[2024-01-24 12:52:51,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,203] [INFO] DQC Reference Directory: /var/lib/cwl/stga43293cd-4564-4185-9071-a7d6998eb003/dqc_reference
[2024-01-24 12:52:53,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,750] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,751] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbf9ce67-8468-4b0d-9b77-faa1dbc83d6e/GCF_031624335.1_ASM3162433v1_genomic.fna.gz | prodigal -d GCF_031624335.1_ASM3162433v1_genomic.fna/cds.fna -a GCF_031624335.1_ASM3162433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:00,164] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:00,164] [INFO] Task started: HMMsearch
[2024-01-24 12:53:00,164] [INFO] Running command: hmmsearch --tblout GCF_031624335.1_ASM3162433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga43293cd-4564-4185-9071-a7d6998eb003/dqc_reference/reference_markers.hmm GCF_031624335.1_ASM3162433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:00,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:00,384] [INFO] Found 6/6 markers.
[2024-01-24 12:53:00,410] [INFO] Query marker FASTA was written to GCF_031624335.1_ASM3162433v1_genomic.fna/markers.fasta
[2024-01-24 12:53:00,410] [INFO] Task started: Blastn
[2024-01-24 12:53:00,410] [INFO] Running command: blastn -query GCF_031624335.1_ASM3162433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43293cd-4564-4185-9071-a7d6998eb003/dqc_reference/reference_markers.fasta -out GCF_031624335.1_ASM3162433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:01,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:01,176] [INFO] Selected 17 target genomes.
[2024-01-24 12:53:01,176] [INFO] Target genome list was writen to GCF_031624335.1_ASM3162433v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:01,224] [INFO] Task started: fastANI
[2024-01-24 12:53:01,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbf9ce67-8468-4b0d-9b77-faa1dbc83d6e/GCF_031624335.1_ASM3162433v1_genomic.fna.gz --refList GCF_031624335.1_ASM3162433v1_genomic.fna/target_genomes.txt --output GCF_031624335.1_ASM3162433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:10,944] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:10,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga43293cd-4564-4185-9071-a7d6998eb003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:10,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga43293cd-4564-4185-9071-a7d6998eb003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:10,956] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:53:10,957] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:53:10,957] [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 marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	87.8376	696	796	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	83.9518	622	796	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	83.9459	647	796	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	80.9722	437	796	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	80.7313	411	796	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	80.7005	412	796	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	80.6532	401	796	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	80.6438	401	796	95	below_threshold
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	79.526	165	796	95	below_threshold
Pseudidiomarina aestuarii	strain=KYW314	GCA_003987355.1	624146	624146	suspected-type	True	78.6033	172	796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:10,958] [INFO] DFAST Taxonomy check result was written to GCF_031624335.1_ASM3162433v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:10,959] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:10,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:10,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga43293cd-4564-4185-9071-a7d6998eb003/dqc_reference/checkm_data
[2024-01-24 12:53:10,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:10,986] [INFO] Task started: CheckM
[2024-01-24 12:53:10,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031624335.1_ASM3162433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031624335.1_ASM3162433v1_genomic.fna/checkm_input GCF_031624335.1_ASM3162433v1_genomic.fna/checkm_result
[2024-01-24 12:53:35,897] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:35,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:35,918] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:35,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:35,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031624335.1_ASM3162433v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:35,920] [INFO] Task started: Blastn
[2024-01-24 12:53:35,920] [INFO] Running command: blastn -query GCF_031624335.1_ASM3162433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga43293cd-4564-4185-9071-a7d6998eb003/dqc_reference/reference_markers_gtdb.fasta -out GCF_031624335.1_ASM3162433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:37,030] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:37,035] [INFO] Selected 11 target genomes.
[2024-01-24 12:53:37,035] [INFO] Target genome list was writen to GCF_031624335.1_ASM3162433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:37,048] [INFO] Task started: fastANI
[2024-01-24 12:53:37,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbf9ce67-8468-4b0d-9b77-faa1dbc83d6e/GCF_031624335.1_ASM3162433v1_genomic.fna.gz --refList GCF_031624335.1_ASM3162433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031624335.1_ASM3162433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:42,535] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:42,546] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:42,547] [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_009734345.1	s__Pseudidiomarina andamanensis	99.9971	795	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002279005.1	s__Pseudidiomarina sp002279005	91.6071	509	796	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	87.8376	696	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	83.9518	622	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	80.9576	438	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	80.7286	407	796	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	80.706	413	796	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	80.644	399	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000423165.1	s__Pseudidiomarina sediminum	78.9856	184	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987355.1	s__Pseudidiomarina aestuarii	78.62	172	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:42,548] [INFO] GTDB search result was written to GCF_031624335.1_ASM3162433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:42,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:42,552] [INFO] DFAST_QC result json was written to GCF_031624335.1_ASM3162433v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:42,552] [INFO] DFAST_QC completed!
[2024-01-24 12:53:42,552] [INFO] Total running time: 0h0m51s