[2023-03-18 01:59:39,747] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,748] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg945f117a-a8d1-4bca-9d2b-19b35e0d889c/dqc_reference
[2023-03-18 01:59:40,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,986] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,986] [INFO] Running command: cat /var/lib/cwl/stg993a0a58-8a8f-4941-a580-aa0ef29493f2/OceanDNA-b41237.fa | prodigal -d OceanDNA-b41237/cds.fna -a OceanDNA-b41237/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:53,349] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:53,349] [INFO] Task started: HMMsearch
[2023-03-18 01:59:53,349] [INFO] Running command: hmmsearch --tblout OceanDNA-b41237/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg945f117a-a8d1-4bca-9d2b-19b35e0d889c/dqc_reference/reference_markers.hmm OceanDNA-b41237/protein.faa > /dev/null
[2023-03-18 01:59:53,542] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:53,543] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg993a0a58-8a8f-4941-a580-aa0ef29493f2/OceanDNA-b41237.fa]
[2023-03-18 01:59:53,744] [INFO] Query marker FASTA was written to OceanDNA-b41237/markers.fasta
[2023-03-18 01:59:53,745] [INFO] Task started: Blastn
[2023-03-18 01:59:53,746] [INFO] Running command: blastn -query OceanDNA-b41237/markers.fasta -db /var/lib/cwl/stg945f117a-a8d1-4bca-9d2b-19b35e0d889c/dqc_reference/reference_markers.fasta -out OceanDNA-b41237/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:54,559] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:54,561] [INFO] Selected 27 target genomes.
[2023-03-18 01:59:54,562] [INFO] Target genome list was writen to OceanDNA-b41237/target_genomes.txt
[2023-03-18 01:59:54,589] [INFO] Task started: fastANI
[2023-03-18 01:59:54,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg993a0a58-8a8f-4941-a580-aa0ef29493f2/OceanDNA-b41237.fa --refList OceanDNA-b41237/target_genomes.txt --output OceanDNA-b41237/fastani_result.tsv --threads 1
[2023-03-18 02:00:15,471] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:15,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg945f117a-a8d1-4bca-9d2b-19b35e0d889c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:15,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg945f117a-a8d1-4bca-9d2b-19b35e0d889c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:15,482] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 02:00:15,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 02:00:15,482] [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 juntendi	strain=BML3	GCA_009932375.1	2666183	2666183	type	True	97.9334	314	350	95	conclusive
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	88.3246	304	350	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	88.2695	306	350	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	88.2069	305	350	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	88.0491	310	350	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	88.0403	310	350	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	88.0388	311	350	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	88.0106	312	350	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	87.6783	299	350	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	87.473	294	350	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	86.8379	301	350	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.804	304	350	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	86.7834	293	350	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.7324	302	350	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	86.5091	290	350	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	86.4414	289	350	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.4171	287	350	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	79.5324	126	350	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:00:15,487] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41237/tc_result.tsv
[2023-03-18 02:00:15,494] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:15,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:15,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg945f117a-a8d1-4bca-9d2b-19b35e0d889c/dqc_reference/checkm_data
[2023-03-18 02:00:15,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:15,551] [INFO] Task started: CheckM
[2023-03-18 02:00:15,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41237/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41237/checkm_input OceanDNA-b41237/checkm_result
[2023-03-18 02:00:50,599] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:50,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:50,632] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:50,632] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:50,633] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41237/markers.fasta)
[2023-03-18 02:00:50,634] [INFO] Task started: Blastn
[2023-03-18 02:00:50,634] [INFO] Running command: blastn -query OceanDNA-b41237/markers.fasta -db /var/lib/cwl/stg945f117a-a8d1-4bca-9d2b-19b35e0d889c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41237/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:52,193] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:52,197] [INFO] Selected 27 target genomes.
[2023-03-18 02:00:52,197] [INFO] Target genome list was writen to OceanDNA-b41237/target_genomes_gtdb.txt
[2023-03-18 02:00:52,227] [INFO] Task started: fastANI
[2023-03-18 02:00:52,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg993a0a58-8a8f-4941-a580-aa0ef29493f2/OceanDNA-b41237.fa --refList OceanDNA-b41237/target_genomes_gtdb.txt --output OceanDNA-b41237/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:01:15,284] [INFO] Task succeeded: fastANI
[2023-03-18 02:01:15,299] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:01:15,299] [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_009932375.1	s__Pseudomonas_E juntendi	97.8586	315	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	conclusive
GCF_016658545.1	s__Pseudomonas_E sp016658545	89.0892	309	350	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_001642705.1	s__Pseudomonas_E sp001642705	88.6095	297	350	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_000935045.1	s__Pseudomonas_E sp000935045	88.5901	305	350	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_000708715.2	s__Pseudomonas_E putida_R	88.3373	300	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.68	95.68	0.85	0.85	2	-
GCF_003205205.1	s__Pseudomonas_E sp003205205	88.3025	299	350	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	88.2912	310	350	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	88.2069	305	350	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_013393325.1	s__Pseudomonas_E putida_P	88.1569	306	350	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_015680405.1	s__Pseudomonas_E pudica	88.1254	300	350	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_003331055.1	s__Pseudomonas_E sp003331055	87.9819	302	350	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_002165135.1	s__Pseudomonas_E sp002165135	87.9566	300	350	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_003671955.1	s__Pseudomonas_E hunanensis	87.7993	308	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_002356095.1	s__Pseudomonas_E putida_H	87.72	317	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.35	0.91	0.82	20	-
GCF_012975065.1	s__Pseudomonas_E sp012975065	87.6804	300	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.74	0.94	0.94	3	-
GCF_013179515.1	s__Pseudomonas_E sp013179515	87.4801	296	350	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_013373935.1	s__Pseudomonas_E sp002438125	86.7834	293	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_015680235.1	s__Pseudomonas_E guariconensis_A	85.2129	277	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.73	0.91	0.90	4	-
GCF_900536025.1	s__Pseudomonas_E reidholzensis	85.1406	284	350	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_004214895.1	s__Pseudomonas_E sp004214895	83.4372	248	350	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_007858275.1	s__Pseudomonas_E proteolytica	81.0891	211	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	-
GCF_000802155.2	s__Pseudomonas_E frederiksbergensis_A	80.9783	203	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.21	99.12	0.93	0.92	4	-
GCF_008801475.1	s__Pseudomonas_E moorei	80.7904	204	350	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_003732265.1	s__Pseudomonas_E brassicacearum_D	80.4424	205	350	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_018449655.1	s__Pseudomonas_E sp018449655	80.3392	178	350	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_008041835.1	s__Pseudomonas_E sp002282595	80.3248	156	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_003325755.1	s__Pseudomonas_A sp003325755	78.695	106	350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:01:15,300] [INFO] GTDB search result was written to OceanDNA-b41237/result_gtdb.tsv
[2023-03-18 02:01:15,303] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:01:15,308] [INFO] DFAST_QC result json was written to OceanDNA-b41237/dqc_result.json
[2023-03-18 02:01:15,308] [INFO] DFAST_QC completed!
[2023-03-18 02:01:15,308] [INFO] Total running time: 0h1m36s