[2024-01-24 10:57:50,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,260] [INFO] DQC Reference Directory: /var/lib/cwl/stgf126fcad-3e39-4be9-a82c-d9a7867dbfe5/dqc_reference
[2024-01-24 10:57:52,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,644] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,645] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6994eb7-b70c-46c5-827b-be0fe65c441a/GCF_016908935.1_ASM1690893v1_genomic.fna.gz | prodigal -d GCF_016908935.1_ASM1690893v1_genomic.fna/cds.fna -a GCF_016908935.1_ASM1690893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:59,807] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:59,807] [INFO] Task started: HMMsearch
[2024-01-24 10:57:59,808] [INFO] Running command: hmmsearch --tblout GCF_016908935.1_ASM1690893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf126fcad-3e39-4be9-a82c-d9a7867dbfe5/dqc_reference/reference_markers.hmm GCF_016908935.1_ASM1690893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:00,065] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:00,067] [INFO] Found 6/6 markers.
[2024-01-24 10:58:00,100] [INFO] Query marker FASTA was written to GCF_016908935.1_ASM1690893v1_genomic.fna/markers.fasta
[2024-01-24 10:58:00,101] [INFO] Task started: Blastn
[2024-01-24 10:58:00,101] [INFO] Running command: blastn -query GCF_016908935.1_ASM1690893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf126fcad-3e39-4be9-a82c-d9a7867dbfe5/dqc_reference/reference_markers.fasta -out GCF_016908935.1_ASM1690893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:00,687] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:00,691] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:00,692] [INFO] Target genome list was writen to GCF_016908935.1_ASM1690893v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:00,741] [INFO] Task started: fastANI
[2024-01-24 10:58:00,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6994eb7-b70c-46c5-827b-be0fe65c441a/GCF_016908935.1_ASM1690893v1_genomic.fna.gz --refList GCF_016908935.1_ASM1690893v1_genomic.fna/target_genomes.txt --output GCF_016908935.1_ASM1690893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:13,852] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:13,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf126fcad-3e39-4be9-a82c-d9a7867dbfe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:13,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf126fcad-3e39-4be9-a82c-d9a7867dbfe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:13,862] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:13,862] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:13,862] [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
Sporolactobacillus spathodeae	strain=DSM 100968	GCA_016908935.1	1465502	1465502	type	True	100.0	939	944	95	conclusive
Sporolactobacillus laevolacticus	strain=DSM 442	GCA_000497245.1	33018	33018	type	True	78.1638	132	944	95	below_threshold
Sporolactobacillus vineae	strain=SL153	GCA_000246965.2	444463	444463	type	True	77.4523	116	944	95	below_threshold
Sporolactobacillus vineae	strain=DSM 21990	GCA_000377985.1	444463	444463	type	True	77.3828	116	944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:13,864] [INFO] DFAST Taxonomy check result was written to GCF_016908935.1_ASM1690893v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:13,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:13,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:13,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf126fcad-3e39-4be9-a82c-d9a7867dbfe5/dqc_reference/checkm_data
[2024-01-24 10:58:13,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:13,902] [INFO] Task started: CheckM
[2024-01-24 10:58:13,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908935.1_ASM1690893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908935.1_ASM1690893v1_genomic.fna/checkm_input GCF_016908935.1_ASM1690893v1_genomic.fna/checkm_result
[2024-01-24 10:58:41,545] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:41,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:41,567] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:41,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:41,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908935.1_ASM1690893v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:41,568] [INFO] Task started: Blastn
[2024-01-24 10:58:41,568] [INFO] Running command: blastn -query GCF_016908935.1_ASM1690893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf126fcad-3e39-4be9-a82c-d9a7867dbfe5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908935.1_ASM1690893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:42,345] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:42,350] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:42,350] [INFO] Target genome list was writen to GCF_016908935.1_ASM1690893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:42,378] [INFO] Task started: fastANI
[2024-01-24 10:58:42,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6994eb7-b70c-46c5-827b-be0fe65c441a/GCF_016908935.1_ASM1690893v1_genomic.fna.gz --refList GCF_016908935.1_ASM1690893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908935.1_ASM1690893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:54,321] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:54,332] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:54,332] [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_016908935.1	s__Sporolactobacillus spathodeae	100.0	939	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000497245.1	s__Sporolactobacillus laevolacticus	78.1031	134	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377985.1	s__Sporolactobacillus vineae	77.3828	116	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_004153225.1	s__Sporolactobacillus sp004153225	77.1666	70	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153195.1	s__Sporolactobacillus sp004153195	77.165	98	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543345.1	s__Sporolactobacillus sp900543345	75.6644	61	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:54,334] [INFO] GTDB search result was written to GCF_016908935.1_ASM1690893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:54,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:54,337] [INFO] DFAST_QC result json was written to GCF_016908935.1_ASM1690893v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:54,337] [INFO] DFAST_QC completed!
[2024-01-24 10:58:54,337] [INFO] Total running time: 0h1m4s