[2024-01-25 20:05:35,505] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:35,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:35,506] [INFO] DQC Reference Directory: /var/lib/cwl/stgab9e4f16-2d73-415b-9983-4e928a048a1d/dqc_reference
[2024-01-25 20:05:36,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:36,607] [INFO] Task started: Prodigal
[2024-01-25 20:05:36,607] [INFO] Running command: gunzip -c /var/lib/cwl/stge68e2420-1b41-48c8-807b-89800ae1ea86/GCF_016861845.1_ASM1686184v1_genomic.fna.gz | prodigal -d GCF_016861845.1_ASM1686184v1_genomic.fna/cds.fna -a GCF_016861845.1_ASM1686184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:43,576] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:43,576] [INFO] Task started: HMMsearch
[2024-01-25 20:05:43,576] [INFO] Running command: hmmsearch --tblout GCF_016861845.1_ASM1686184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab9e4f16-2d73-415b-9983-4e928a048a1d/dqc_reference/reference_markers.hmm GCF_016861845.1_ASM1686184v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:43,776] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:43,777] [INFO] Found 6/6 markers.
[2024-01-25 20:05:43,800] [INFO] Query marker FASTA was written to GCF_016861845.1_ASM1686184v1_genomic.fna/markers.fasta
[2024-01-25 20:05:43,800] [INFO] Task started: Blastn
[2024-01-25 20:05:43,800] [INFO] Running command: blastn -query GCF_016861845.1_ASM1686184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab9e4f16-2d73-415b-9983-4e928a048a1d/dqc_reference/reference_markers.fasta -out GCF_016861845.1_ASM1686184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:44,337] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:44,340] [INFO] Selected 25 target genomes.
[2024-01-25 20:05:44,340] [INFO] Target genome list was writen to GCF_016861845.1_ASM1686184v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:44,348] [INFO] Task started: fastANI
[2024-01-25 20:05:44,348] [INFO] Running command: fastANI --query /var/lib/cwl/stge68e2420-1b41-48c8-807b-89800ae1ea86/GCF_016861845.1_ASM1686184v1_genomic.fna.gz --refList GCF_016861845.1_ASM1686184v1_genomic.fna/target_genomes.txt --output GCF_016861845.1_ASM1686184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:56,802] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:56,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab9e4f16-2d73-415b-9983-4e928a048a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:56,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab9e4f16-2d73-415b-9983-4e928a048a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:56,810] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:56,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:56,810] [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
Lacticaseibacillus suilingensis	strain=ZW152	GCA_016861845.1	2799577	2799577	type	True	100.0	867	867	95	conclusive
Lacticaseibacillus suibinensis	strain=247-3	GCA_003946175.1	2486011	2486011	type	True	92.2803	718	867	95	below_threshold
Lacticaseibacillus camelliae	strain=DSM 22697	GCA_001436615.1	381742	381742	type	True	78.748	250	867	95	below_threshold
Lacticaseibacillus hegangensis	strain=73-4	GCA_003946465.1	2486010	2486010	type	True	78.725	258	867	95	below_threshold
Lacticaseibacillus camelliae	strain=JCM 13995	GCA_001311195.1	381742	381742	type	True	78.6732	245	867	95	below_threshold
Lacticaseibacillus jixianensis	strain=159-4	GCA_003946485.1	2486012	2486012	type	True	78.5701	250	867	95	below_threshold
Lacticaseibacillus daqingensis	strain=143-4(a)	GCA_003946115.1	2486014	2486014	type	True	78.4801	180	867	95	below_threshold
Lacticaseibacillus nasuensis	strain=JCM 17158	GCA_001434705.1	944671	944671	type	True	77.8714	158	867	95	below_threshold
Lacticaseibacillus nasuensis	strain=JCM 17158	GCA_001311255.1	944671	944671	type	True	77.8418	146	867	95	below_threshold
Lacticaseibacillus saniviri	strain=JCM 17471	GCA_001311785.1	931533	931533	type	True	77.4501	69	867	95	below_threshold
Lacticaseibacillus saniviri	strain=DSM 24301	GCA_001437465.1	931533	931533	type	True	77.3109	73	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:56,812] [INFO] DFAST Taxonomy check result was written to GCF_016861845.1_ASM1686184v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:56,812] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:56,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:56,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab9e4f16-2d73-415b-9983-4e928a048a1d/dqc_reference/checkm_data
[2024-01-25 20:05:56,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:56,841] [INFO] Task started: CheckM
[2024-01-25 20:05:56,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016861845.1_ASM1686184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016861845.1_ASM1686184v1_genomic.fna/checkm_input GCF_016861845.1_ASM1686184v1_genomic.fna/checkm_result
[2024-01-25 20:06:22,596] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:22,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:22,634] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:22,634] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:22,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016861845.1_ASM1686184v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:22,635] [INFO] Task started: Blastn
[2024-01-25 20:06:22,635] [INFO] Running command: blastn -query GCF_016861845.1_ASM1686184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab9e4f16-2d73-415b-9983-4e928a048a1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016861845.1_ASM1686184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:23,419] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:23,422] [INFO] Selected 18 target genomes.
[2024-01-25 20:06:23,422] [INFO] Target genome list was writen to GCF_016861845.1_ASM1686184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:23,469] [INFO] Task started: fastANI
[2024-01-25 20:06:23,469] [INFO] Running command: fastANI --query /var/lib/cwl/stge68e2420-1b41-48c8-807b-89800ae1ea86/GCF_016861845.1_ASM1686184v1_genomic.fna.gz --refList GCF_016861845.1_ASM1686184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016861845.1_ASM1686184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:32,504] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:32,511] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:32,511] [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_016861845.1	s__Lacticaseibacillus sp900540605	100.0	867	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.61	99.51	0.94	0.94	3	conclusive
GCF_003946175.1	s__Lacticaseibacillus suibinensis	92.2446	720	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.05	98.05	0.90	0.90	2	-
GCF_003946465.1	s__Lacticaseibacillus hegangensis	78.7163	258	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
GCF_001311195.1	s__Lacticaseibacillus camelliae	78.6674	245	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	1.00	1.00	2	-
GCF_003946165.1	s__Lacticaseibacillus baoqingensis	78.6588	127	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946485.1	s__Lacticaseibacillus jixianensis	78.5543	251	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946115.1	s__Lacticaseibacillus daqingensis	78.501	179	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407595.1	s__Lacticaseibacillus absianus	78.1393	126	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434705.1	s__Lacticaseibacillus nasuensis	77.8776	160	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.88	99.88	1.00	1.00	2	-
GCF_001311785.1	s__Lacticaseibacillus saniviri	77.4501	69	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.88	99.88	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:32,513] [INFO] GTDB search result was written to GCF_016861845.1_ASM1686184v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:32,513] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:32,516] [INFO] DFAST_QC result json was written to GCF_016861845.1_ASM1686184v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:32,516] [INFO] DFAST_QC completed!
[2024-01-25 20:06:32,516] [INFO] Total running time: 0h0m57s