[2024-01-24 13:33:10,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:10,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:10,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgd10092ef-d106-43c4-9771-7ca87636121f/dqc_reference
[2024-01-24 13:33:11,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:11,916] [INFO] Task started: Prodigal
[2024-01-24 13:33:11,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg772d9a24-42e0-4da9-a419-3a21859fcd31/GCF_007992015.1_ASM799201v1_genomic.fna.gz | prodigal -d GCF_007992015.1_ASM799201v1_genomic.fna/cds.fna -a GCF_007992015.1_ASM799201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:18,330] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:18,330] [INFO] Task started: HMMsearch
[2024-01-24 13:33:18,330] [INFO] Running command: hmmsearch --tblout GCF_007992015.1_ASM799201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd10092ef-d106-43c4-9771-7ca87636121f/dqc_reference/reference_markers.hmm GCF_007992015.1_ASM799201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:18,570] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:18,574] [INFO] Found 6/6 markers.
[2024-01-24 13:33:18,605] [INFO] Query marker FASTA was written to GCF_007992015.1_ASM799201v1_genomic.fna/markers.fasta
[2024-01-24 13:33:18,605] [INFO] Task started: Blastn
[2024-01-24 13:33:18,605] [INFO] Running command: blastn -query GCF_007992015.1_ASM799201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd10092ef-d106-43c4-9771-7ca87636121f/dqc_reference/reference_markers.fasta -out GCF_007992015.1_ASM799201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:19,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:19,261] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:19,262] [INFO] Target genome list was writen to GCF_007992015.1_ASM799201v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:19,274] [INFO] Task started: fastANI
[2024-01-24 13:33:19,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg772d9a24-42e0-4da9-a419-3a21859fcd31/GCF_007992015.1_ASM799201v1_genomic.fna.gz --refList GCF_007992015.1_ASM799201v1_genomic.fna/target_genomes.txt --output GCF_007992015.1_ASM799201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:27,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:27,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd10092ef-d106-43c4-9771-7ca87636121f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:27,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd10092ef-d106-43c4-9771-7ca87636121f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:27,121] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:27,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:27,121] [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
Levilactobacillus namurensis	strain=DSM 19117	GCA_001434785.1	380393	380393	type	True	99.9961	762	764	95	conclusive
Levilactobacillus spicheri	strain=DSM 15429	GCA_001435095.1	216463	216463	type	True	81.7274	500	764	95	below_threshold
Levilactobacillus zymae	strain=DSM 19395	GCA_001434115.1	267363	267363	type	True	80.5603	380	764	95	below_threshold
Levilactobacillus acidifarinae	strain=DSM 19394	GCA_001434835.1	267364	267364	type	True	80.3179	367	764	95	below_threshold
Levilactobacillus suantsaii	strain=BCRC 12945	GCA_004115745.1	2292255	2292255	type	True	79.6858	310	764	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	79.6546	294	764	95	below_threshold
Levilactobacillus hammesii	strain=DSM 16381	GCA_001434395.1	267633	267633	type	True	79.6082	252	764	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	79.5051	269	764	95	below_threshold
Levilactobacillus fuyuanensis	strain=244-4	GCA_003946395.1	2486022	2486022	type	True	79.4919	259	764	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	79.4834	309	764	95	below_threshold
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	79.069	223	764	95	below_threshold
Levilactobacillus tangyuanensis	strain=137-3	GCA_003946545.1	2486021	2486021	type	True	79.036	226	764	95	below_threshold
Levilactobacillus parabrevis	strain=ATCC 53295	GCA_001434055.1	357278	357278	type	True	78.9818	268	764	95	below_threshold
Secundilactobacillus oryzae	strain=JCM 18671	GCA_001311525.1	1202668	1202668	type	True	78.2258	56	764	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:27,123] [INFO] DFAST Taxonomy check result was written to GCF_007992015.1_ASM799201v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:27,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:27,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:27,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd10092ef-d106-43c4-9771-7ca87636121f/dqc_reference/checkm_data
[2024-01-24 13:33:27,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:27,160] [INFO] Task started: CheckM
[2024-01-24 13:33:27,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992015.1_ASM799201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992015.1_ASM799201v1_genomic.fna/checkm_input GCF_007992015.1_ASM799201v1_genomic.fna/checkm_result
[2024-01-24 13:33:52,128] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:52,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:52,148] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:52,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:52,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992015.1_ASM799201v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:52,150] [INFO] Task started: Blastn
[2024-01-24 13:33:52,150] [INFO] Running command: blastn -query GCF_007992015.1_ASM799201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd10092ef-d106-43c4-9771-7ca87636121f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992015.1_ASM799201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:52,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:52,976] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:52,976] [INFO] Target genome list was writen to GCF_007992015.1_ASM799201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:52,990] [INFO] Task started: fastANI
[2024-01-24 13:33:52,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg772d9a24-42e0-4da9-a419-3a21859fcd31/GCF_007992015.1_ASM799201v1_genomic.fna.gz --refList GCF_007992015.1_ASM799201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992015.1_ASM799201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:59,582] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:59,599] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:59,599] [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_001434785.1	s__Levilactobacillus namurensis	99.9961	762	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	96.48	95.39	0.91	0.87	6	conclusive
GCF_001435095.1	s__Levilactobacillus spicheri	81.7418	499	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	98.77	97.54	0.95	0.91	3	-
GCA_019113985.1	s__Levilactobacillus faecigallinarum	81.3733	298	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434115.1	s__Levilactobacillus zymae	80.5603	380	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.08	97.26	0.95	0.86	4	-
GCF_001434835.1	s__Levilactobacillus acidifarinae	80.3098	368	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003666485.1	s__Levilactobacillus brevis_A	79.7115	308	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946085.1	s__Levilactobacillus angrenensis	79.6546	294	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434395.1	s__Levilactobacillus hammesii	79.6082	252	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435525.1	s__Levilactobacillus koreensis	79.5051	269	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003946395.1	s__Levilactobacillus fuyuanensis	79.4883	260	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	79.4673	310	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641185.1	s__Levilactobacillus sp012641185	79.0481	224	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.99	95.94	0.88	0.87	3	-
GCF_003946545.1	s__Levilactobacillus tangyuanensis	79.036	226	764	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:59,601] [INFO] GTDB search result was written to GCF_007992015.1_ASM799201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:59,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:59,606] [INFO] DFAST_QC result json was written to GCF_007992015.1_ASM799201v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:59,606] [INFO] DFAST_QC completed!
[2024-01-24 13:33:59,606] [INFO] Total running time: 0h0m49s