[2024-01-24 13:55:58,094] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:58,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:58,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg6648beea-1809-4d0d-a2f7-7b6825dbceaf/dqc_reference
[2024-01-24 13:55:59,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,301] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d62fa45-095b-4ee7-86e3-d77ecdb417a4/GCF_021608225.1_ASM2160822v1_genomic.fna.gz | prodigal -d GCF_021608225.1_ASM2160822v1_genomic.fna/cds.fna -a GCF_021608225.1_ASM2160822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:07,014] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:07,015] [INFO] Task started: HMMsearch
[2024-01-24 13:56:07,015] [INFO] Running command: hmmsearch --tblout GCF_021608225.1_ASM2160822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6648beea-1809-4d0d-a2f7-7b6825dbceaf/dqc_reference/reference_markers.hmm GCF_021608225.1_ASM2160822v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:07,284] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:07,285] [INFO] Found 6/6 markers.
[2024-01-24 13:56:07,317] [INFO] Query marker FASTA was written to GCF_021608225.1_ASM2160822v1_genomic.fna/markers.fasta
[2024-01-24 13:56:07,317] [INFO] Task started: Blastn
[2024-01-24 13:56:07,317] [INFO] Running command: blastn -query GCF_021608225.1_ASM2160822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6648beea-1809-4d0d-a2f7-7b6825dbceaf/dqc_reference/reference_markers.fasta -out GCF_021608225.1_ASM2160822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:07,926] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:07,930] [INFO] Selected 26 target genomes.
[2024-01-24 13:56:07,931] [INFO] Target genome list was writen to GCF_021608225.1_ASM2160822v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:08,039] [INFO] Task started: fastANI
[2024-01-24 13:56:08,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d62fa45-095b-4ee7-86e3-d77ecdb417a4/GCF_021608225.1_ASM2160822v1_genomic.fna.gz --refList GCF_021608225.1_ASM2160822v1_genomic.fna/target_genomes.txt --output GCF_021608225.1_ASM2160822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:24,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:24,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6648beea-1809-4d0d-a2f7-7b6825dbceaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:24,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6648beea-1809-4d0d-a2f7-7b6825dbceaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:24,760] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:24,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:24,761] [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
Pseudalkalibacillus berkeleyi	strain=KCTC 12718	GCA_021608225.1	1069813	1069813	type	True	100.0	1159	1161	95	conclusive
Pseudalkalibacillus caeni	strain=HB172195	GCA_005747095.1	2574798	2574798	type	True	77.2315	52	1161	95	below_threshold
Fictibacillus barbaricus	strain=DSM 14730	GCA_017052555.1	182136	182136	type	True	76.5164	67	1161	95	below_threshold
Fictibacillus barbaricus	strain=CCM 4982	GCA_014635025.1	182136	182136	type	True	76.5164	67	1161	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	76.43	56	1161	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	75.8633	50	1161	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	75.8421	56	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:24,762] [INFO] DFAST Taxonomy check result was written to GCF_021608225.1_ASM2160822v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:24,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:24,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:24,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6648beea-1809-4d0d-a2f7-7b6825dbceaf/dqc_reference/checkm_data
[2024-01-24 13:56:24,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:24,804] [INFO] Task started: CheckM
[2024-01-24 13:56:24,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021608225.1_ASM2160822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021608225.1_ASM2160822v1_genomic.fna/checkm_input GCF_021608225.1_ASM2160822v1_genomic.fna/checkm_result
[2024-01-24 13:56:53,772] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:53,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:53,796] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:53,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:53,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021608225.1_ASM2160822v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:53,797] [INFO] Task started: Blastn
[2024-01-24 13:56:53,798] [INFO] Running command: blastn -query GCF_021608225.1_ASM2160822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6648beea-1809-4d0d-a2f7-7b6825dbceaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_021608225.1_ASM2160822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:54,563] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:54,566] [INFO] Selected 31 target genomes.
[2024-01-24 13:56:54,567] [INFO] Target genome list was writen to GCF_021608225.1_ASM2160822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:54,612] [INFO] Task started: fastANI
[2024-01-24 13:56:54,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d62fa45-095b-4ee7-86e3-d77ecdb417a4/GCF_021608225.1_ASM2160822v1_genomic.fna.gz --refList GCF_021608225.1_ASM2160822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021608225.1_ASM2160822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:14,765] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:14,786] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:57:14,787] [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
GCA_017052515.1	s__Fictibacillus nanhaiensis_B	77.1372	54	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262935.1	s__Lottiidibacillus patelloidae	76.8883	57	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_E;f__SA5d-4;g__Lottiidibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335805.1	s__FJAT-45350 sp002335805	76.7547	53	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303315.1	s__Anaerobacillus_A sp017303315	76.713	62	1161	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_014635025.1	s__Fictibacillus barbaricus	76.5164	67	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	76.4088	52	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	76.3392	62	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363695.1	s__Sutcliffiella_A sp009363695	76.0518	56	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	75.6963	52	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116295.1	s__Bacillus_A sp900116295	75.6007	50	1161	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:14,788] [INFO] GTDB search result was written to GCF_021608225.1_ASM2160822v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:14,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:14,793] [INFO] DFAST_QC result json was written to GCF_021608225.1_ASM2160822v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:14,793] [INFO] DFAST_QC completed!
[2024-01-24 13:57:14,793] [INFO] Total running time: 0h1m17s