[2023-06-18 17:26:39,505] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:26:39,507] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:26:39,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6f585e0-8f0d-49fa-bfe2-a3129eb18ccd/dqc_reference
[2023-06-18 17:26:40,631] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:26:40,632] [INFO] Task started: Prodigal
[2023-06-18 17:26:40,632] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb39cbe7-0de8-4b79-8f2c-ef36b02fa7f6/GCA_018222985.1_ASM1822298v1_genomic.fna.gz | prodigal -d GCA_018222985.1_ASM1822298v1_genomic.fna/cds.fna -a GCA_018222985.1_ASM1822298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:26:46,435] [INFO] Task succeeded: Prodigal
[2023-06-18 17:26:46,436] [INFO] Task started: HMMsearch
[2023-06-18 17:26:46,436] [INFO] Running command: hmmsearch --tblout GCA_018222985.1_ASM1822298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6f585e0-8f0d-49fa-bfe2-a3129eb18ccd/dqc_reference/reference_markers.hmm GCA_018222985.1_ASM1822298v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:26:46,618] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:26:46,618] [INFO] Found 6/6 markers.
[2023-06-18 17:26:46,640] [INFO] Query marker FASTA was written to GCA_018222985.1_ASM1822298v1_genomic.fna/markers.fasta
[2023-06-18 17:26:46,640] [INFO] Task started: Blastn
[2023-06-18 17:26:46,640] [INFO] Running command: blastn -query GCA_018222985.1_ASM1822298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f585e0-8f0d-49fa-bfe2-a3129eb18ccd/dqc_reference/reference_markers.fasta -out GCA_018222985.1_ASM1822298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:26:47,340] [INFO] Task succeeded: Blastn
[2023-06-18 17:26:47,343] [INFO] Selected 13 target genomes.
[2023-06-18 17:26:47,343] [INFO] Target genome list was writen to GCA_018222985.1_ASM1822298v1_genomic.fna/target_genomes.txt
[2023-06-18 17:26:47,346] [INFO] Task started: fastANI
[2023-06-18 17:26:47,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb39cbe7-0de8-4b79-8f2c-ef36b02fa7f6/GCA_018222985.1_ASM1822298v1_genomic.fna.gz --refList GCA_018222985.1_ASM1822298v1_genomic.fna/target_genomes.txt --output GCA_018222985.1_ASM1822298v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:26:54,782] [INFO] Task succeeded: fastANI
[2023-06-18 17:26:54,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6f585e0-8f0d-49fa-bfe2-a3129eb18ccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:26:54,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6f585e0-8f0d-49fa-bfe2-a3129eb18ccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:26:54,789] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:26:54,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:26:54,790] [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
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	91.975	713	809	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	91.9504	714	809	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	89.4494	712	809	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	89.4494	712	809	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	80.5206	411	809	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	80.471	395	809	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	80.3901	403	809	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	80.3507	403	809	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.1248	60	809	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:26:54,804] [INFO] DFAST Taxonomy check result was written to GCA_018222985.1_ASM1822298v1_genomic.fna/tc_result.tsv
[2023-06-18 17:26:54,806] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:26:54,806] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:26:54,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6f585e0-8f0d-49fa-bfe2-a3129eb18ccd/dqc_reference/checkm_data
[2023-06-18 17:26:54,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:26:54,836] [INFO] Task started: CheckM
[2023-06-18 17:26:54,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018222985.1_ASM1822298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018222985.1_ASM1822298v1_genomic.fna/checkm_input GCA_018222985.1_ASM1822298v1_genomic.fna/checkm_result
[2023-06-18 17:27:16,320] [INFO] Task succeeded: CheckM
[2023-06-18 17:27:16,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:27:16,347] [INFO] ===== Completeness check finished =====
[2023-06-18 17:27:16,347] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:27:16,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018222985.1_ASM1822298v1_genomic.fna/markers.fasta)
[2023-06-18 17:27:16,348] [INFO] Task started: Blastn
[2023-06-18 17:27:16,348] [INFO] Running command: blastn -query GCA_018222985.1_ASM1822298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f585e0-8f0d-49fa-bfe2-a3129eb18ccd/dqc_reference/reference_markers_gtdb.fasta -out GCA_018222985.1_ASM1822298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:27:17,457] [INFO] Task succeeded: Blastn
[2023-06-18 17:27:17,485] [INFO] Selected 10 target genomes.
[2023-06-18 17:27:17,485] [INFO] Target genome list was writen to GCA_018222985.1_ASM1822298v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:27:17,489] [INFO] Task started: fastANI
[2023-06-18 17:27:17,489] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb39cbe7-0de8-4b79-8f2c-ef36b02fa7f6/GCA_018222985.1_ASM1822298v1_genomic.fna.gz --refList GCA_018222985.1_ASM1822298v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018222985.1_ASM1822298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:27:22,688] [INFO] Task succeeded: fastANI
[2023-06-18 17:27:22,696] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:27:22,697] [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
GCA_018222985.1	s__Pseudidiomarina sp018222985	100.0	808	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900116895.1	s__Pseudidiomarina donghaiensis	91.975	713	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001418345.1	s__Pseudidiomarina woesei	89.4494	712	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	81.0095	324	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	80.6987	418	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987045.1	s__Pseudidiomarina marina	80.4712	395	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	80.3901	403	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	80.3792	401	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_003987225.1	s__Pseudidiomarina homiensis	79.3292	193	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	78.0594	184	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:27:22,698] [INFO] GTDB search result was written to GCA_018222985.1_ASM1822298v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:27:22,701] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:27:22,707] [INFO] DFAST_QC result json was written to GCA_018222985.1_ASM1822298v1_genomic.fna/dqc_result.json
[2023-06-18 17:27:22,708] [INFO] DFAST_QC completed!
[2023-06-18 17:27:22,708] [INFO] Total running time: 0h0m43s