[2024-01-24 12:54:39,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg9362fd5e-26f9-4039-9a02-4416503bd933/dqc_reference
[2024-01-24 12:54:41,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:41,061] [INFO] Task started: Prodigal
[2024-01-24 12:54:41,061] [INFO] Running command: gunzip -c /var/lib/cwl/stgd22c1991-0f11-4f9b-80ea-988108784386/GCF_030814955.1_ASM3081495v1_genomic.fna.gz | prodigal -d GCF_030814955.1_ASM3081495v1_genomic.fna/cds.fna -a GCF_030814955.1_ASM3081495v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:52,339] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:52,339] [INFO] Task started: HMMsearch
[2024-01-24 12:54:52,339] [INFO] Running command: hmmsearch --tblout GCF_030814955.1_ASM3081495v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9362fd5e-26f9-4039-9a02-4416503bd933/dqc_reference/reference_markers.hmm GCF_030814955.1_ASM3081495v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:52,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:52,619] [INFO] Found 6/6 markers.
[2024-01-24 12:54:52,656] [INFO] Query marker FASTA was written to GCF_030814955.1_ASM3081495v1_genomic.fna/markers.fasta
[2024-01-24 12:54:52,656] [INFO] Task started: Blastn
[2024-01-24 12:54:52,656] [INFO] Running command: blastn -query GCF_030814955.1_ASM3081495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9362fd5e-26f9-4039-9a02-4416503bd933/dqc_reference/reference_markers.fasta -out GCF_030814955.1_ASM3081495v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:53,283] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:53,288] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:53,289] [INFO] Target genome list was writen to GCF_030814955.1_ASM3081495v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:53,293] [INFO] Task started: fastANI
[2024-01-24 12:54:53,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgd22c1991-0f11-4f9b-80ea-988108784386/GCF_030814955.1_ASM3081495v1_genomic.fna.gz --refList GCF_030814955.1_ASM3081495v1_genomic.fna/target_genomes.txt --output GCF_030814955.1_ASM3081495v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:01,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:01,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9362fd5e-26f9-4039-9a02-4416503bd933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:01,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9362fd5e-26f9-4039-9a02-4416503bd933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:01,156] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:55:01,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:55:01,157] [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
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	94.9932	1116	1254	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	83.7641	858	1254	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	83.6486	900	1254	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	82.6309	865	1254	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	81.3657	635	1254	95	below_threshold
Planococcus faecalis	strain=CECT 8759	GCA_001856115.1	1598147	1598147	suspected-type	True	81.319	617	1254	95	below_threshold
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	81.2342	661	1254	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	79.1194	394	1254	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	79.0532	391	1254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:01,159] [INFO] DFAST Taxonomy check result was written to GCF_030814955.1_ASM3081495v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:01,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:01,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:01,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9362fd5e-26f9-4039-9a02-4416503bd933/dqc_reference/checkm_data
[2024-01-24 12:55:01,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:01,200] [INFO] Task started: CheckM
[2024-01-24 12:55:01,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814955.1_ASM3081495v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814955.1_ASM3081495v1_genomic.fna/checkm_input GCF_030814955.1_ASM3081495v1_genomic.fna/checkm_result
[2024-01-24 12:55:36,770] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:36,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:36,797] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:36,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:36,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814955.1_ASM3081495v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:36,799] [INFO] Task started: Blastn
[2024-01-24 12:55:36,799] [INFO] Running command: blastn -query GCF_030814955.1_ASM3081495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9362fd5e-26f9-4039-9a02-4416503bd933/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814955.1_ASM3081495v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:37,581] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:37,584] [INFO] Selected 7 target genomes.
[2024-01-24 12:55:37,584] [INFO] Target genome list was writen to GCF_030814955.1_ASM3081495v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:37,604] [INFO] Task started: fastANI
[2024-01-24 12:55:37,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgd22c1991-0f11-4f9b-80ea-988108784386/GCF_030814955.1_ASM3081495v1_genomic.fna.gz --refList GCF_030814955.1_ASM3081495v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814955.1_ASM3081495v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:43,688] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:43,700] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:55:43,701] [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_016881065.1	s__Planococcus soli	94.9932	1116	1254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018613575.1	s__Planococcus sp018613575	85.7988	904	1254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687565.2	s__Planococcus antarcticus	83.646	900	1254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.42	99.42	0.95	0.95	2	-
GCF_007859295.1	s__Planococcus sp007859295	83.1699	919	1254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836985.1	s__Planococcus sp014836985	82.631	865	1254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.16	97.16	0.91	0.91	2	-
GCF_001465835.2	s__Planococcus kocurii	81.2618	660	1254	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	98.39	98.00	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:43,702] [INFO] GTDB search result was written to GCF_030814955.1_ASM3081495v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:43,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:43,706] [INFO] DFAST_QC result json was written to GCF_030814955.1_ASM3081495v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:43,706] [INFO] DFAST_QC completed!
[2024-01-24 12:55:43,706] [INFO] Total running time: 0h1m4s