[2024-01-24 13:52:12,557] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ff86d3a-8a3d-4276-bacf-07d9050d3326/dqc_reference
[2024-01-24 13:52:13,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,791] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg8266697d-a525-4ac3-a9f6-301e61644634/GCF_016820495.1_ASM1682049v1_genomic.fna.gz | prodigal -d GCF_016820495.1_ASM1682049v1_genomic.fna/cds.fna -a GCF_016820495.1_ASM1682049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:22,376] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:22,377] [INFO] Task started: HMMsearch
[2024-01-24 13:52:22,377] [INFO] Running command: hmmsearch --tblout GCF_016820495.1_ASM1682049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ff86d3a-8a3d-4276-bacf-07d9050d3326/dqc_reference/reference_markers.hmm GCF_016820495.1_ASM1682049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:22,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:22,641] [INFO] Found 6/6 markers.
[2024-01-24 13:52:22,675] [INFO] Query marker FASTA was written to GCF_016820495.1_ASM1682049v1_genomic.fna/markers.fasta
[2024-01-24 13:52:22,676] [INFO] Task started: Blastn
[2024-01-24 13:52:22,676] [INFO] Running command: blastn -query GCF_016820495.1_ASM1682049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ff86d3a-8a3d-4276-bacf-07d9050d3326/dqc_reference/reference_markers.fasta -out GCF_016820495.1_ASM1682049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:23,279] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:23,284] [INFO] Selected 20 target genomes.
[2024-01-24 13:52:23,284] [INFO] Target genome list was writen to GCF_016820495.1_ASM1682049v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:23,303] [INFO] Task started: fastANI
[2024-01-24 13:52:23,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg8266697d-a525-4ac3-a9f6-301e61644634/GCF_016820495.1_ASM1682049v1_genomic.fna.gz --refList GCF_016820495.1_ASM1682049v1_genomic.fna/target_genomes.txt --output GCF_016820495.1_ASM1682049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:34,487] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:34,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ff86d3a-8a3d-4276-bacf-07d9050d3326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:34,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ff86d3a-8a3d-4276-bacf-07d9050d3326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:34,504] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:52:34,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:52:34,504] [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 salinarum	strain=ISL-16	GCA_003428865.1	622695	622695	type	True	81.0035	564	1056	95	below_threshold
Planococcus salinarum	strain=KCTC 13584	GCA_007004625.1	622695	622695	type	True	80.9444	560	1056	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	79.0966	291	1056	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	78.9382	333	1056	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	78.8841	340	1056	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.8833	341	1056	95	below_threshold
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	78.8821	183	1056	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	78.8481	333	1056	95	below_threshold
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	78.835	328	1056	95	below_threshold
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	78.7551	348	1056	95	below_threshold
Planococcus salinus	strain=LCB217	GCA_003719725.1	1848460	1848460	type	True	78.6477	290	1056	95	below_threshold
Planococcus citreus	strain=DSM 20549	GCA_003664125.1	1373	1373	type	True	78.4376	281	1056	95	below_threshold
Planococcus plakortidis	strain=DSM 23997	GCA_001687605.2	1038856	1038856	type	True	78.4116	297	1056	95	below_threshold
Planococcus citreus	strain=DSM 20549	GCA_004761885.1	1373	1373	type	True	78.3595	268	1056	95	below_threshold
Planococcus rifietoensis	strain=M8	GCA_001465795.2	200991	200991	type	True	78.2473	278	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:34,506] [INFO] DFAST Taxonomy check result was written to GCF_016820495.1_ASM1682049v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:34,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:34,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:34,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ff86d3a-8a3d-4276-bacf-07d9050d3326/dqc_reference/checkm_data
[2024-01-24 13:52:34,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:34,539] [INFO] Task started: CheckM
[2024-01-24 13:52:34,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820495.1_ASM1682049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820495.1_ASM1682049v1_genomic.fna/checkm_input GCF_016820495.1_ASM1682049v1_genomic.fna/checkm_result
[2024-01-24 13:53:05,424] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:05,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:05,443] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:05,443] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:05,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820495.1_ASM1682049v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:05,444] [INFO] Task started: Blastn
[2024-01-24 13:53:05,444] [INFO] Running command: blastn -query GCF_016820495.1_ASM1682049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ff86d3a-8a3d-4276-bacf-07d9050d3326/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820495.1_ASM1682049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:06,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:06,250] [INFO] Selected 8 target genomes.
[2024-01-24 13:53:06,250] [INFO] Target genome list was writen to GCF_016820495.1_ASM1682049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:06,260] [INFO] Task started: fastANI
[2024-01-24 13:53:06,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg8266697d-a525-4ac3-a9f6-301e61644634/GCF_016820495.1_ASM1682049v1_genomic.fna.gz --refList GCF_016820495.1_ASM1682049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820495.1_ASM1682049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:12,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:12,806] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:12,806] [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_016820495.1	s__Planococcus sp016820495	100.0	1055	1056	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000775575.1	s__Planococcus sp000775575	83.5102	639	1056	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_017873465.1	s__Planococcus mcmeekinii	82.0645	677	1056	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_003428875.1	s__Planococcus okeanokoites	81.5797	638	1056	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_003289955.1	s__Planococcus halotolerans	81.5433	650	1056	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_003668635.1	s__Planococcus sp003668635	81.4304	627	1056	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_007004625.1	s__Planococcus salinarum	81.0114	554	1056	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_018613655.1	s__Planococcus sp018613655	78.3018	261	1056	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:12,808] [INFO] GTDB search result was written to GCF_016820495.1_ASM1682049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:12,808] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:12,811] [INFO] DFAST_QC result json was written to GCF_016820495.1_ASM1682049v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:12,811] [INFO] DFAST_QC completed!
[2024-01-24 13:53:12,811] [INFO] Total running time: 0h1m0s