[2024-01-24 12:31:56,188] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:56,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:56,190] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcb81eb9-3443-478c-9e49-18bd526b890f/dqc_reference
[2024-01-24 12:31:57,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:57,445] [INFO] Task started: Prodigal
[2024-01-24 12:31:57,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg49812585-2c43-434c-9085-3496177f8248/GCF_019586025.1_ASM1958602v1_genomic.fna.gz | prodigal -d GCF_019586025.1_ASM1958602v1_genomic.fna/cds.fna -a GCF_019586025.1_ASM1958602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:02,489] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:02,489] [INFO] Task started: HMMsearch
[2024-01-24 12:32:02,489] [INFO] Running command: hmmsearch --tblout GCF_019586025.1_ASM1958602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcb81eb9-3443-478c-9e49-18bd526b890f/dqc_reference/reference_markers.hmm GCF_019586025.1_ASM1958602v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:02,775] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:02,776] [INFO] Found 6/6 markers.
[2024-01-24 12:32:02,798] [INFO] Query marker FASTA was written to GCF_019586025.1_ASM1958602v1_genomic.fna/markers.fasta
[2024-01-24 12:32:02,799] [INFO] Task started: Blastn
[2024-01-24 12:32:02,799] [INFO] Running command: blastn -query GCF_019586025.1_ASM1958602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb81eb9-3443-478c-9e49-18bd526b890f/dqc_reference/reference_markers.fasta -out GCF_019586025.1_ASM1958602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:03,418] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:03,422] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:03,422] [INFO] Target genome list was writen to GCF_019586025.1_ASM1958602v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:03,429] [INFO] Task started: fastANI
[2024-01-24 12:32:03,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg49812585-2c43-434c-9085-3496177f8248/GCF_019586025.1_ASM1958602v1_genomic.fna.gz --refList GCF_019586025.1_ASM1958602v1_genomic.fna/target_genomes.txt --output GCF_019586025.1_ASM1958602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:08,650] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:08,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcb81eb9-3443-478c-9e49-18bd526b890f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:08,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcb81eb9-3443-478c-9e49-18bd526b890f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:08,657] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:08,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:08,658] [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
Lactococcus laudensis	strain=LMG 28353	GCA_019586025.1	1494461	1494461	type	True	100.0	712	715	95	conclusive
Lactococcus laudensis	strain=DSM 28961	GCA_013449735.1	1494461	1494461	type	True	99.9896	703	715	95	conclusive
Lactococcus chungangensis	strain=DSM 22330	GCA_002441885.1	451457	451457	type	True	91.911	536	715	95	below_threshold
Lactococcus chungangensis	strain=DSM 22330	GCA_900119835.1	451457	451457	type	True	91.838	541	715	95	below_threshold
Lactococcus raffinolactis	strain=ATCC 43920	GCA_002441745.1	1366	1366	type	True	87.9004	523	715	95	below_threshold
Lactococcus raffinolactis	strain=NBRC 100932	GCA_001591765.1	1366	1366	type	True	87.7513	523	715	95	below_threshold
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	79.2935	258	715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:08,663] [INFO] DFAST Taxonomy check result was written to GCF_019586025.1_ASM1958602v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:08,664] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:08,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:08,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcb81eb9-3443-478c-9e49-18bd526b890f/dqc_reference/checkm_data
[2024-01-24 12:32:08,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:08,706] [INFO] Task started: CheckM
[2024-01-24 12:32:08,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019586025.1_ASM1958602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019586025.1_ASM1958602v1_genomic.fna/checkm_input GCF_019586025.1_ASM1958602v1_genomic.fna/checkm_result
[2024-01-24 12:32:31,319] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:31,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:31,342] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:31,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:31,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019586025.1_ASM1958602v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:31,343] [INFO] Task started: Blastn
[2024-01-24 12:32:31,344] [INFO] Running command: blastn -query GCF_019586025.1_ASM1958602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb81eb9-3443-478c-9e49-18bd526b890f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019586025.1_ASM1958602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:32,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:32,195] [INFO] Selected 10 target genomes.
[2024-01-24 12:32:32,195] [INFO] Target genome list was writen to GCF_019586025.1_ASM1958602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:32,202] [INFO] Task started: fastANI
[2024-01-24 12:32:32,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg49812585-2c43-434c-9085-3496177f8248/GCF_019586025.1_ASM1958602v1_genomic.fna.gz --refList GCF_019586025.1_ASM1958602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019586025.1_ASM1958602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:37,176] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:37,185] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:37,185] [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_013449735.1	s__Lactococcus_A laudensis	99.9896	703	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	97.98	97.98	0.86	0.86	2	conclusive
GCF_002441885.1	s__Lactococcus_A chungangensis	91.9279	535	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.24	98.46	0.92	0.88	4	-
GCF_001591765.1	s__Lactococcus_A raffinolactis	87.7399	523	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.11	98.57	0.92	0.88	14	-
GCF_002260845.1	s__Lactococcus_A reticulitermitis	85.0342	478	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002441695.1	s__Lactococcus_A piscium	79.562	264	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006770285.1	s__Lactococcus_A paracarnosus	79.3126	257	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.90	99.90	0.97	0.97	2	-
GCF_006770265.1	s__Lactococcus_A carnosus	79.2319	249	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	97.28	95.96	0.91	0.89	5	-
GCF_011170065.1	s__Lactococcus_A insecticola	79.1521	205	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011170085.1	s__Lactococcus_A hodotermopsidis	78.5069	191	715	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:37,187] [INFO] GTDB search result was written to GCF_019586025.1_ASM1958602v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:37,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:37,190] [INFO] DFAST_QC result json was written to GCF_019586025.1_ASM1958602v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:37,190] [INFO] DFAST_QC completed!
[2024-01-24 12:32:37,190] [INFO] Total running time: 0h0m41s