[2024-01-24 14:15:02,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg29686947-da8f-49ab-a85d-41cb71bbaab2/dqc_reference
[2024-01-24 14:15:03,849] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:03,850] [INFO] Task started: Prodigal
[2024-01-24 14:15:03,850] [INFO] Running command: gunzip -c /var/lib/cwl/stg9221f13d-61ae-4b0a-b0aa-fa082b50a1b4/GCF_003987045.1_ASM398704v1_genomic.fna.gz | prodigal -d GCF_003987045.1_ASM398704v1_genomic.fna/cds.fna -a GCF_003987045.1_ASM398704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:10,841] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:10,841] [INFO] Task started: HMMsearch
[2024-01-24 14:15:10,841] [INFO] Running command: hmmsearch --tblout GCF_003987045.1_ASM398704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29686947-da8f-49ab-a85d-41cb71bbaab2/dqc_reference/reference_markers.hmm GCF_003987045.1_ASM398704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:11,100] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:11,102] [INFO] Found 6/6 markers.
[2024-01-24 14:15:11,130] [INFO] Query marker FASTA was written to GCF_003987045.1_ASM398704v1_genomic.fna/markers.fasta
[2024-01-24 14:15:11,130] [INFO] Task started: Blastn
[2024-01-24 14:15:11,130] [INFO] Running command: blastn -query GCF_003987045.1_ASM398704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29686947-da8f-49ab-a85d-41cb71bbaab2/dqc_reference/reference_markers.fasta -out GCF_003987045.1_ASM398704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:11,976] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:11,979] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:11,980] [INFO] Target genome list was writen to GCF_003987045.1_ASM398704v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:11,988] [INFO] Task started: fastANI
[2024-01-24 14:15:11,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg9221f13d-61ae-4b0a-b0aa-fa082b50a1b4/GCF_003987045.1_ASM398704v1_genomic.fna.gz --refList GCF_003987045.1_ASM398704v1_genomic.fna/target_genomes.txt --output GCF_003987045.1_ASM398704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:22,311] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:22,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29686947-da8f-49ab-a85d-41cb71bbaab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:22,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29686947-da8f-49ab-a85d-41cb71bbaab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:22,320] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:22,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:22,320] [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	100.0	799	799	95	conclusive
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	84.0687	616	799	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	83.6346	634	799	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	81.1025	404	799	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	81.0544	405	799	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	80.9786	440	799	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	80.9511	398	799	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	80.9511	398	799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:22,322] [INFO] DFAST Taxonomy check result was written to GCF_003987045.1_ASM398704v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:22,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:22,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:22,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29686947-da8f-49ab-a85d-41cb71bbaab2/dqc_reference/checkm_data
[2024-01-24 14:15:22,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:22,351] [INFO] Task started: CheckM
[2024-01-24 14:15:22,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987045.1_ASM398704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987045.1_ASM398704v1_genomic.fna/checkm_input GCF_003987045.1_ASM398704v1_genomic.fna/checkm_result
[2024-01-24 14:15:48,660] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:48,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:48,680] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:48,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:48,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987045.1_ASM398704v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:48,681] [INFO] Task started: Blastn
[2024-01-24 14:15:48,681] [INFO] Running command: blastn -query GCF_003987045.1_ASM398704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29686947-da8f-49ab-a85d-41cb71bbaab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987045.1_ASM398704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:49,977] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:49,981] [INFO] Selected 11 target genomes.
[2024-01-24 14:15:49,981] [INFO] Target genome list was writen to GCF_003987045.1_ASM398704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:49,994] [INFO] Task started: fastANI
[2024-01-24 14:15:49,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg9221f13d-61ae-4b0a-b0aa-fa082b50a1b4/GCF_003987045.1_ASM398704v1_genomic.fna.gz --refList GCF_003987045.1_ASM398704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987045.1_ASM398704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:56,267] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:56,277] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:56,278] [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_003987045.1	s__Pseudidiomarina marina	100.0	799	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	conclusive
GCF_009734345.1	s__Pseudidiomarina andamanensis	87.9837	674	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	87.5775	486	799	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	84.0687	616	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	81.1188	403	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	80.9786	440	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418345.1	s__Pseudidiomarina woesei	80.9672	397	799	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	80.5341	390	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	79.8055	198	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:56,279] [INFO] GTDB search result was written to GCF_003987045.1_ASM398704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:56,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:56,283] [INFO] DFAST_QC result json was written to GCF_003987045.1_ASM398704v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:56,283] [INFO] DFAST_QC completed!
[2024-01-24 14:15:56,283] [INFO] Total running time: 0h0m54s