[2024-01-24 11:52:49,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:49,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:49,635] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8b19c67-7b6c-49be-aa68-758261094a9d/dqc_reference
[2024-01-24 11:52:50,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:50,858] [INFO] Task started: Prodigal
[2024-01-24 11:52:50,859] [INFO] Running command: gunzip -c /var/lib/cwl/stgc08d9e7c-cc5d-40ed-a34f-8d989c47e51c/GCF_003967595.1_ASM396759v1_genomic.fna.gz | prodigal -d GCF_003967595.1_ASM396759v1_genomic.fna/cds.fna -a GCF_003967595.1_ASM396759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:55,523] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:55,524] [INFO] Task started: HMMsearch
[2024-01-24 11:52:55,524] [INFO] Running command: hmmsearch --tblout GCF_003967595.1_ASM396759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8b19c67-7b6c-49be-aa68-758261094a9d/dqc_reference/reference_markers.hmm GCF_003967595.1_ASM396759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:55,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:55,745] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc08d9e7c-cc5d-40ed-a34f-8d989c47e51c/GCF_003967595.1_ASM396759v1_genomic.fna.gz]
[2024-01-24 11:52:55,766] [INFO] Query marker FASTA was written to GCF_003967595.1_ASM396759v1_genomic.fna/markers.fasta
[2024-01-24 11:52:55,767] [INFO] Task started: Blastn
[2024-01-24 11:52:55,767] [INFO] Running command: blastn -query GCF_003967595.1_ASM396759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8b19c67-7b6c-49be-aa68-758261094a9d/dqc_reference/reference_markers.fasta -out GCF_003967595.1_ASM396759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:56,361] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:56,365] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:56,365] [INFO] Target genome list was writen to GCF_003967595.1_ASM396759v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:56,373] [INFO] Task started: fastANI
[2024-01-24 11:52:56,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08d9e7c-cc5d-40ed-a34f-8d989c47e51c/GCF_003967595.1_ASM396759v1_genomic.fna.gz --refList GCF_003967595.1_ASM396759v1_genomic.fna/target_genomes.txt --output GCF_003967595.1_ASM396759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:05,425] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:05,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8b19c67-7b6c-49be-aa68-758261094a9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:05,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8b19c67-7b6c-49be-aa68-758261094a9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:05,439] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:53:05,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:05,440] [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 musae	strain=NBRC 112868	GCA_003967595.1	1903258	1903258	type	True	100.0	776	777	95	conclusive
Companilactobacillus musae	strain=313	GCA_003573575.1	1903258	1903258	type	True	99.9961	775	777	95	conclusive
Companilactobacillus crustorum	strain=JCM 15951	GCA_001434585.1	392416	392416	type	True	83.8849	483	777	95	below_threshold
Companilactobacillus crustorum	strain=LMG 23699	GCA_001438825.1	392416	392416	type	True	83.7801	487	777	95	below_threshold
Companilactobacillus nantensis	strain=DSM 16982	GCA_001435815.1	305793	305793	type	True	83.2433	508	777	95	below_threshold
Companilactobacillus zhachilii	strain=HBUAS52074	GCA_003606365.2	2304606	2304606	type	True	83.2071	483	777	95	below_threshold
Companilactobacillus formosensis	strain=NBRC 109509	GCA_005405305.1	1617889	1617889	type	True	83.0005	479	777	95	below_threshold
Companilactobacillus formosensis	strain=S215	GCA_003573535.1	1617889	1617889	type	True	82.9561	473	777	95	below_threshold
Companilactobacillus futsaii	strain=JCM 17355	GCA_001435505.1	938155	938155	type	True	82.8781	456	777	95	below_threshold
Companilactobacillus heilongjiangensis	strain=S4-3	GCA_005405325.1	1074467	1074467	type	True	82.8658	485	777	95	below_threshold
Companilactobacillus heilongjiangensis	strain=DSM 28069	GCA_000831645.3	1074467	1074467	type	True	82.7585	499	777	95	below_threshold
Companilactobacillus nuruki	strain=SYF10-1a	GCA_002872255.1	1993540	1993540	type	True	82.6206	466	777	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	82.5342	443	777	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	82.3496	438	777	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.3093	257	777	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	78.9235	197	777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:05,442] [INFO] DFAST Taxonomy check result was written to GCF_003967595.1_ASM396759v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:05,442] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:05,442] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:05,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8b19c67-7b6c-49be-aa68-758261094a9d/dqc_reference/checkm_data
[2024-01-24 11:53:05,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:05,471] [INFO] Task started: CheckM
[2024-01-24 11:53:05,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967595.1_ASM396759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967595.1_ASM396759v1_genomic.fna/checkm_input GCF_003967595.1_ASM396759v1_genomic.fna/checkm_result
[2024-01-24 11:53:26,550] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:26,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:26,572] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:26,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:26,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967595.1_ASM396759v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:26,574] [INFO] Task started: Blastn
[2024-01-24 11:53:26,574] [INFO] Running command: blastn -query GCF_003967595.1_ASM396759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8b19c67-7b6c-49be-aa68-758261094a9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967595.1_ASM396759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:27,405] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:27,410] [INFO] Selected 12 target genomes.
[2024-01-24 11:53:27,410] [INFO] Target genome list was writen to GCF_003967595.1_ASM396759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:27,433] [INFO] Task started: fastANI
[2024-01-24 11:53:27,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08d9e7c-cc5d-40ed-a34f-8d989c47e51c/GCF_003967595.1_ASM396759v1_genomic.fna.gz --refList GCF_003967595.1_ASM396759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967595.1_ASM396759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:34,594] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:34,615] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:34,615] [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_003967595.1	s__Companilactobacillus musae	100.0	776	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001434585.1	s__Companilactobacillus crustorum	83.8659	484	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.76	99.52	0.96	0.87	5	-
GCF_001435815.1	s__Companilactobacillus nantensis	83.2433	508	777	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	83.2071	483	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.75	97.75	0.87	0.87	2	-
GCF_014058425.1	s__Companilactobacillus pabuli	83.197	485	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.23	98.09	0.94	0.87	5	-
GCF_001438805.1	s__Companilactobacillus kimchiensis	83.1372	496	777	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	83.0182	478	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001435505.1	s__Companilactobacillus futsaii	82.9148	454	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.20	98.55	0.91	0.87	7	-
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	82.759	499	777	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	82.7535	461	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872255.1	s__Companilactobacillus nuruki	82.6035	467	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116025.1	s__Companilactobacillus pullicola	81.5437	425	777	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:34,617] [INFO] GTDB search result was written to GCF_003967595.1_ASM396759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:34,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:34,622] [INFO] DFAST_QC result json was written to GCF_003967595.1_ASM396759v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:34,622] [INFO] DFAST_QC completed!
[2024-01-24 11:53:34,622] [INFO] Total running time: 0h0m45s