[2024-01-25 20:07:20,415] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:20,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:20,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg525a47a7-1946-48e2-8525-81aaab6d97a2/dqc_reference
[2024-01-25 20:07:21,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:21,568] [INFO] Task started: Prodigal
[2024-01-25 20:07:21,568] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6819798-6849-49a2-b85c-fb1999fb81c1/GCF_001687565.2_ASM168756v2_genomic.fna.gz | prodigal -d GCF_001687565.2_ASM168756v2_genomic.fna/cds.fna -a GCF_001687565.2_ASM168756v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:30,287] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:30,288] [INFO] Task started: HMMsearch
[2024-01-25 20:07:30,288] [INFO] Running command: hmmsearch --tblout GCF_001687565.2_ASM168756v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg525a47a7-1946-48e2-8525-81aaab6d97a2/dqc_reference/reference_markers.hmm GCF_001687565.2_ASM168756v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:30,505] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:30,506] [INFO] Found 6/6 markers.
[2024-01-25 20:07:30,536] [INFO] Query marker FASTA was written to GCF_001687565.2_ASM168756v2_genomic.fna/markers.fasta
[2024-01-25 20:07:30,536] [INFO] Task started: Blastn
[2024-01-25 20:07:30,536] [INFO] Running command: blastn -query GCF_001687565.2_ASM168756v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg525a47a7-1946-48e2-8525-81aaab6d97a2/dqc_reference/reference_markers.fasta -out GCF_001687565.2_ASM168756v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:31,082] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:31,084] [INFO] Selected 13 target genomes.
[2024-01-25 20:07:31,085] [INFO] Target genome list was writen to GCF_001687565.2_ASM168756v2_genomic.fna/target_genomes.txt
[2024-01-25 20:07:31,090] [INFO] Task started: fastANI
[2024-01-25 20:07:31,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6819798-6849-49a2-b85c-fb1999fb81c1/GCF_001687565.2_ASM168756v2_genomic.fna.gz --refList GCF_001687565.2_ASM168756v2_genomic.fna/target_genomes.txt --output GCF_001687565.2_ASM168756v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:41,993] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:41,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg525a47a7-1946-48e2-8525-81aaab6d97a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:41,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg525a47a7-1946-48e2-8525-81aaab6d97a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:42,001] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:07:42,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:42,002] [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 antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	100.0	1263	1267	95	conclusive
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	99.4195	1120	1267	95	conclusive
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	83.741	887	1267	95	below_threshold
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	82.5372	768	1267	95	below_threshold
Planococcus faecalis	strain=CECT 8759	GCA_001856115.1	1598147	1598147	suspected-type	True	82.4433	747	1267	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	81.7889	755	1267	95	below_threshold
Planococcus versutus	strain=L10.15	GCA_001186155.3	1302659	1302659	type	True	81.5368	656	1267	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	81.5363	697	1267	95	below_threshold
Planococcus halocryophilus	strain=Or1	GCA_000342445.1	1215089	1215089	type	True	81.1686	682	1267	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.9007	313	1267	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	77.3963	51	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:42,003] [INFO] DFAST Taxonomy check result was written to GCF_001687565.2_ASM168756v2_genomic.fna/tc_result.tsv
[2024-01-25 20:07:42,003] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:42,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:42,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg525a47a7-1946-48e2-8525-81aaab6d97a2/dqc_reference/checkm_data
[2024-01-25 20:07:42,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:42,044] [INFO] Task started: CheckM
[2024-01-25 20:07:42,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001687565.2_ASM168756v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001687565.2_ASM168756v2_genomic.fna/checkm_input GCF_001687565.2_ASM168756v2_genomic.fna/checkm_result
[2024-01-25 20:08:10,807] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:10,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:10,824] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:10,824] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:10,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001687565.2_ASM168756v2_genomic.fna/markers.fasta)
[2024-01-25 20:08:10,825] [INFO] Task started: Blastn
[2024-01-25 20:08:10,825] [INFO] Running command: blastn -query GCF_001687565.2_ASM168756v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg525a47a7-1946-48e2-8525-81aaab6d97a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001687565.2_ASM168756v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:11,579] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:11,582] [INFO] Selected 10 target genomes.
[2024-01-25 20:08:11,582] [INFO] Target genome list was writen to GCF_001687565.2_ASM168756v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:11,593] [INFO] Task started: fastANI
[2024-01-25 20:08:11,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6819798-6849-49a2-b85c-fb1999fb81c1/GCF_001687565.2_ASM168756v2_genomic.fna.gz --refList GCF_001687565.2_ASM168756v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001687565.2_ASM168756v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:20,661] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:20,668] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:20,669] [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_001687565.2	s__Planococcus antarcticus	100.0	1264	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.42	99.42	0.95	0.95	2	conclusive
GCF_018613575.1	s__Planococcus sp018613575	84.544	906	1267	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_016881065.1	s__Planococcus soli	83.7307	888	1267	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_001465835.2	s__Planococcus kocurii	82.7102	777	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	98.39	98.00	0.92	0.89	4	-
GCF_007859295.1	s__Planococcus sp007859295	82.2947	823	1267	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	81.7889	755	1267	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_001687665.2	s__Planococcus donghaensis	81.561	627	1267	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_001687585.2	s__Planococcus halocryophilus	81.5105	699	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_000785555.1	s__Planococcus sp000785555	81.4772	630	1267	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_000189395.1	s__Planococcus donghaensis_B	81.036	627	1267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:20,670] [INFO] GTDB search result was written to GCF_001687565.2_ASM168756v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:20,670] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:20,673] [INFO] DFAST_QC result json was written to GCF_001687565.2_ASM168756v2_genomic.fna/dqc_result.json
[2024-01-25 20:08:20,673] [INFO] DFAST_QC completed!
[2024-01-25 20:08:20,673] [INFO] Total running time: 0h1m0s