[2024-01-24 14:06:06,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,322] [INFO] DQC Reference Directory: /var/lib/cwl/stge06894d4-c0b6-4373-905b-625a4a119f8f/dqc_reference
[2024-01-24 14:06:07,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,600] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c92e636-f5c7-4b06-ad11-1b03896367c0/GCF_020180945.1_ASM2018094v1_genomic.fna.gz | prodigal -d GCF_020180945.1_ASM2018094v1_genomic.fna/cds.fna -a GCF_020180945.1_ASM2018094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,374] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,375] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,375] [INFO] Running command: hmmsearch --tblout GCF_020180945.1_ASM2018094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge06894d4-c0b6-4373-905b-625a4a119f8f/dqc_reference/reference_markers.hmm GCF_020180945.1_ASM2018094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:16,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:16,625] [INFO] Found 6/6 markers.
[2024-01-24 14:06:16,651] [INFO] Query marker FASTA was written to GCF_020180945.1_ASM2018094v1_genomic.fna/markers.fasta
[2024-01-24 14:06:16,651] [INFO] Task started: Blastn
[2024-01-24 14:06:16,651] [INFO] Running command: blastn -query GCF_020180945.1_ASM2018094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge06894d4-c0b6-4373-905b-625a4a119f8f/dqc_reference/reference_markers.fasta -out GCF_020180945.1_ASM2018094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,346] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,349] [INFO] Selected 21 target genomes.
[2024-01-24 14:06:17,349] [INFO] Target genome list was writen to GCF_020180945.1_ASM2018094v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,384] [INFO] Task started: fastANI
[2024-01-24 14:06:17,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c92e636-f5c7-4b06-ad11-1b03896367c0/GCF_020180945.1_ASM2018094v1_genomic.fna.gz --refList GCF_020180945.1_ASM2018094v1_genomic.fna/target_genomes.txt --output GCF_020180945.1_ASM2018094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:31,087] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:31,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge06894d4-c0b6-4373-905b-625a4a119f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:31,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge06894d4-c0b6-4373-905b-625a4a119f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:31,103] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:31,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:31,103] [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 daqingensis	strain=143-4(a)	GCA_003946115.1	2486014	2486014	type	True	80.9163	417	925	95	below_threshold
Lacticaseibacillus absianus	strain=YH-lac23	GCA_013407595.1	2729623	2729623	type	True	80.3177	405	925	95	below_threshold
Lacticaseibacillus jixianensis	strain=159-4	GCA_003946485.1	2486012	2486012	type	True	79.0449	320	925	95	below_threshold
Lacticaseibacillus manihotivorans	strain=JCM 12514	GCA_001311155.1	88233	88233	type	True	78.8089	86	925	95	below_threshold
Lacticaseibacillus camelliae	strain=JCM 13995	GCA_001311195.1	381742	381742	type	True	78.6619	256	925	95	below_threshold
Lacticaseibacillus camelliae	strain=DSM 22697	GCA_001436615.1	381742	381742	type	True	78.6491	273	925	95	below_threshold
Lacticaseibacillus suilingensis	strain=ZW152	GCA_016861845.1	2799577	2799577	type	True	78.637	171	925	95	below_threshold
Lacticaseibacillus suibinensis	strain=247-3	GCA_003946175.1	2486011	2486011	type	True	78.553	171	925	95	below_threshold
Lacticaseibacillus hegangensis	strain=73-4	GCA_003946465.1	2486010	2486010	type	True	78.5461	277	925	95	below_threshold
Lacticaseibacillus yichunensis	strain=33-1	GCA_003946405.1	2486015	2486015	type	True	78.2113	212	925	95	below_threshold
Lacticaseibacillus nasuensis	strain=JCM 17158	GCA_001434705.1	944671	944671	type	True	77.797	234	925	95	below_threshold
Lacticaseibacillus nasuensis	strain=JCM 17158	GCA_001311255.1	944671	944671	type	True	77.7237	214	925	95	below_threshold
Lacticaseibacillus hulanensis	strain=ZW163	GCA_004010095.1	2493111	2493111	type	True	77.6248	82	925	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.2618	68	925	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	75.0955	68	925	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	74.9808	51	925	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.9296	79	925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:31,105] [INFO] DFAST Taxonomy check result was written to GCF_020180945.1_ASM2018094v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:31,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:31,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:31,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge06894d4-c0b6-4373-905b-625a4a119f8f/dqc_reference/checkm_data
[2024-01-24 14:06:31,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:31,136] [INFO] Task started: CheckM
[2024-01-24 14:06:31,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020180945.1_ASM2018094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020180945.1_ASM2018094v1_genomic.fna/checkm_input GCF_020180945.1_ASM2018094v1_genomic.fna/checkm_result
[2024-01-24 14:07:01,839] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:01,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,858] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:01,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:01,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020180945.1_ASM2018094v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:01,859] [INFO] Task started: Blastn
[2024-01-24 14:07:01,859] [INFO] Running command: blastn -query GCF_020180945.1_ASM2018094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge06894d4-c0b6-4373-905b-625a4a119f8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_020180945.1_ASM2018094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:02,823] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:02,826] [INFO] Selected 14 target genomes.
[2024-01-24 14:07:02,826] [INFO] Target genome list was writen to GCF_020180945.1_ASM2018094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:02,841] [INFO] Task started: fastANI
[2024-01-24 14:07:02,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c92e636-f5c7-4b06-ad11-1b03896367c0/GCF_020180945.1_ASM2018094v1_genomic.fna.gz --refList GCF_020180945.1_ASM2018094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020180945.1_ASM2018094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:09,691] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:09,708] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:09,708] [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_003946115.1	s__Lacticaseibacillus daqingensis	80.8795	419	925	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	80.3171	405	925	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	79.0108	323	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311195.1	s__Lacticaseibacillus camelliae	78.6451	257	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	1.00	1.00	2	-
GCF_016861845.1	s__Lacticaseibacillus sp900540605	78.637	171	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.61	99.51	0.94	0.94	3	-
GCF_003946175.1	s__Lacticaseibacillus suibinensis	78.5616	172	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.05	98.05	0.90	0.90	2	-
GCF_001435035.1	s__Lacticaseibacillus manihotivorans	78.5527	88	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.87	99.83	0.97	0.96	3	-
GCF_003946465.1	s__Lacticaseibacillus hegangensis	78.5404	278	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
GCF_003946405.1	s__Lacticaseibacillus yichunensis	78.2291	211	925	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	77.7921	236	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.88	99.88	1.00	1.00	2	-
GCF_004010095.1	s__Lacticaseibacillus hulanensis	77.6179	83	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214545.1	s__Lactobacillus sp905214545	75.9453	52	925	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:09,709] [INFO] GTDB search result was written to GCF_020180945.1_ASM2018094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:09,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:09,713] [INFO] DFAST_QC result json was written to GCF_020180945.1_ASM2018094v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:09,714] [INFO] DFAST_QC completed!
[2024-01-24 14:07:09,714] [INFO] Total running time: 0h1m3s