[2024-01-25 17:41:05,761] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:05,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:05,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg09796f63-286f-40c1-a6e5-ec14c99076e9/dqc_reference
[2024-01-25 17:41:06,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:06,875] [INFO] Task started: Prodigal
[2024-01-25 17:41:06,875] [INFO] Running command: gunzip -c /var/lib/cwl/stgea130500-0989-4015-bbd0-19938db99076/GCF_001418345.1_ASM141834v1_genomic.fna.gz | prodigal -d GCF_001418345.1_ASM141834v1_genomic.fna/cds.fna -a GCF_001418345.1_ASM141834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:12,552] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:12,552] [INFO] Task started: HMMsearch
[2024-01-25 17:41:12,552] [INFO] Running command: hmmsearch --tblout GCF_001418345.1_ASM141834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09796f63-286f-40c1-a6e5-ec14c99076e9/dqc_reference/reference_markers.hmm GCF_001418345.1_ASM141834v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:12,751] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:12,752] [INFO] Found 6/6 markers.
[2024-01-25 17:41:12,775] [INFO] Query marker FASTA was written to GCF_001418345.1_ASM141834v1_genomic.fna/markers.fasta
[2024-01-25 17:41:12,775] [INFO] Task started: Blastn
[2024-01-25 17:41:12,775] [INFO] Running command: blastn -query GCF_001418345.1_ASM141834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09796f63-286f-40c1-a6e5-ec14c99076e9/dqc_reference/reference_markers.fasta -out GCF_001418345.1_ASM141834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:13,502] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:13,505] [INFO] Selected 12 target genomes.
[2024-01-25 17:41:13,505] [INFO] Target genome list was writen to GCF_001418345.1_ASM141834v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:13,525] [INFO] Task started: fastANI
[2024-01-25 17:41:13,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgea130500-0989-4015-bbd0-19938db99076/GCF_001418345.1_ASM141834v1_genomic.fna.gz --refList GCF_001418345.1_ASM141834v1_genomic.fna/target_genomes.txt --output GCF_001418345.1_ASM141834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:21,147] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:21,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09796f63-286f-40c1-a6e5-ec14c99076e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:21,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09796f63-286f-40c1-a6e5-ec14c99076e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:21,154] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:41:21,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:21,154] [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 woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	100.0	803	804	95	conclusive
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	100.0	803	804	95	conclusive
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	91.1884	747	804	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	91.1267	752	804	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	81.0657	380	804	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	80.9468	388	804	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	78.5546	191	804	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.6264	55	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:21,155] [INFO] DFAST Taxonomy check result was written to GCF_001418345.1_ASM141834v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:21,157] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:21,157] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:21,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09796f63-286f-40c1-a6e5-ec14c99076e9/dqc_reference/checkm_data
[2024-01-25 17:41:21,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:21,190] [INFO] Task started: CheckM
[2024-01-25 17:41:21,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418345.1_ASM141834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418345.1_ASM141834v1_genomic.fna/checkm_input GCF_001418345.1_ASM141834v1_genomic.fna/checkm_result
[2024-01-25 17:41:42,618] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:42,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:42,639] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:42,639] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:42,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418345.1_ASM141834v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:42,640] [INFO] Task started: Blastn
[2024-01-25 17:41:42,640] [INFO] Running command: blastn -query GCF_001418345.1_ASM141834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09796f63-286f-40c1-a6e5-ec14c99076e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418345.1_ASM141834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:43,831] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:43,834] [INFO] Selected 13 target genomes.
[2024-01-25 17:41:43,834] [INFO] Target genome list was writen to GCF_001418345.1_ASM141834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:43,847] [INFO] Task started: fastANI
[2024-01-25 17:41:43,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgea130500-0989-4015-bbd0-19938db99076/GCF_001418345.1_ASM141834v1_genomic.fna.gz --refList GCF_001418345.1_ASM141834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418345.1_ASM141834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:51,451] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:51,458] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:51,459] [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_001418345.1	s__Pseudidiomarina woesei	100.0	803	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900116895.1	s__Pseudidiomarina donghaiensis	91.1884	747	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	89.6834	680	804	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	81.2515	380	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_003987045.1	s__Pseudidiomarina marina	80.9404	388	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	80.8859	312	804	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	80.8341	402	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	80.4548	401	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987225.1	s__Pseudidiomarina homiensis	79.8325	190	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423165.1	s__Pseudidiomarina sediminum	78.5355	190	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000753715.1	s__Pseudidiomarina salinarum	77.8753	142	804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:51,460] [INFO] GTDB search result was written to GCF_001418345.1_ASM141834v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:51,460] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:51,464] [INFO] DFAST_QC result json was written to GCF_001418345.1_ASM141834v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:51,465] [INFO] DFAST_QC completed!
[2024-01-25 17:41:51,465] [INFO] Total running time: 0h0m46s