[2023-03-15 23:56:02,561] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:56:02,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:56:02,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg75ef1e16-002e-4e20-b237-cdd9bbbe6a90/dqc_reference
[2023-03-15 23:56:03,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:56:03,685] [INFO] Task started: Prodigal
[2023-03-15 23:56:03,685] [INFO] Running command: cat /var/lib/cwl/stg3aa630bc-dac3-49ce-81d9-57af29ab2825/OceanDNA-b41313.fa | prodigal -d OceanDNA-b41313/cds.fna -a OceanDNA-b41313/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:56:32,824] [INFO] Task succeeded: Prodigal
[2023-03-15 23:56:32,824] [INFO] Task started: HMMsearch
[2023-03-15 23:56:32,824] [INFO] Running command: hmmsearch --tblout OceanDNA-b41313/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75ef1e16-002e-4e20-b237-cdd9bbbe6a90/dqc_reference/reference_markers.hmm OceanDNA-b41313/protein.faa > /dev/null
[2023-03-15 23:56:33,051] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:56:33,052] [INFO] Found 6/6 markers.
[2023-03-15 23:56:33,080] [INFO] Query marker FASTA was written to OceanDNA-b41313/markers.fasta
[2023-03-15 23:56:33,081] [INFO] Task started: Blastn
[2023-03-15 23:56:33,081] [INFO] Running command: blastn -query OceanDNA-b41313/markers.fasta -db /var/lib/cwl/stg75ef1e16-002e-4e20-b237-cdd9bbbe6a90/dqc_reference/reference_markers.fasta -out OceanDNA-b41313/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:56:33,888] [INFO] Task succeeded: Blastn
[2023-03-15 23:56:33,889] [INFO] Selected 18 target genomes.
[2023-03-15 23:56:33,889] [INFO] Target genome list was writen to OceanDNA-b41313/target_genomes.txt
[2023-03-15 23:56:33,925] [INFO] Task started: fastANI
[2023-03-15 23:56:33,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aa630bc-dac3-49ce-81d9-57af29ab2825/OceanDNA-b41313.fa --refList OceanDNA-b41313/target_genomes.txt --output OceanDNA-b41313/fastani_result.tsv --threads 1
[2023-03-15 23:56:53,547] [INFO] Task succeeded: fastANI
[2023-03-15 23:56:53,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75ef1e16-002e-4e20-b237-cdd9bbbe6a90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:56:53,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75ef1e16-002e-4e20-b237-cdd9bbbe6a90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:56:53,558] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:56:53,558] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:56:53,558] [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 benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	85.2748	1131	1511	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	84.7949	1063	1511	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	84.6799	1051	1511	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.2567	990	1511	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	83.9188	956	1511	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	83.8573	970	1511	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	83.364	1041	1511	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	82.7998	850	1511	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	82.7353	974	1511	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.7326	995	1511	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.5917	909	1511	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	82.0045	870	1511	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	81.9364	812	1511	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	81.9078	824	1511	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	81.8529	945	1511	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	81.4851	778	1511	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	81.2346	689	1511	95	below_threshold
Pseudomonas guariconensis	strain=LMG 27394	GCA_900102675.1	1288410	1288410	suspected-type	True	79.9985	638	1511	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:56:53,622] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41313/tc_result.tsv
[2023-03-15 23:56:53,624] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:56:53,624] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:56:53,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75ef1e16-002e-4e20-b237-cdd9bbbe6a90/dqc_reference/checkm_data
[2023-03-15 23:56:53,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:56:53,643] [INFO] Task started: CheckM
[2023-03-15 23:56:53,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41313/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41313/checkm_input OceanDNA-b41313/checkm_result
[2023-03-15 23:58:03,665] [INFO] Task succeeded: CheckM
[2023-03-15 23:58:03,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:58:03,671] [INFO] ===== Completeness check finished =====
[2023-03-15 23:58:03,671] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:58:03,671] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41313/markers.fasta)
[2023-03-15 23:58:03,673] [INFO] Task started: Blastn
[2023-03-15 23:58:03,673] [INFO] Running command: blastn -query OceanDNA-b41313/markers.fasta -db /var/lib/cwl/stg75ef1e16-002e-4e20-b237-cdd9bbbe6a90/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41313/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:58:05,046] [INFO] Task succeeded: Blastn
[2023-03-15 23:58:05,047] [INFO] Selected 22 target genomes.
[2023-03-15 23:58:05,047] [INFO] Target genome list was writen to OceanDNA-b41313/target_genomes_gtdb.txt
[2023-03-15 23:58:05,060] [INFO] Task started: fastANI
[2023-03-15 23:58:05,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aa630bc-dac3-49ce-81d9-57af29ab2825/OceanDNA-b41313.fa --refList OceanDNA-b41313/target_genomes_gtdb.txt --output OceanDNA-b41313/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:58:28,751] [INFO] Task succeeded: fastANI
[2023-03-15 23:58:28,763] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:58:28,763] [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
GCA_002354655.1	s__Pseudomonas_E sp002354655	99.9771	1484	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	conclusive
GCF_900100495.1	s__Pseudomonas_E benzenivorans	85.2602	1132	1511	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	84.7758	1065	1511	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_900115555.1	s__Pseudomonas_E borbori	84.6839	1052	1511	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_002840155.1	s__Pseudomonas_E sp002840155	84.5997	1013	1511	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_002025205.1	s__Pseudomonas_E sp002025205	83.9674	1023	1511	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_900099645.1	s__Pseudomonas_E peli	83.8573	970	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_900105355.1	s__Pseudomonas_E anguilliseptica	83.7776	961	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCF_007993865.1	s__Pseudomonas_E sp007993865	83.6658	1074	1511	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_018827205.1	s__Pseudomonas_E sp018827205	83.3896	853	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_000498575.2	s__Pseudomonas_E taeanensis	83.3685	1042	1511	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_009763245.1	s__Pseudomonas_E sp009763245	83.226	860	1511	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_902506505.1	s__Pseudomonas_E sp902506505	83.0997	893	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	83.0956	801	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	82.4882	845	1511	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_000213805.1	s__Pseudomonas_E fulva_B	82.0384	819	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_900112645.1	s__Pseudomonas_E straminea	81.7253	804	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.94	0.94	2	-
GCF_001945395.1	s__Pseudomonas_E sp001945395	81.6082	813	1511	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_013408425.1	s__Pseudomonas_E fulva_A	81.5194	803	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	99.00	0.95	0.95	2	-
GCF_900102335.1	s__Pseudomonas_E seleniipraecipitans	81.3626	729	1511	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_902506535.1	s__Pseudomonas_E sp902506535	81.2949	818	1511	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_002286785.1	s__Pseudomonas_M sp002286785	81.2631	897	1511	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:58:28,765] [INFO] GTDB search result was written to OceanDNA-b41313/result_gtdb.tsv
[2023-03-15 23:58:28,765] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:58:28,769] [INFO] DFAST_QC result json was written to OceanDNA-b41313/dqc_result.json
[2023-03-15 23:58:28,769] [INFO] DFAST_QC completed!
[2023-03-15 23:58:28,769] [INFO] Total running time: 0h2m26s