[2024-01-24 12:37:37,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,927] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc957ab3-f0c7-4b0e-84ea-836447d7ad7c/dqc_reference
[2024-01-24 12:37:41,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,018] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg1685f871-20a1-4e0f-b9f2-e6711f114140/GCF_005405165.1_ASM540516v1_genomic.fna.gz | prodigal -d GCF_005405165.1_ASM540516v1_genomic.fna/cds.fna -a GCF_005405165.1_ASM540516v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:47,060] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:47,061] [INFO] Task started: HMMsearch
[2024-01-24 12:37:47,061] [INFO] Running command: hmmsearch --tblout GCF_005405165.1_ASM540516v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc957ab3-f0c7-4b0e-84ea-836447d7ad7c/dqc_reference/reference_markers.hmm GCF_005405165.1_ASM540516v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:47,312] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:47,313] [INFO] Found 6/6 markers.
[2024-01-24 12:37:47,338] [INFO] Query marker FASTA was written to GCF_005405165.1_ASM540516v1_genomic.fna/markers.fasta
[2024-01-24 12:37:47,338] [INFO] Task started: Blastn
[2024-01-24 12:37:47,338] [INFO] Running command: blastn -query GCF_005405165.1_ASM540516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc957ab3-f0c7-4b0e-84ea-836447d7ad7c/dqc_reference/reference_markers.fasta -out GCF_005405165.1_ASM540516v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:48,508] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:48,511] [INFO] Selected 11 target genomes.
[2024-01-24 12:37:48,511] [INFO] Target genome list was writen to GCF_005405165.1_ASM540516v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:48,549] [INFO] Task started: fastANI
[2024-01-24 12:37:48,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg1685f871-20a1-4e0f-b9f2-e6711f114140/GCF_005405165.1_ASM540516v1_genomic.fna.gz --refList GCF_005405165.1_ASM540516v1_genomic.fna/target_genomes.txt --output GCF_005405165.1_ASM540516v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:53,791] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:53,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc957ab3-f0c7-4b0e-84ea-836447d7ad7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:53,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc957ab3-f0c7-4b0e-84ea-836447d7ad7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:53,803] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:53,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:53,804] [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
Loigolactobacillus binensis	strain=735-2	GCA_005405165.1	2559922	2559922	type	True	100.0	905	910	95	conclusive
Loigolactobacillus coryniformis subsp. torquens	strain=DSM 20004	GCA_002706705.1	115542	1610	type	True	81.6259	475	910	95	below_threshold
Loigolactobacillus coryniformis subsp. coryniformis	strain=KCTC 3167	GCA_000166795.1	115541	1610	type	True	81.5307	479	910	95	below_threshold
Loigolactobacillus coryniformis subsp. torquens	strain=KCTC 3535	GCA_000184285.2	115542	1610	type	True	81.4778	412	910	95	below_threshold
Loigolactobacillus coryniformis subsp. coryniformis	strain=DSM 20001	GCA_002706425.1	115541	1610	type	True	81.4602	473	910	95	below_threshold
Loigolactobacillus coryniformis subsp. coryniformis	strain=DSM 20001	GCA_001433765.1	115541	1610	type	True	81.4143	439	910	95	below_threshold
Loigolactobacillus coryniformis subsp. torquens	strain=DSM 20004	GCA_001435425.1	115542	1610	type	True	81.3588	405	910	95	below_threshold
Loigolactobacillus jiayinensis	strain=257-1	GCA_003946445.1	2486016	2486016	type	True	80.4076	414	910	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:53,806] [INFO] DFAST Taxonomy check result was written to GCF_005405165.1_ASM540516v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:53,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:53,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:53,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc957ab3-f0c7-4b0e-84ea-836447d7ad7c/dqc_reference/checkm_data
[2024-01-24 12:37:53,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:53,838] [INFO] Task started: CheckM
[2024-01-24 12:37:53,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405165.1_ASM540516v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405165.1_ASM540516v1_genomic.fna/checkm_input GCF_005405165.1_ASM540516v1_genomic.fna/checkm_result
[2024-01-24 12:38:18,872] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:18,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:18,906] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:18,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:18,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405165.1_ASM540516v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:18,907] [INFO] Task started: Blastn
[2024-01-24 12:38:18,907] [INFO] Running command: blastn -query GCF_005405165.1_ASM540516v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc957ab3-f0c7-4b0e-84ea-836447d7ad7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405165.1_ASM540516v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:19,768] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:19,772] [INFO] Selected 14 target genomes.
[2024-01-24 12:38:19,772] [INFO] Target genome list was writen to GCF_005405165.1_ASM540516v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:19,783] [INFO] Task started: fastANI
[2024-01-24 12:38:19,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg1685f871-20a1-4e0f-b9f2-e6711f114140/GCF_005405165.1_ASM540516v1_genomic.fna.gz --refList GCF_005405165.1_ASM540516v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405165.1_ASM540516v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:26,696] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:26,702] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:26,703] [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_005405165.1	s__Loigolactobacillus binensis	100.0	905	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002706425.1	s__Loigolactobacillus coryniformis	81.487	471	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	98.39	97.42	0.89	0.81	10	-
GCF_003946385.1	s__Loigolactobacillus zhaoyuanensis	80.7913	417	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946445.1	s__Loigolactobacillus jiayinensis	80.3932	415	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946275.1	s__Loigolactobacillus backii	78.2543	139	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	99.33	98.15	0.95	0.91	9	-
GCF_001436505.1	s__Loigolactobacillus rennini	77.8325	163	910	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:26,704] [INFO] GTDB search result was written to GCF_005405165.1_ASM540516v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:26,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:26,708] [INFO] DFAST_QC result json was written to GCF_005405165.1_ASM540516v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:26,708] [INFO] DFAST_QC completed!
[2024-01-24 12:38:26,708] [INFO] Total running time: 0h0m49s