[2024-01-24 14:31:28,843] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:28,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:28,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg907413f5-cd47-4231-85bd-fa446f5525f5/dqc_reference
[2024-01-24 14:31:29,981] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:29,982] [INFO] Task started: Prodigal
[2024-01-24 14:31:29,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e98ec53-b8d3-4cbc-97d5-cc68813ff17a/GCF_003987065.1_ASM398706v1_genomic.fna.gz | prodigal -d GCF_003987065.1_ASM398706v1_genomic.fna/cds.fna -a GCF_003987065.1_ASM398706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:36,020] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:36,021] [INFO] Task started: HMMsearch
[2024-01-24 14:31:36,021] [INFO] Running command: hmmsearch --tblout GCF_003987065.1_ASM398706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg907413f5-cd47-4231-85bd-fa446f5525f5/dqc_reference/reference_markers.hmm GCF_003987065.1_ASM398706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:36,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:36,213] [INFO] Found 6/6 markers.
[2024-01-24 14:31:36,234] [INFO] Query marker FASTA was written to GCF_003987065.1_ASM398706v1_genomic.fna/markers.fasta
[2024-01-24 14:31:36,234] [INFO] Task started: Blastn
[2024-01-24 14:31:36,234] [INFO] Running command: blastn -query GCF_003987065.1_ASM398706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg907413f5-cd47-4231-85bd-fa446f5525f5/dqc_reference/reference_markers.fasta -out GCF_003987065.1_ASM398706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:36,952] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:36,955] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:36,955] [INFO] Target genome list was writen to GCF_003987065.1_ASM398706v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:37,303] [INFO] Task started: fastANI
[2024-01-24 14:31:37,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e98ec53-b8d3-4cbc-97d5-cc68813ff17a/GCF_003987065.1_ASM398706v1_genomic.fna.gz --refList GCF_003987065.1_ASM398706v1_genomic.fna/target_genomes.txt --output GCF_003987065.1_ASM398706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:46,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:46,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg907413f5-cd47-4231-85bd-fa446f5525f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:46,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg907413f5-cd47-4231-85bd-fa446f5525f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:46,259] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:46,259] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:46,259] [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 insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	100.0	842	843	95	conclusive
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	79.9457	387	843	95	below_threshold
Pseudidiomarina homiensis	strain=PO-M2	GCA_003987225.1	364198	364198	type	True	79.8309	370	843	95	below_threshold
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	79.256	333	843	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	79.1265	300	843	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	79.122	163	843	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	79.0685	298	843	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	78.7887	281	843	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_003987105.1	435908	435908	type	True	78.7284	196	843	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_000753715.1	435908	435908	type	True	78.5565	196	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:46,261] [INFO] DFAST Taxonomy check result was written to GCF_003987065.1_ASM398706v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:46,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:46,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:46,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg907413f5-cd47-4231-85bd-fa446f5525f5/dqc_reference/checkm_data
[2024-01-24 14:31:46,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:46,290] [INFO] Task started: CheckM
[2024-01-24 14:31:46,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987065.1_ASM398706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987065.1_ASM398706v1_genomic.fna/checkm_input GCF_003987065.1_ASM398706v1_genomic.fna/checkm_result
[2024-01-24 14:32:09,158] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:09,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:09,173] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:09,173] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:09,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987065.1_ASM398706v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:09,174] [INFO] Task started: Blastn
[2024-01-24 14:32:09,174] [INFO] Running command: blastn -query GCF_003987065.1_ASM398706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg907413f5-cd47-4231-85bd-fa446f5525f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987065.1_ASM398706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:10,336] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:10,338] [INFO] Selected 15 target genomes.
[2024-01-24 14:32:10,338] [INFO] Target genome list was writen to GCF_003987065.1_ASM398706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:10,346] [INFO] Task started: fastANI
[2024-01-24 14:32:10,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e98ec53-b8d3-4cbc-97d5-cc68813ff17a/GCF_003987065.1_ASM398706v1_genomic.fna.gz --refList GCF_003987065.1_ASM398706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987065.1_ASM398706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:18,008] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:18,016] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:18,016] [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_003987065.1	s__Pseudidiomarina insulisalsae	100.0	842	843	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_003987395.1	s__Pseudidiomarina aquimaris	79.96	386	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_003987225.1	s__Pseudidiomarina homiensis	79.8309	370	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987215.1	s__Pseudidiomarina halophila	79.2419	334	843	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	79.0822	165	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_000423165.1	s__Pseudidiomarina sediminum	79.0589	297	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000753735.1	s__Pseudidiomarina atlantica	78.7887	281	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	78.7675	183	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	78.7244	185	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753715.1	s__Pseudidiomarina salinarum	78.5565	196	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	78.4419	178	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987185.1	s__Idiomarina aquatica	77.8338	107	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:18,017] [INFO] GTDB search result was written to GCF_003987065.1_ASM398706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:18,018] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:18,021] [INFO] DFAST_QC result json was written to GCF_003987065.1_ASM398706v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:18,021] [INFO] DFAST_QC completed!
[2024-01-24 14:32:18,021] [INFO] Total running time: 0h0m49s