[2023-03-18 23:17:05,019] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:17:05,019] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:17:05,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5ca341a-f84f-490a-8ceb-749b6338cf7b/dqc_reference
[2023-03-18 23:17:06,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:17:06,107] [INFO] Task started: Prodigal
[2023-03-18 23:17:06,107] [INFO] Running command: cat /var/lib/cwl/stgd7993540-d779-4089-ac0e-97f2f2d2ffb3/OceanDNA-b41272.fa | prodigal -d OceanDNA-b41272/cds.fna -a OceanDNA-b41272/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:17:35,482] [INFO] Task succeeded: Prodigal
[2023-03-18 23:17:35,482] [INFO] Task started: HMMsearch
[2023-03-18 23:17:35,482] [INFO] Running command: hmmsearch --tblout OceanDNA-b41272/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5ca341a-f84f-490a-8ceb-749b6338cf7b/dqc_reference/reference_markers.hmm OceanDNA-b41272/protein.faa > /dev/null
[2023-03-18 23:17:35,705] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:17:35,705] [INFO] Found 6/6 markers.
[2023-03-18 23:17:35,732] [INFO] Query marker FASTA was written to OceanDNA-b41272/markers.fasta
[2023-03-18 23:17:35,733] [INFO] Task started: Blastn
[2023-03-18 23:17:35,734] [INFO] Running command: blastn -query OceanDNA-b41272/markers.fasta -db /var/lib/cwl/stgb5ca341a-f84f-490a-8ceb-749b6338cf7b/dqc_reference/reference_markers.fasta -out OceanDNA-b41272/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:17:36,768] [INFO] Task succeeded: Blastn
[2023-03-18 23:17:36,769] [INFO] Selected 21 target genomes.
[2023-03-18 23:17:36,770] [INFO] Target genome list was writen to OceanDNA-b41272/target_genomes.txt
[2023-03-18 23:17:36,795] [INFO] Task started: fastANI
[2023-03-18 23:17:36,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7993540-d779-4089-ac0e-97f2f2d2ffb3/OceanDNA-b41272.fa --refList OceanDNA-b41272/target_genomes.txt --output OceanDNA-b41272/fastani_result.tsv --threads 1
[2023-03-18 23:17:56,541] [INFO] Task succeeded: fastANI
[2023-03-18 23:17:56,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5ca341a-f84f-490a-8ceb-749b6338cf7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:17:56,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5ca341a-f84f-490a-8ceb-749b6338cf7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:17:56,606] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:17:56,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:17:56,607] [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
Pseudomonas marincola	strain=JCM 14761	GCA_900116605.1	437900	437900	type	True	97.6531	1414	1516	95	conclusive
Pseudomonas segetis	strain=CIP 108523	GCA_900188155.1	298908	298908	type	True	80.0269	700	1516	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	79.9195	660	1516	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	79.5302	681	1516	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	79.5243	632	1516	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	79.5195	685	1516	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	79.3087	597	1516	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	79.1942	630	1516	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	79.1616	533	1516	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	79.0747	543	1516	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	79.0735	540	1516	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	79.0529	542	1516	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	79.0445	582	1516	95	below_threshold
Pseudomonas punonensis	strain=CECT 8089	GCA_900142655.1	1220495	1220495	type	True	79.0172	560	1516	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	78.7976	526	1516	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	78.7859	500	1516	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.7218	568	1516	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	78.677	446	1516	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	78.6522	508	1516	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	78.6224	508	1516	95	below_threshold
Pseudomonas trivialis	strain=DSM 14937	GCA_001439805.1	200450	200450	type	True	78.5888	471	1516	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:17:56,607] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41272/tc_result.tsv
[2023-03-18 23:17:56,607] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:17:56,608] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:17:56,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5ca341a-f84f-490a-8ceb-749b6338cf7b/dqc_reference/checkm_data
[2023-03-18 23:17:56,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:17:56,614] [INFO] Task started: CheckM
[2023-03-18 23:17:56,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41272/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41272/checkm_input OceanDNA-b41272/checkm_result
[2023-03-18 23:19:10,415] [INFO] Task succeeded: CheckM
[2023-03-18 23:19:10,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:19:10,418] [INFO] ===== Completeness check finished =====
[2023-03-18 23:19:10,418] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:19:10,418] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41272/markers.fasta)
[2023-03-18 23:19:10,419] [INFO] Task started: Blastn
[2023-03-18 23:19:10,420] [INFO] Running command: blastn -query OceanDNA-b41272/markers.fasta -db /var/lib/cwl/stgb5ca341a-f84f-490a-8ceb-749b6338cf7b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41272/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:19:12,036] [INFO] Task succeeded: Blastn
[2023-03-18 23:19:12,037] [INFO] Selected 23 target genomes.
[2023-03-18 23:19:12,037] [INFO] Target genome list was writen to OceanDNA-b41272/target_genomes_gtdb.txt
[2023-03-18 23:19:12,295] [INFO] Task started: fastANI
[2023-03-18 23:19:12,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7993540-d779-4089-ac0e-97f2f2d2ffb3/OceanDNA-b41272.fa --refList OceanDNA-b41272/target_genomes_gtdb.txt --output OceanDNA-b41272/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:19:34,308] [INFO] Task succeeded: fastANI
[2023-03-18 23:19:34,321] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:19:34,321] [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_900116605.1	s__Pseudomonas_E marincola	97.6531	1414	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.48	97.31	0.90	0.86	9	conclusive
GCF_002163625.1	s__Pseudomonas_E sp002163625	80.0978	628	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188155.1	s__Pseudomonas_E segetis	80.0237	700	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.92	98.92	0.93	0.93	2	-
GCF_900115555.1	s__Pseudomonas_E borbori	79.9194	660	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	79.9063	726	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCA_002840155.1	s__Pseudomonas_E sp002840155	79.8992	683	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993865.1	s__Pseudomonas_E sp007993865	79.5802	637	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498575.2	s__Pseudomonas_E taeanensis	79.54	630	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184545.1	s__Pseudomonas_E sp013184545	79.5181	685	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	79.5152	682	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567565.1	s__Pseudomonas_E composti_A	79.2954	612	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	79.1943	630	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_003253735.1	s__Pseudomonas_E sp003253735	79.1055	559	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.17	0.95	0.95	2	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	79.0524	581	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327355.1	s__Pseudomonas_E dryadis	79.0078	596	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	79.0019	558	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142655.1	s__Pseudomonas_E punonensis	78.9914	562	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102335.1	s__Pseudomonas_E seleniipraecipitans	78.9875	528	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.05	0.91	0.90	3	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	78.7192	569	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000397205.1	s__Pseudomonas_E protegens	78.6557	507	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	-
GCF_002304225.1	s__Pseudomonas_E sp002304225	78.5887	456	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
GCF_009905615.1	s__Pseudomonas_E sp009905615	78.564	436	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353925.1	s__Pseudomonas_E sp004353925	78.4578	470	1516	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:19:34,321] [INFO] GTDB search result was written to OceanDNA-b41272/result_gtdb.tsv
[2023-03-18 23:19:34,322] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:19:34,324] [INFO] DFAST_QC result json was written to OceanDNA-b41272/dqc_result.json
[2023-03-18 23:19:34,324] [INFO] DFAST_QC completed!
[2023-03-18 23:19:34,324] [INFO] Total running time: 0h2m29s