gz | prodigal -d GCF_000429705.1_ASM42970v1_genomic.fna/cds.fna -a GCF_000429705.1_ASM42970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:33,702] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:33,703] [INFO] Task started: HMMsearch
[2024-01-24 12:54:33,703] [INFO] Running command: hmmsearch --tblout GCF_000429705.1_ASM42970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c3134ee-d1a6-4e4d-a695-d508c226ce71/dqc_reference/reference_markers.hmm GCF_000429705.1_ASM42970v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:34,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:34,030] [INFO] Found 6/6 markers.
[2024-01-24 12:54:34,073] [INFO] Query marker FASTA was written to GCF_000429705.1_ASM42970v1_genomic.fna/markers.fasta
[2024-01-24 12:54:34,073] [INFO] Task started: Blastn
[2024-01-24 12:54:34,074] [INFO] Running command: blastn -query GCF_000429705.1_ASM42970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c3134ee-d1a6-4e4d-a695-d508c226ce71/dqc_reference/reference_markers.fasta -out GCF_000429705.1_ASM42970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:34,671] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:34,677] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:34,678] [INFO] Target genome list was writen to GCF_000429705.1_ASM42970v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:34,696] [INFO] Task started: fastANI
[2024-01-24 12:54:34,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg9acead8e-6fc2-4a64-9bbd-0930c6216613/GCF_000429705.1_ASM42970v1_genomic.fna.gz --refList GCF_000429705.1_ASM42970v1_genomic.fna/target_genomes.txt --output GCF_000429705.1_ASM42970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:48,941] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:48,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c3134ee-d1a6-4e4d-a695-d508c226ce71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:48,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c3134ee-d1a6-4e4d-a695-d508c226ce71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:48,954] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:48,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:48,954] [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
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	100.0	1333	1333	95	conclusive
Alteribacter keqinensis	strain=KQ-3	GCA_003710255.1	2483800	2483800	type	True	80.1365	640	1333	95	below_threshold
Alteribacter salitolerans	strain=APA H-16(1)	GCA_016901055.1	2912333	2912333	type	True	80.0139	641	1333	95	below_threshold
Alteribacter populi	strain=FJAT-45347	GCA_002352765.2	2011011	2011011	type	True	78.3291	259	1333	95	below_threshold
Alteribacter lacisalsi	strain=YSP-3	GCA_003226345.1	2045244	2045244	type	True	78.0472	227	1333	95	below_threshold
Paenalkalicoccus suaedae	strain=M4U3P1	GCA_006965545.2	2592382	2592382	type	True	77.7018	74	1333	95	below_threshold
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	77.5151	222	1333	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	77.4706	109	1333	95	below_threshold
Evansella tamaricis	strain=CGMCC 1.15917	GCA_019042215.1	2069301	2069301	type	True	77.1818	62	1333	95	below_threshold
Salipaludibacillus neizhouensis	strain=DSM 19794	GCA_002886185.1	885475	885475	type	True	76.9827	67	1333	95	below_threshold
Salipaludibacillus neizhouensis	strain=KCTC 13187	GCA_003615245.1	885475	885475	type	True	76.8922	64	1333	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	76.5546	56	1333	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.1183	58	1333	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:48,956] [INFO] DFAST Taxonomy check result was written to GCF_000429705.1_ASM42970v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:48,957] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:48,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:48,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c3134ee-d1a6-4e4d-a695-d508c226ce71/dqc_reference/checkm_data
[2024-01-24 12:54:48,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:48,998] [INFO] Task started: CheckM
[2024-01-24 12:54:48,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429705.1_ASM42970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429705.1_ASM42970v1_genomic.fna/checkm_input GCF_000429705.1_ASM42970v1_genomic.fna/checkm_result
[2024-01-24 12:55:22,952] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:22,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:22,973] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:22,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:22,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429705.1_ASM42970v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:22,974] [INFO] Task started: Blastn
[2024-01-24 12:55:22,974] [INFO] Running command: blastn -query GCF_000429705.1_ASM42970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c3134ee-d1a6-4e4d-a695-d508c226ce71/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429705.1_ASM42970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:23,791] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:23,795] [INFO] Selected 25 target genomes.
[2024-01-24 12:55:23,796] [INFO] Target genome list was writen to GCF_000429705.1_ASM42970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:23,814] [INFO] Task started: fastANI
[2024-01-24 12:55:23,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg9acead8e-6fc2-4a64-9bbd-0930c6216613/GCF_000429705.1_ASM42970v1_genomic.fna.gz --refList GCF_000429705.1_ASM42970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429705.1_ASM42970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:41,162] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:41,176] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:41,177] [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_000429705.1	s__Alteribacter aurantiacus	100.0	1333	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003710255.1	s__Alteribacter sp003710255	80.151	639	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	98.04	98.04	0.95	0.95	2	-
GCF_002352765.1	s__Alteribacter populi	78.3462	260	1333	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_003226345.1	s__Alteribacter lacisalsi	78.0472	227	1333	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_006965545.2	s__Alkalicoccus sp006965545	77.6585	73	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006007885.1	s__Alteribacter natronophilus	77.5416	220	1333	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_000177235.2	s__Evansella cellulosilytica	77.4407	70	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019042215.1	s__Evansella tamaricis	77.2312	63	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000005825.2	s__Bacillus_S pseudofirmus	77.1372	66	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002019735.1	s__Salipaludibacillus agaradhaerens	77.0975	67	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886185.1	s__Salipaludibacillus neizhouensis	76.9656	64	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004116265.1	s__Anaerobacillus alkaliphilus	76.5551	56	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144865.1	s__Anaerobacillus_A hwajinpoensis_A	76.5342	54	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024285.1	s__Bacillus_BH sp019024285	76.1659	59	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:41,178] [INFO] GTDB search result was written to GCF_000429705.1_ASM42970v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:41,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:41,183] [INFO] DFAST_QC result json was written to GCF_000429705.1_ASM42970v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:41,183] [INFO] DFAST_QC completed!
[2024-01-24 12:55:41,183] [INFO] Total running time: 0h1m19s