[2023-03-14 11:14:12,736] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,736] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg599d6a9f-1417-4e59-9260-25c7df45dc1b/dqc_reference
[2023-03-14 11:14:14,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,205] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,205] [INFO] Running command: cat /var/lib/cwl/stg78c30ab1-736b-4d7f-90b1-e193a1ce8151/OceanDNA-b41270.fa | prodigal -d OceanDNA-b41270/cds.fna -a OceanDNA-b41270/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:27,860] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:27,861] [INFO] Task started: HMMsearch
[2023-03-14 11:14:27,861] [INFO] Running command: hmmsearch --tblout OceanDNA-b41270/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg599d6a9f-1417-4e59-9260-25c7df45dc1b/dqc_reference/reference_markers.hmm OceanDNA-b41270/protein.faa > /dev/null
[2023-03-14 11:14:28,071] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:28,071] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg78c30ab1-736b-4d7f-90b1-e193a1ce8151/OceanDNA-b41270.fa]
[2023-03-14 11:14:28,087] [INFO] Query marker FASTA was written to OceanDNA-b41270/markers.fasta
[2023-03-14 11:14:28,087] [INFO] Task started: Blastn
[2023-03-14 11:14:28,087] [INFO] Running command: blastn -query OceanDNA-b41270/markers.fasta -db /var/lib/cwl/stg599d6a9f-1417-4e59-9260-25c7df45dc1b/dqc_reference/reference_markers.fasta -out OceanDNA-b41270/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:28,886] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:28,887] [INFO] Selected 12 target genomes.
[2023-03-14 11:14:28,887] [INFO] Target genome list was writen to OceanDNA-b41270/target_genomes.txt
[2023-03-14 11:14:28,897] [INFO] Task started: fastANI
[2023-03-14 11:14:28,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg78c30ab1-736b-4d7f-90b1-e193a1ce8151/OceanDNA-b41270.fa --refList OceanDNA-b41270/target_genomes.txt --output OceanDNA-b41270/fastani_result.tsv --threads 1
[2023-03-14 11:14:43,193] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:43,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg599d6a9f-1417-4e59-9260-25c7df45dc1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:43,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg599d6a9f-1417-4e59-9260-25c7df45dc1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:43,201] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2023-03-14 11:14:43,201] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-14 11:14:43,201] [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 atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	96.7472	690	712	95	inconclusive
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	96.5844	655	712	95	inconclusive
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	96.5483	661	712	95	inconclusive
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	96.4777	674	712	95	inconclusive
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	90.5111	659	712	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	89.3043	660	712	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.9445	656	712	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	83.8452	555	712	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	83.7231	523	712	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_001645105.1	298	298	suspected-type	True	83.7109	533	712	95	below_threshold
Pseudomonas asgharzadehiana	strain=SWRI132	GCA_019139815.1	2842349	2842349	type	True	83.4126	549	712	95	below_threshold
Pseudomonas pisciculturae	strain=P115	GCA_015461805.1	2730413	2730413	type	True	83.2495	556	712	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:43,202] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41270/tc_result.tsv
[2023-03-14 11:14:43,202] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:43,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:43,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg599d6a9f-1417-4e59-9260-25c7df45dc1b/dqc_reference/checkm_data
[2023-03-14 11:14:43,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:43,224] [INFO] Task started: CheckM
[2023-03-14 11:14:43,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41270/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41270/checkm_input OceanDNA-b41270/checkm_result
[2023-03-14 11:15:20,392] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:20,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:20,394] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:20,394] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:20,394] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41270/markers.fasta)
[2023-03-14 11:15:20,395] [INFO] Task started: Blastn
[2023-03-14 11:15:20,395] [INFO] Running command: blastn -query OceanDNA-b41270/markers.fasta -db /var/lib/cwl/stg599d6a9f-1417-4e59-9260-25c7df45dc1b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41270/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:21,706] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:21,706] [INFO] Selected 12 target genomes.
[2023-03-14 11:15:21,707] [INFO] Target genome list was writen to OceanDNA-b41270/target_genomes_gtdb.txt
[2023-03-14 11:15:21,722] [INFO] Task started: fastANI
[2023-03-14 11:15:21,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg78c30ab1-736b-4d7f-90b1-e193a1ce8151/OceanDNA-b41270.fa --refList OceanDNA-b41270/target_genomes_gtdb.txt --output OceanDNA-b41270/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:35,232] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:35,240] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-14 11:15:35,240] [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_004801935.1	s__Pseudomonas_E atacamensis	96.7472	690	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	97.08	95.72	0.92	0.89	59	inconclusive
GCF_001605965.1	s__Pseudomonas_E koreensis_C	95.9384	692	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	98.03	96.36	0.95	0.90	10	inconclusive
GCF_000817895.1	s__Pseudomonas_E fluorescens_AO	94.9301	667	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.16	98.16	0.95	0.95	2	-
GCF_900105805.1	s__Pseudomonas_E moraviensis_A	93.3411	674	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
GCF_002836515.1	s__Pseudomonas_E sp002836515	93.2494	662	712	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_900582195.1	s__Pseudomonas_E sp900582195	89.3102	663	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.42	0.95	0.95	2	-
GCF_000292795.1	s__Pseudomonas_E fluorescens_H	89.044	639	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
GCF_900105325.1	s__Pseudomonas_E marginalis	83.8626	559	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_001269925.1	s__Pseudomonas_E sp001269925	83.6526	555	712	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_015163715.1	s__Pseudomonas_E cyclaminis	83.6474	538	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	95.83	0.83	0.80	14	-
GCF_007858185.1	s__Pseudomonas_E grimontii	83.6242	558	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013778505.1	s__Pseudomonas_E sivasensis	83.2298	561	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.92	98.83	0.93	0.91	13	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:35,241] [INFO] GTDB search result was written to OceanDNA-b41270/result_gtdb.tsv
[2023-03-14 11:15:35,241] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:35,242] [INFO] DFAST_QC result json was written to OceanDNA-b41270/dqc_result.json
[2023-03-14 11:15:35,242] [INFO] DFAST_QC completed!
[2023-03-14 11:15:35,242] [INFO] Total running time: 0h1m23s