[2024-01-25 18:09:05,517] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:05,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:05,518] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8a60c36-d48b-48ba-a8dd-f69315e1cdd6/dqc_reference
[2024-01-25 18:09:06,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:06,663] [INFO] Task started: Prodigal
[2024-01-25 18:09:06,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg55164bb8-537b-41af-9f88-571c3a6e217b/GCF_000425545.1_ASM42554v1_genomic.fna.gz | prodigal -d GCF_000425545.1_ASM42554v1_genomic.fna/cds.fna -a GCF_000425545.1_ASM42554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:13,523] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:13,523] [INFO] Task started: HMMsearch
[2024-01-25 18:09:13,523] [INFO] Running command: hmmsearch --tblout GCF_000425545.1_ASM42554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8a60c36-d48b-48ba-a8dd-f69315e1cdd6/dqc_reference/reference_markers.hmm GCF_000425545.1_ASM42554v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:13,755] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:13,756] [INFO] Found 6/6 markers.
[2024-01-25 18:09:13,783] [INFO] Query marker FASTA was written to GCF_000425545.1_ASM42554v1_genomic.fna/markers.fasta
[2024-01-25 18:09:13,783] [INFO] Task started: Blastn
[2024-01-25 18:09:13,784] [INFO] Running command: blastn -query GCF_000425545.1_ASM42554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8a60c36-d48b-48ba-a8dd-f69315e1cdd6/dqc_reference/reference_markers.fasta -out GCF_000425545.1_ASM42554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:14,326] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:14,329] [INFO] Selected 25 target genomes.
[2024-01-25 18:09:14,329] [INFO] Target genome list was writen to GCF_000425545.1_ASM42554v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:14,360] [INFO] Task started: fastANI
[2024-01-25 18:09:14,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg55164bb8-537b-41af-9f88-571c3a6e217b/GCF_000425545.1_ASM42554v1_genomic.fna.gz --refList GCF_000425545.1_ASM42554v1_genomic.fna/target_genomes.txt --output GCF_000425545.1_ASM42554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:27,630] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:27,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8a60c36-d48b-48ba-a8dd-f69315e1cdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:27,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8a60c36-d48b-48ba-a8dd-f69315e1cdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:27,639] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:27,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:27,639] [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
Sporosarcina ureae	strain=DSM 2281	GCA_000425545.1	1571	1571	suspected-type	True	100.0	1086	1088	95	conclusive
Sporosarcina gallistercoris	strain=Sa3CUA8	GCA_014836415.1	2762245	2762245	type	True	77.7376	79	1088	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	77.4026	91	1088	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	77.3695	56	1088	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	77.1122	55	1088	95	below_threshold
Sporosarcina luteola	strain=NBRC 105378	GCA_007991495.1	582850	582850	type	True	77.0261	103	1088	95	below_threshold
Savagea serpentis	strain=SN6	GCA_015351395.1	2785297	2785297	type	True	76.8913	56	1088	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	76.6424	66	1088	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	76.5636	69	1088	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	76.5257	69	1088	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	76.306	55	1088	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	76.3045	55	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:27,640] [INFO] DFAST Taxonomy check result was written to GCF_000425545.1_ASM42554v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:27,641] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:27,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:27,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8a60c36-d48b-48ba-a8dd-f69315e1cdd6/dqc_reference/checkm_data
[2024-01-25 18:09:27,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:27,676] [INFO] Task started: CheckM
[2024-01-25 18:09:27,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425545.1_ASM42554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425545.1_ASM42554v1_genomic.fna/checkm_input GCF_000425545.1_ASM42554v1_genomic.fna/checkm_result
[2024-01-25 18:09:53,066] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:53,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:53,082] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:53,082] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:53,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425545.1_ASM42554v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:53,082] [INFO] Task started: Blastn
[2024-01-25 18:09:53,082] [INFO] Running command: blastn -query GCF_000425545.1_ASM42554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8a60c36-d48b-48ba-a8dd-f69315e1cdd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425545.1_ASM42554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:53,874] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:53,877] [INFO] Selected 7 target genomes.
[2024-01-25 18:09:53,877] [INFO] Target genome list was writen to GCF_000425545.1_ASM42554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:53,884] [INFO] Task started: fastANI
[2024-01-25 18:09:53,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg55164bb8-537b-41af-9f88-571c3a6e217b/GCF_000425545.1_ASM42554v1_genomic.fna.gz --refList GCF_000425545.1_ASM42554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425545.1_ASM42554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:00,247] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:00,253] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:00,253] [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_000425545.1	s__Sporosarcina ureae	100.0	1086	1088	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	97.73	96.74	0.92	0.89	7	conclusive
GCF_002082015.1	s__Sporosarcina ureae_A	90.4874	952	1088	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	97.43	97.43	0.91	0.91	2	-
GCF_002743335.1	s__Sporosarcina sp002743335	90.1867	915	1088	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.80	96.09	0.96	0.91	5	-
GCF_002101375.1	s__Sporosarcina ureae_B	88.4984	873	1088	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.89	98.86	0.95	0.94	5	-
GCF_002743255.1	s__Sporosarcina sp002743255	88.2145	885	1088	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	97.62	97.10	0.91	0.90	4	-
GCF_002743375.1	s__Sporosarcina sp002743375	87.7294	870	1088	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002109325.1	s__Sporosarcina ureae_C	85.4593	878	1088	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.86	98.81	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:00,255] [INFO] GTDB search result was written to GCF_000425545.1_ASM42554v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:00,255] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:00,258] [INFO] DFAST_QC result json was written to GCF_000425545.1_ASM42554v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:00,259] [INFO] DFAST_QC completed!
[2024-01-25 18:10:00,259] [INFO] Total running time: 0h0m55s