[2023-03-15 14:47:21,424] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:47:21,428] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:47:21,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg727dc464-1eaf-4933-8ff0-38c236c6568d/dqc_reference
[2023-03-15 14:47:22,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:47:22,552] [INFO] Task started: Prodigal
[2023-03-15 14:47:22,552] [INFO] Running command: cat /var/lib/cwl/stgdc8badb2-cfae-4c67-b871-6af0417242b2/OceanDNA-b41315.fa | prodigal -d OceanDNA-b41315/cds.fna -a OceanDNA-b41315/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:47:27,039] [INFO] Task succeeded: Prodigal
[2023-03-15 14:47:27,039] [INFO] Task started: HMMsearch
[2023-03-15 14:47:27,039] [INFO] Running command: hmmsearch --tblout OceanDNA-b41315/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg727dc464-1eaf-4933-8ff0-38c236c6568d/dqc_reference/reference_markers.hmm OceanDNA-b41315/protein.faa > /dev/null
[2023-03-15 14:47:27,166] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:47:27,166] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdc8badb2-cfae-4c67-b871-6af0417242b2/OceanDNA-b41315.fa]
[2023-03-15 14:47:27,203] [INFO] Query marker FASTA was written to OceanDNA-b41315/markers.fasta
[2023-03-15 14:47:27,205] [INFO] Task started: Blastn
[2023-03-15 14:47:27,205] [INFO] Running command: blastn -query OceanDNA-b41315/markers.fasta -db /var/lib/cwl/stg727dc464-1eaf-4933-8ff0-38c236c6568d/dqc_reference/reference_markers.fasta -out OceanDNA-b41315/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:27,730] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:27,741] [INFO] Selected 10 target genomes.
[2023-03-15 14:47:27,742] [INFO] Target genome list was writen to OceanDNA-b41315/target_genomes.txt
[2023-03-15 14:47:27,748] [INFO] Task started: fastANI
[2023-03-15 14:47:27,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc8badb2-cfae-4c67-b871-6af0417242b2/OceanDNA-b41315.fa --refList OceanDNA-b41315/target_genomes.txt --output OceanDNA-b41315/fastani_result.tsv --threads 1
[2023-03-15 14:47:36,811] [INFO] Task succeeded: fastANI
[2023-03-15 14:47:36,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg727dc464-1eaf-4933-8ff0-38c236c6568d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:47:36,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg727dc464-1eaf-4933-8ff0-38c236c6568d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:47:36,818] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2023-03-15 14:47:36,818] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-15 14:47:36,819] [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 paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	97.6302	199	202	95	inconclusive
Pseudomonas lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	96.1079	199	202	95	inconclusive
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	95.8447	198	202	95	inconclusive
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	92.0389	198	202	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	90.3213	193	202	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	90.2999	193	202	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	90.2817	190	202	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	90.0351	193	202	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	88.1025	194	202	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	87.3006	184	202	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:47:36,823] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41315/tc_result.tsv
[2023-03-15 14:47:36,830] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:47:36,830] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:47:36,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg727dc464-1eaf-4933-8ff0-38c236c6568d/dqc_reference/checkm_data
[2023-03-15 14:47:36,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:47:36,929] [INFO] Task started: CheckM
[2023-03-15 14:47:36,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41315/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41315/checkm_input OceanDNA-b41315/checkm_result
[2023-03-15 14:47:54,124] [INFO] Task succeeded: CheckM
[2023-03-15 14:47:54,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:47:54,229] [INFO] ===== Completeness check finished =====
[2023-03-15 14:47:54,229] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:47:54,229] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41315/markers.fasta)
[2023-03-15 14:47:54,230] [INFO] Task started: Blastn
[2023-03-15 14:47:54,230] [INFO] Running command: blastn -query OceanDNA-b41315/markers.fasta -db /var/lib/cwl/stg727dc464-1eaf-4933-8ff0-38c236c6568d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41315/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:55,020] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:55,034] [INFO] Selected 9 target genomes.
[2023-03-15 14:47:55,034] [INFO] Target genome list was writen to OceanDNA-b41315/target_genomes_gtdb.txt
[2023-03-15 14:47:55,089] [INFO] Task started: fastANI
[2023-03-15 14:47:55,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc8badb2-cfae-4c67-b871-6af0417242b2/OceanDNA-b41315.fa --refList OceanDNA-b41315/target_genomes_gtdb.txt --output OceanDNA-b41315/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:48:03,410] [INFO] Task succeeded: fastANI
[2023-03-15 14:48:03,416] [INFO] Found 9 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-15 14:48:03,416] [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_904063055.1	s__Pseudomonas_E paracarnis	97.6302	199	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	95.59	0.90	0.84	86	inconclusive
GCF_001902145.1	s__Pseudomonas_E fluorescens_BV	96.3711	200	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.76	95.23	0.87	0.84	22	inconclusive
GCF_001439845.1	s__Pseudomonas_E lactis	96.1079	199	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	inconclusive
GCF_000263715.2	s__Pseudomonas_E synxantha_A	92.2739	196	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_009659625.1	s__Pseudomonas_E haemolytica	92.0615	196	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	-
GCF_900105675.1	s__Pseudomonas_E synxantha	91.7338	197	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
GCF_003851495.1	s__Pseudomonas_E fluorescens_BB	91.7014	197	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3929	98.85	97.70	0.94	0.89	3	-
GCF_002934065.1	s__Pseudomonas_E orientalis_A	90.4684	191	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.15	95.96	0.86	0.83	21	-
GCF_002563895.1	s__Pseudomonas_E lurida	90.2817	190	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
--------------------------------------------------------------------------------
[2023-03-15 14:48:03,417] [INFO] GTDB search result was written to OceanDNA-b41315/result_gtdb.tsv
[2023-03-15 14:48:03,422] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:48:03,427] [INFO] DFAST_QC result json was written to OceanDNA-b41315/dqc_result.json
[2023-03-15 14:48:03,427] [INFO] DFAST_QC completed!
[2023-03-15 14:48:03,427] [INFO] Total running time: 0h0m42s