[2024-01-24 13:31:32,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:32,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:32,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0bf64e9-b7e6-4cdd-bd83-4f0dd0694462/dqc_reference
[2024-01-24 13:31:33,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:33,874] [INFO] Task started: Prodigal
[2024-01-24 13:31:33,874] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0fafade-0694-49be-b3f9-ccca6f6855a5/GCF_007293315.1_ASM729331v1_genomic.fna.gz | prodigal -d GCF_007293315.1_ASM729331v1_genomic.fna/cds.fna -a GCF_007293315.1_ASM729331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:43,706] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:43,707] [INFO] Task started: HMMsearch
[2024-01-24 13:31:43,707] [INFO] Running command: hmmsearch --tblout GCF_007293315.1_ASM729331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0bf64e9-b7e6-4cdd-bd83-4f0dd0694462/dqc_reference/reference_markers.hmm GCF_007293315.1_ASM729331v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:44,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:44,008] [INFO] Found 6/6 markers.
[2024-01-24 13:31:44,050] [INFO] Query marker FASTA was written to GCF_007293315.1_ASM729331v1_genomic.fna/markers.fasta
[2024-01-24 13:31:44,050] [INFO] Task started: Blastn
[2024-01-24 13:31:44,050] [INFO] Running command: blastn -query GCF_007293315.1_ASM729331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0bf64e9-b7e6-4cdd-bd83-4f0dd0694462/dqc_reference/reference_markers.fasta -out GCF_007293315.1_ASM729331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:44,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:44,660] [INFO] Selected 31 target genomes.
[2024-01-24 13:31:44,660] [INFO] Target genome list was writen to GCF_007293315.1_ASM729331v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:44,677] [INFO] Task started: fastANI
[2024-01-24 13:31:44,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0fafade-0694-49be-b3f9-ccca6f6855a5/GCF_007293315.1_ASM729331v1_genomic.fna.gz --refList GCF_007293315.1_ASM729331v1_genomic.fna/target_genomes.txt --output GCF_007293315.1_ASM729331v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:02,200] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:02,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0bf64e9-b7e6-4cdd-bd83-4f0dd0694462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:02,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0bf64e9-b7e6-4cdd-bd83-4f0dd0694462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:02,209] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:02,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:02,209] [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
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	77.4304	73	1404	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.3642	71	1404	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.1588	79	1404	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	77.1455	79	1404	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	77.1455	79	1404	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	76.8352	79	1404	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.7553	84	1404	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.559	72	1404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:02,211] [INFO] DFAST Taxonomy check result was written to GCF_007293315.1_ASM729331v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:02,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:02,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:02,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0bf64e9-b7e6-4cdd-bd83-4f0dd0694462/dqc_reference/checkm_data
[2024-01-24 13:32:02,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:02,260] [INFO] Task started: CheckM
[2024-01-24 13:32:02,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007293315.1_ASM729331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007293315.1_ASM729331v1_genomic.fna/checkm_input GCF_007293315.1_ASM729331v1_genomic.fna/checkm_result
[2024-01-24 13:32:36,303] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:36,305] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:36,338] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:36,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:36,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007293315.1_ASM729331v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:36,339] [INFO] Task started: Blastn
[2024-01-24 13:32:36,339] [INFO] Running command: blastn -query GCF_007293315.1_ASM729331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0bf64e9-b7e6-4cdd-bd83-4f0dd0694462/dqc_reference/reference_markers_gtdb.fasta -out GCF_007293315.1_ASM729331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:37,062] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:37,067] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:37,067] [INFO] Target genome list was writen to GCF_007293315.1_ASM729331v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:37,095] [INFO] Task started: fastANI
[2024-01-24 13:32:37,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0fafade-0694-49be-b3f9-ccca6f6855a5/GCF_007293315.1_ASM729331v1_genomic.fna.gz --refList GCF_007293315.1_ASM729331v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007293315.1_ASM729331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:56,248] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:56,257] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:56,258] [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_007293315.1	s__Alkalihalobacillus_A sp007293315	100.0	1404	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016798245.1	s__Alkalihalobacillus_A gibsonii_A	78.8625	383	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002109385.1	s__Bacillus_L krulwichiae	77.4986	72	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002156385.1	s__45385 sp002156385	77.2835	72	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797325.1	s__Bacillus_S sp002797325	77.2476	71	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797395.1	s__45385 sp002797395	77.244	83	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	77.1294	79	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	76.8576	79	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_000474275.2	s__Bacillus_S marmarensis	76.7804	83	1404	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:56,260] [INFO] GTDB search result was written to GCF_007293315.1_ASM729331v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:56,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:56,264] [INFO] DFAST_QC result json was written to GCF_007293315.1_ASM729331v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:56,265] [INFO] DFAST_QC completed!
[2024-01-24 13:32:56,265] [INFO] Total running time: 0h1m24s