[2024-01-24 12:44:43,744] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgd95d471f-2059-45f6-a58b-4a6ab437dd1d/dqc_reference
[2024-01-24 12:44:45,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,109] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,109] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d65de64-461b-429e-83b5-390adf52732b/GCF_002167005.1_ASM216700v1_genomic.fna.gz | prodigal -d GCF_002167005.1_ASM216700v1_genomic.fna/cds.fna -a GCF_002167005.1_ASM216700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:53,578] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:53,578] [INFO] Task started: HMMsearch
[2024-01-24 12:44:53,579] [INFO] Running command: hmmsearch --tblout GCF_002167005.1_ASM216700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd95d471f-2059-45f6-a58b-4a6ab437dd1d/dqc_reference/reference_markers.hmm GCF_002167005.1_ASM216700v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:53,911] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:53,913] [INFO] Found 6/6 markers.
[2024-01-24 12:44:53,958] [INFO] Query marker FASTA was written to GCF_002167005.1_ASM216700v1_genomic.fna/markers.fasta
[2024-01-24 12:44:53,958] [INFO] Task started: Blastn
[2024-01-24 12:44:53,959] [INFO] Running command: blastn -query GCF_002167005.1_ASM216700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95d471f-2059-45f6-a58b-4a6ab437dd1d/dqc_reference/reference_markers.fasta -out GCF_002167005.1_ASM216700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:54,602] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:54,605] [INFO] Selected 30 target genomes.
[2024-01-24 12:44:54,606] [INFO] Target genome list was writen to GCF_002167005.1_ASM216700v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:54,673] [INFO] Task started: fastANI
[2024-01-24 12:44:54,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d65de64-461b-429e-83b5-390adf52732b/GCF_002167005.1_ASM216700v1_genomic.fna.gz --refList GCF_002167005.1_ASM216700v1_genomic.fna/target_genomes.txt --output GCF_002167005.1_ASM216700v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:14,470] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:14,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd95d471f-2059-45f6-a58b-4a6ab437dd1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:14,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd95d471f-2059-45f6-a58b-4a6ab437dd1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:14,481] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:14,481] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:14,481] [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 plakortidis	strain=DSM 23997	GCA_001687605.2	1038856	1038856	type	True	77.0023	145	968	95	below_threshold
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	76.9325	107	968	95	below_threshold
Planococcus maitriensis	strain=S1	GCA_003289925.1	221799	221799	type	True	76.8834	150	968	95	below_threshold
Planococcus rifietoensis	strain=M8	GCA_001465795.2	200991	200991	type	True	76.8373	120	968	95	below_threshold
Planococcus maritimus	strain=DSM 17275	GCA_001687625.2	192421	192421	type	True	76.8286	94	968	95	below_threshold
Planococcus citreus	strain=DSM 20549	GCA_004761885.1	1373	1373	type	True	76.8036	114	968	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	76.7763	116	968	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	76.6587	121	968	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	76.5304	83	968	95	below_threshold
Bhargavaea beijingensis	strain=CGMCC 1.6762	GCA_900101985.1	426756	426756	type	True	76.3976	83	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:14,483] [INFO] DFAST Taxonomy check result was written to GCF_002167005.1_ASM216700v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:14,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:14,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:14,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd95d471f-2059-45f6-a58b-4a6ab437dd1d/dqc_reference/checkm_data
[2024-01-24 12:45:14,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:14,517] [INFO] Task started: CheckM
[2024-01-24 12:45:14,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002167005.1_ASM216700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002167005.1_ASM216700v1_genomic.fna/checkm_input GCF_002167005.1_ASM216700v1_genomic.fna/checkm_result
[2024-01-24 12:45:44,809] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:44,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:44,830] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:44,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:44,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002167005.1_ASM216700v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:44,831] [INFO] Task started: Blastn
[2024-01-24 12:45:44,831] [INFO] Running command: blastn -query GCF_002167005.1_ASM216700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95d471f-2059-45f6-a58b-4a6ab437dd1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002167005.1_ASM216700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:45,624] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:45,627] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:45,627] [INFO] Target genome list was writen to GCF_002167005.1_ASM216700v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:45,658] [INFO] Task started: fastANI
[2024-01-24 12:45:45,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d65de64-461b-429e-83b5-390adf52732b/GCF_002167005.1_ASM216700v1_genomic.fna.gz --refList GCF_002167005.1_ASM216700v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002167005.1_ASM216700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:58,117] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:58,141] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:58,141] [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_002167005.1	s__Indiicoccus explosivorum	100.0	966	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Indiicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001999905.1	s__Indiicoccus sp001999905	78.3098	390	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Indiicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775575.1	s__Planococcus sp000775575	77.019	105	968	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_003289955.1	s__Planococcus halotolerans	76.9918	104	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.14	99.14	0.94	0.94	2	-
GCF_000826125.2	s__Bhargavaea cecembensis_B	76.9746	112	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664125.1	s__Planococcus citreus	76.9382	120	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003428875.1	s__Planococcus okeanokoites	76.8848	122	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.50	97.25	0.88	0.87	3	-
GCF_016908095.1	s__Planococcus chinensis	76.8632	171	968	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_004761975.1	s__Planococcus koreensis	76.8524	112	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001465795.2	s__Planococcus rifietoensis	76.8406	118	968	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_001687625.2	s__Planococcus maritimus	76.8327	92	968	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_009707665.1	s__Planococcus sp009707665	76.7898	107	968	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_900156305.1	s__Bhargavaea lindanitolerans	76.6176	88	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101985.1	s__Bhargavaea beijingensis	76.4008	84	968	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Bhargavaea	95.0	99.27	99.27	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:58,150] [INFO] GTDB search result was written to GCF_002167005.1_ASM216700v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:58,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:58,158] [INFO] DFAST_QC result json was written to GCF_002167005.1_ASM216700v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:58,159] [INFO] DFAST_QC completed!
[2024-01-24 12:45:58,159] [INFO] Total running time: 0h1m14s