[2024-01-24 13:41:20,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,477] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg90efb4bc-cc98-4b77-bd32-6d578d02c0d2/dqc_reference
[2024-01-24 13:41:21,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,974] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg385cd107-3d39-4dc7-89d3-4d1e416b9552/GCF_002441695.1_ASM244169v1_genomic.fna.gz | prodigal -d GCF_002441695.1_ASM244169v1_genomic.fna/cds.fna -a GCF_002441695.1_ASM244169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:26,800] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:26,800] [INFO] Task started: HMMsearch
[2024-01-24 13:41:26,801] [INFO] Running command: hmmsearch --tblout GCF_002441695.1_ASM244169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90efb4bc-cc98-4b77-bd32-6d578d02c0d2/dqc_reference/reference_markers.hmm GCF_002441695.1_ASM244169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:27,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:27,143] [INFO] Found 6/6 markers.
[2024-01-24 13:41:27,166] [INFO] Query marker FASTA was written to GCF_002441695.1_ASM244169v1_genomic.fna/markers.fasta
[2024-01-24 13:41:27,166] [INFO] Task started: Blastn
[2024-01-24 13:41:27,167] [INFO] Running command: blastn -query GCF_002441695.1_ASM244169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90efb4bc-cc98-4b77-bd32-6d578d02c0d2/dqc_reference/reference_markers.fasta -out GCF_002441695.1_ASM244169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:27,744] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:27,747] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:27,747] [INFO] Target genome list was writen to GCF_002441695.1_ASM244169v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:27,753] [INFO] Task started: fastANI
[2024-01-24 13:41:27,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg385cd107-3d39-4dc7-89d3-4d1e416b9552/GCF_002441695.1_ASM244169v1_genomic.fna.gz --refList GCF_002441695.1_ASM244169v1_genomic.fna/target_genomes.txt --output GCF_002441695.1_ASM244169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:35,106] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:35,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90efb4bc-cc98-4b77-bd32-6d578d02c0d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:35,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90efb4bc-cc98-4b77-bd32-6d578d02c0d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:35,116] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:35,117] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:35,117] [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 piscium	strain=DSM 6634	GCA_002441695.1	1364	1364	suspected-type	True	100.0	766	770	95	conclusive
Lactococcus carnosus	strain=TMW 2.1612	GCA_006770265.1	2749961	2749961	type	True	94.704	609	770	95	below_threshold
Lactococcus paracarnosus	strain=TMW 2.1615	GCA_006770285.1	2749962	2749962	type	True	92.7684	626	770	95	below_threshold
Lactococcus raffinolactis	strain=ATCC 43920	GCA_002441745.1	1366	1366	type	True	80.0727	249	770	95	below_threshold
Lactococcus plantarum	strain=DSM 20686	GCA_002441715.1	1365	1365	type	True	79.9935	317	770	95	below_threshold
Lactococcus laudensis	strain=LMG 28353	GCA_019586025.1	1494461	1494461	type	True	79.8443	256	770	95	below_threshold
Lactococcus chungangensis	strain=DSM 22330	GCA_900119835.1	451457	451457	type	True	79.7306	237	770	95	below_threshold
Lactococcus raffinolactis	strain=NBRC 100932	GCA_001591765.1	1366	1366	type	True	79.7227	246	770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:35,121] [INFO] DFAST Taxonomy check result was written to GCF_002441695.1_ASM244169v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:35,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:35,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:35,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90efb4bc-cc98-4b77-bd32-6d578d02c0d2/dqc_reference/checkm_data
[2024-01-24 13:41:35,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:35,153] [INFO] Task started: CheckM
[2024-01-24 13:41:35,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002441695.1_ASM244169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002441695.1_ASM244169v1_genomic.fna/checkm_input GCF_002441695.1_ASM244169v1_genomic.fna/checkm_result
[2024-01-24 13:41:57,300] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:57,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:57,322] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:57,322] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:57,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002441695.1_ASM244169v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:57,323] [INFO] Task started: Blastn
[2024-01-24 13:41:57,323] [INFO] Running command: blastn -query GCF_002441695.1_ASM244169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90efb4bc-cc98-4b77-bd32-6d578d02c0d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002441695.1_ASM244169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:58,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:58,126] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:58,127] [INFO] Target genome list was writen to GCF_002441695.1_ASM244169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:58,135] [INFO] Task started: fastANI
[2024-01-24 13:41:58,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg385cd107-3d39-4dc7-89d3-4d1e416b9552/GCF_002441695.1_ASM244169v1_genomic.fna.gz --refList GCF_002441695.1_ASM244169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002441695.1_ASM244169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:03,809] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:03,817] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:03,817] [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_002441695.1	s__Lactococcus_A piscium	100.0	766	770	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006770265.1	s__Lactococcus_A carnosus	94.704	609	770	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_006770285.1	s__Lactococcus_A paracarnosus	92.7576	627	770	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_013449735.1	s__Lactococcus_A laudensis	80.1193	259	770	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	97.98	97.98	0.86	0.86	2	-
GCF_002441715.1	s__Lactococcus_A plantarum	79.9935	317	770	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A	95.0	99.99	99.98	1.00	0.99	3	-
GCF_002441885.1	s__Lactococcus_A chungangensis	79.7837	239	770	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	79.7443	245	770	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_011170065.1	s__Lactococcus_A insecticola	78.8041	152	770	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 13:42:03,819] [INFO] GTDB search result was written to GCF_002441695.1_ASM244169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:03,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:03,823] [INFO] DFAST_QC result json was written to GCF_002441695.1_ASM244169v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:03,823] [INFO] DFAST_QC completed!
[2024-01-24 13:42:03,823] [INFO] Total running time: 0h0m43s