[2024-01-24 13:25:47,659] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg073ae3cb-be4f-47dc-8e35-eae659c7afbb/dqc_reference
[2024-01-24 13:25:48,974] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,975] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg79040833-ea5d-4c4a-b31f-06c42d5806c5/GCF_007992035.1_ASM799203v1_genomic.fna.gz | prodigal -d GCF_007992035.1_ASM799203v1_genomic.fna/cds.fna -a GCF_007992035.1_ASM799203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:52,888] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:52,889] [INFO] Task started: HMMsearch
[2024-01-24 13:25:52,889] [INFO] Running command: hmmsearch --tblout GCF_007992035.1_ASM799203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg073ae3cb-be4f-47dc-8e35-eae659c7afbb/dqc_reference/reference_markers.hmm GCF_007992035.1_ASM799203v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:53,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:53,136] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg79040833-ea5d-4c4a-b31f-06c42d5806c5/GCF_007992035.1_ASM799203v1_genomic.fna.gz]
[2024-01-24 13:25:53,175] [INFO] Query marker FASTA was written to GCF_007992035.1_ASM799203v1_genomic.fna/markers.fasta
[2024-01-24 13:25:53,176] [INFO] Task started: Blastn
[2024-01-24 13:25:53,176] [INFO] Running command: blastn -query GCF_007992035.1_ASM799203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg073ae3cb-be4f-47dc-8e35-eae659c7afbb/dqc_reference/reference_markers.fasta -out GCF_007992035.1_ASM799203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:53,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:53,831] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:53,831] [INFO] Target genome list was writen to GCF_007992035.1_ASM799203v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:53,839] [INFO] Task started: fastANI
[2024-01-24 13:25:53,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg79040833-ea5d-4c4a-b31f-06c42d5806c5/GCF_007992035.1_ASM799203v1_genomic.fna.gz --refList GCF_007992035.1_ASM799203v1_genomic.fna/target_genomes.txt --output GCF_007992035.1_ASM799203v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:00,808] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:00,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg073ae3cb-be4f-47dc-8e35-eae659c7afbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:00,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg073ae3cb-be4f-47dc-8e35-eae659c7afbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:00,824] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:00,824] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:00,824] [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
Companilactobacillus crustorum	strain=LMG 23699	GCA_001438825.1	392416	392416	type	True	99.9951	673	675	95	conclusive
Companilactobacillus crustorum	strain=JCM 15951	GCA_001434585.1	392416	392416	type	True	99.9934	671	675	95	conclusive
Companilactobacillus musae	strain=313	GCA_003573575.1	1903258	1903258	type	True	83.9614	480	675	95	below_threshold
Companilactobacillus musae	strain=NBRC 112868	GCA_003967595.1	1903258	1903258	type	True	83.8678	484	675	95	below_threshold
Companilactobacillus nuruki	strain=SYF10-1a	GCA_002872255.1	1993540	1993540	type	True	82.6532	428	675	95	below_threshold
Companilactobacillus zhachilii	strain=HBUAS52074	GCA_003606365.2	2304606	2304606	type	True	82.5004	443	675	95	below_threshold
Companilactobacillus heilongjiangensis	strain=S4-3	GCA_005405325.1	1074467	1074467	type	True	82.2561	433	675	95	below_threshold
Companilactobacillus heilongjiangensis	strain=DSM 28069	GCA_000831645.3	1074467	1074467	type	True	82.2109	446	675	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	81.8704	392	675	95	below_threshold
Companilactobacillus bobalius	strain=DSM 19674	GCA_001434855.1	2801451	2801451	type	True	81.8556	385	675	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	81.793	388	675	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.4543	227	675	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	79.0232	173	675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:00,826] [INFO] DFAST Taxonomy check result was written to GCF_007992035.1_ASM799203v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:00,827] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:00,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:00,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg073ae3cb-be4f-47dc-8e35-eae659c7afbb/dqc_reference/checkm_data
[2024-01-24 13:26:00,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:00,853] [INFO] Task started: CheckM
[2024-01-24 13:26:00,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992035.1_ASM799203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992035.1_ASM799203v1_genomic.fna/checkm_input GCF_007992035.1_ASM799203v1_genomic.fna/checkm_result
[2024-01-24 13:26:20,503] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:20,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:20,523] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:20,523] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:20,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992035.1_ASM799203v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:20,524] [INFO] Task started: Blastn
[2024-01-24 13:26:20,525] [INFO] Running command: blastn -query GCF_007992035.1_ASM799203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg073ae3cb-be4f-47dc-8e35-eae659c7afbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992035.1_ASM799203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:21,264] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:21,267] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:21,268] [INFO] Target genome list was writen to GCF_007992035.1_ASM799203v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:21,281] [INFO] Task started: fastANI
[2024-01-24 13:26:21,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg79040833-ea5d-4c4a-b31f-06c42d5806c5/GCF_007992035.1_ASM799203v1_genomic.fna.gz --refList GCF_007992035.1_ASM799203v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992035.1_ASM799203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:26,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:26,872] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:26,873] [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_001434585.1	s__Companilactobacillus crustorum	99.9934	671	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.76	99.52	0.96	0.87	5	conclusive
GCF_003967595.1	s__Companilactobacillus musae	83.8678	484	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002872255.1	s__Companilactobacillus nuruki	82.6532	428	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435815.1	s__Companilactobacillus nantensis	82.507	451	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003606365.2	s__Companilactobacillus zhachilii	82.5003	443	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.75	97.75	0.87	0.87	2	-
GCF_001438805.1	s__Companilactobacillus kimchiensis	82.3439	433	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	82.2109	446	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005404815.1	s__Companilactobacillus huachuanensis	82.1603	450	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405305.1	s__Companilactobacillus formosensis	82.1036	435	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009764355.1	s__Companilactobacillus paralimentarius_A	81.8184	392	675	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.92	99.92	1.00	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:26,874] [INFO] GTDB search result was written to GCF_007992035.1_ASM799203v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:26,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:26,880] [INFO] DFAST_QC result json was written to GCF_007992035.1_ASM799203v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:26,880] [INFO] DFAST_QC completed!
[2024-01-24 13:26:26,880] [INFO] Total running time: 0h0m39s