[2024-01-25 19:07:35,406] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:35,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:35,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg32759098-9d27-4b91-9539-a5cae8877034/dqc_reference
[2024-01-25 19:07:36,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:36,521] [INFO] Task started: Prodigal
[2024-01-25 19:07:36,522] [INFO] Running command: gunzip -c /var/lib/cwl/stge39a8504-8e01-4b69-9115-0ddb2582c302/GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna.gz | prodigal -d GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/cds.fna -a GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:44,801] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:44,801] [INFO] Task started: HMMsearch
[2024-01-25 19:07:44,801] [INFO] Running command: hmmsearch --tblout GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32759098-9d27-4b91-9539-a5cae8877034/dqc_reference/reference_markers.hmm GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:45,012] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:45,013] [INFO] Found 6/6 markers.
[2024-01-25 19:07:45,041] [INFO] Query marker FASTA was written to GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/markers.fasta
[2024-01-25 19:07:45,041] [INFO] Task started: Blastn
[2024-01-25 19:07:45,041] [INFO] Running command: blastn -query GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32759098-9d27-4b91-9539-a5cae8877034/dqc_reference/reference_markers.fasta -out GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:45,603] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:45,606] [INFO] Selected 13 target genomes.
[2024-01-25 19:07:45,606] [INFO] Target genome list was writen to GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:45,619] [INFO] Task started: fastANI
[2024-01-25 19:07:45,619] [INFO] Running command: fastANI --query /var/lib/cwl/stge39a8504-8e01-4b69-9115-0ddb2582c302/GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna.gz --refList GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/target_genomes.txt --output GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:54,636] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:54,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32759098-9d27-4b91-9539-a5cae8877034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:54,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32759098-9d27-4b91-9539-a5cae8877034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:54,644] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:07:54,644] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:07:54,644] [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 massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	100.0	1119	1119	95	inconclusive
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	97.8952	1041	1119	95	inconclusive
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	80.1781	547	1119	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	79.6655	418	1119	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	79.6464	419	1119	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	79.339	389	1119	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	78.855	394	1119	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	78.716	54	1119	95	below_threshold
Planococcus citreus	strain=DSM 20549	GCA_003664125.1	1373	1373	type	True	78.6627	323	1119	95	below_threshold
Planococcus citreus	strain=DSM 20549	GCA_004761885.1	1373	1373	type	True	78.5347	303	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:54,645] [INFO] DFAST Taxonomy check result was written to GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:54,646] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:54,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:54,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32759098-9d27-4b91-9539-a5cae8877034/dqc_reference/checkm_data
[2024-01-25 19:07:54,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:54,681] [INFO] Task started: CheckM
[2024-01-25 19:07:54,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/checkm_input GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/checkm_result
[2024-01-25 19:08:23,175] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:23,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:23,206] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:23,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:23,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/markers.fasta)
[2024-01-25 19:08:23,208] [INFO] Task started: Blastn
[2024-01-25 19:08:23,208] [INFO] Running command: blastn -query GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32759098-9d27-4b91-9539-a5cae8877034/dqc_reference/reference_markers_gtdb.fasta -out GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:24,009] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:24,012] [INFO] Selected 16 target genomes.
[2024-01-25 19:08:24,012] [INFO] Target genome list was writen to GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:24,033] [INFO] Task started: fastANI
[2024-01-25 19:08:24,033] [INFO] Running command: fastANI --query /var/lib/cwl/stge39a8504-8e01-4b69-9115-0ddb2582c302/GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna.gz --refList GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:35,393] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:35,403] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:35,404] [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_000821325.1	s__Planococcus massiliensis	100.0	1119	1119	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900099655.1	s__Planococcus glaciei	80.1783	547	1119	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.05	96.92	0.90	0.89	5	-
GCF_004761975.1	s__Planococcus koreensis	79.6629	419	1119	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_016908095.1	s__Planococcus chinensis	79.6558	455	1119	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_000785555.1	s__Planococcus sp000785555	79.3701	266	1119	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	79.3387	389	1119	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_007859275.1	s__Planococcus sp007859275	79.3185	381	1119	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_007859295.1	s__Planococcus sp007859295	79.2413	376	1119	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_003014655.1	s__Planococcus soli_A	79.222	346	1119	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	79.193	339	1119	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_007859395.1	s__Planococcus sp007859395	79.174	378	1119	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_018283455.1	s__Planococcus sp018283455	79.0118	313	1119	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	78.8891	360	1119	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	78.8601	392	1119	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_016820495.1	s__Planococcus sp016820495	78.6775	341	1119	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_018613655.1	s__Planococcus sp018613655	78.3999	283	1119	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 19:08:35,405] [INFO] GTDB search result was written to GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:35,408] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:35,415] [INFO] DFAST_QC result json was written to GCF_000821325.1_PRJEB6479_assembly_1_genomic.fna/dqc_result.json
[2024-01-25 19:08:35,415] [INFO] DFAST_QC completed!
[2024-01-25 19:08:35,415] [INFO] Total running time: 0h1m0s