[2023-03-16 18:27:01,717] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:27:01,717] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:27:01,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg1451a4d7-d642-4d74-8231-ea9dfa7c6dd1/dqc_reference
[2023-03-16 18:27:02,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:27:02,832] [INFO] Task started: Prodigal
[2023-03-16 18:27:02,832] [INFO] Running command: cat /var/lib/cwl/stg9d916afb-c7b7-4c79-9dd1-a57a26ff0161/OceanDNA-b41273.fa | prodigal -d OceanDNA-b41273/cds.fna -a OceanDNA-b41273/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:27:27,194] [INFO] Task succeeded: Prodigal
[2023-03-16 18:27:27,194] [INFO] Task started: HMMsearch
[2023-03-16 18:27:27,194] [INFO] Running command: hmmsearch --tblout OceanDNA-b41273/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1451a4d7-d642-4d74-8231-ea9dfa7c6dd1/dqc_reference/reference_markers.hmm OceanDNA-b41273/protein.faa > /dev/null
[2023-03-16 18:27:27,650] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:27:27,651] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9d916afb-c7b7-4c79-9dd1-a57a26ff0161/OceanDNA-b41273.fa]
[2023-03-16 18:27:27,668] [INFO] Query marker FASTA was written to OceanDNA-b41273/markers.fasta
[2023-03-16 18:27:27,668] [INFO] Task started: Blastn
[2023-03-16 18:27:27,668] [INFO] Running command: blastn -query OceanDNA-b41273/markers.fasta -db /var/lib/cwl/stg1451a4d7-d642-4d74-8231-ea9dfa7c6dd1/dqc_reference/reference_markers.fasta -out OceanDNA-b41273/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:27:29,541] [INFO] Task succeeded: Blastn
[2023-03-16 18:27:29,542] [INFO] Selected 21 target genomes.
[2023-03-16 18:27:29,542] [INFO] Target genome list was writen to OceanDNA-b41273/target_genomes.txt
[2023-03-16 18:27:29,552] [INFO] Task started: fastANI
[2023-03-16 18:27:29,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d916afb-c7b7-4c79-9dd1-a57a26ff0161/OceanDNA-b41273.fa --refList OceanDNA-b41273/target_genomes.txt --output OceanDNA-b41273/fastani_result.tsv --threads 1
[2023-03-16 18:27:52,639] [INFO] Task succeeded: fastANI
[2023-03-16 18:27:52,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1451a4d7-d642-4d74-8231-ea9dfa7c6dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:27:52,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1451a4d7-d642-4d74-8231-ea9dfa7c6dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:27:52,649] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 18:27:52,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 18:27:52,649] [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 monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	99.5119	748	758	95	conclusive
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	99.5113	742	758	95	conclusive
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	91.8297	696	758	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	91.7865	708	758	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	91.7703	716	758	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	91.1408	709	758	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	90.1885	704	758	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	90.0944	688	758	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	88.9959	671	758	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	88.9712	653	758	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	88.7597	663	758	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	88.7347	681	758	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	88.5493	676	758	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	88.462	665	758	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	86.9686	632	758	95	below_threshold
Pseudomonas parafulva	strain=NBRC 16636	GCA_000730645.1	157782	157782	suspected-type	True	86.9625	622	758	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:27:52,650] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41273/tc_result.tsv
[2023-03-16 18:27:52,650] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:27:52,650] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:27:52,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1451a4d7-d642-4d74-8231-ea9dfa7c6dd1/dqc_reference/checkm_data
[2023-03-16 18:27:52,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:27:52,655] [INFO] Task started: CheckM
[2023-03-16 18:27:52,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41273/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41273/checkm_input OceanDNA-b41273/checkm_result
[2023-03-16 18:28:39,712] [INFO] Task succeeded: CheckM
[2023-03-16 18:28:39,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:28:39,715] [INFO] ===== Completeness check finished =====
[2023-03-16 18:28:39,715] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:28:39,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41273/markers.fasta)
[2023-03-16 18:28:39,715] [INFO] Task started: Blastn
[2023-03-16 18:28:39,716] [INFO] Running command: blastn -query OceanDNA-b41273/markers.fasta -db /var/lib/cwl/stg1451a4d7-d642-4d74-8231-ea9dfa7c6dd1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41273/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:28:41,174] [INFO] Task succeeded: Blastn
[2023-03-16 18:28:41,174] [INFO] Selected 18 target genomes.
[2023-03-16 18:28:41,175] [INFO] Target genome list was writen to OceanDNA-b41273/target_genomes_gtdb.txt
[2023-03-16 18:28:41,185] [INFO] Task started: fastANI
[2023-03-16 18:28:41,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d916afb-c7b7-4c79-9dd1-a57a26ff0161/OceanDNA-b41273.fa --refList OceanDNA-b41273/target_genomes_gtdb.txt --output OceanDNA-b41273/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:29:05,152] [INFO] Task succeeded: fastANI
[2023-03-16 18:29:05,163] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:29:05,164] [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_000730605.1	s__Pseudomonas_E monteilii	99.5113	742	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	conclusive
GCF_001642705.1	s__Pseudomonas_E sp001642705	91.5969	706	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_013393325.1	s__Pseudomonas_E putida_P	91.5773	721	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	99.27	0.91	0.82	10	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	91.2932	693	758	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_016658545.1	s__Pseudomonas_E sp016658545	91.2474	688	758	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_009932335.1	s__Pseudomonas_E asiatica	91.1577	714	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_900277125.1	s__Pseudomonas_E inefficax	91.1408	709	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_015680405.1	s__Pseudomonas_E pudica	91.128	699	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_002113165.1	s__Pseudomonas_E sp002113165	91.0165	705	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	90.9926	696	758	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_003331055.1	s__Pseudomonas_E sp003331055	90.7428	670	758	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_003205205.1	s__Pseudomonas_E sp003205205	90.5348	687	758	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_013179515.1	s__Pseudomonas_E sp013179515	90.1363	625	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_003097235.1	s__Pseudomonas_E sp003097235	89.0645	693	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009391885.1	s__Pseudomonas_E sp009391885	88.9881	681	758	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_005080685.1	s__Pseudomonas_E putida_V	87.7405	672	758	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_000621225.1	s__Pseudomonas_E mosselii	87.1571	663	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_003231275.1	s__Pseudomonas_E huaxiensis	84.0981	606	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:29:05,164] [INFO] GTDB search result was written to OceanDNA-b41273/result_gtdb.tsv
[2023-03-16 18:29:05,164] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:29:05,171] [INFO] DFAST_QC result json was written to OceanDNA-b41273/dqc_result.json
[2023-03-16 18:29:05,171] [INFO] DFAST_QC completed!
[2023-03-16 18:29:05,173] [INFO] Total running time: 0h2m3s