[2023-03-15 09:48:16,565] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,565] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cb5c99b-4e34-4647-93ad-9d9bb51dec21/dqc_reference
[2023-03-15 09:48:18,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,228] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,229] [INFO] Running command: cat /var/lib/cwl/stg615d4222-c514-440f-8c11-531dc21cd822/OceanDNA-b37592.fa | prodigal -d OceanDNA-b37592/cds.fna -a OceanDNA-b37592/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:43,141] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:43,141] [INFO] Task started: HMMsearch
[2023-03-15 09:48:43,141] [INFO] Running command: hmmsearch --tblout OceanDNA-b37592/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cb5c99b-4e34-4647-93ad-9d9bb51dec21/dqc_reference/reference_markers.hmm OceanDNA-b37592/protein.faa > /dev/null
[2023-03-15 09:48:43,350] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:43,350] [INFO] Found 6/6 markers.
[2023-03-15 09:48:43,371] [INFO] Query marker FASTA was written to OceanDNA-b37592/markers.fasta
[2023-03-15 09:48:43,372] [INFO] Task started: Blastn
[2023-03-15 09:48:43,372] [INFO] Running command: blastn -query OceanDNA-b37592/markers.fasta -db /var/lib/cwl/stg8cb5c99b-4e34-4647-93ad-9d9bb51dec21/dqc_reference/reference_markers.fasta -out OceanDNA-b37592/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:44,035] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:44,036] [INFO] Selected 27 target genomes.
[2023-03-15 09:48:44,036] [INFO] Target genome list was writen to OceanDNA-b37592/target_genomes.txt
[2023-03-15 09:48:44,052] [INFO] Task started: fastANI
[2023-03-15 09:48:44,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg615d4222-c514-440f-8c11-531dc21cd822/OceanDNA-b37592.fa --refList OceanDNA-b37592/target_genomes.txt --output OceanDNA-b37592/fastani_result.tsv --threads 1
[2023-03-15 09:49:02,161] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:02,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cb5c99b-4e34-4647-93ad-9d9bb51dec21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:49:02,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cb5c99b-4e34-4647-93ad-9d9bb51dec21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:49:02,170] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:49:02,171] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:49:02,171] [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
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.0835	223	1308	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.8888	185	1308	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.8607	195	1308	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.851	193	1308	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.8103	161	1308	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.7274	154	1308	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.6832	159	1308	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.6768	164	1308	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.6661	130	1308	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.6507	165	1308	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	76.6388	110	1308	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	75.7906	92	1308	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	75.3204	50	1308	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.3033	56	1308	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.2937	55	1308	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:49:02,171] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37592/tc_result.tsv
[2023-03-15 09:49:02,171] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:49:02,171] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:49:02,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cb5c99b-4e34-4647-93ad-9d9bb51dec21/dqc_reference/checkm_data
[2023-03-15 09:49:02,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:49:02,224] [INFO] Task started: CheckM
[2023-03-15 09:49:02,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37592/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37592/checkm_input OceanDNA-b37592/checkm_result
[2023-03-15 09:50:03,364] [INFO] Task succeeded: CheckM
[2023-03-15 09:50:03,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:50:03,367] [INFO] ===== Completeness check finished =====
[2023-03-15 09:50:03,367] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:50:03,368] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37592/markers.fasta)
[2023-03-15 09:50:03,369] [INFO] Task started: Blastn
[2023-03-15 09:50:03,369] [INFO] Running command: blastn -query OceanDNA-b37592/markers.fasta -db /var/lib/cwl/stg8cb5c99b-4e34-4647-93ad-9d9bb51dec21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37592/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:50:04,496] [INFO] Task succeeded: Blastn
[2023-03-15 09:50:04,497] [INFO] Selected 26 target genomes.
[2023-03-15 09:50:04,497] [INFO] Target genome list was writen to OceanDNA-b37592/target_genomes_gtdb.txt
[2023-03-15 09:50:04,819] [INFO] Task started: fastANI
[2023-03-15 09:50:04,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg615d4222-c514-440f-8c11-531dc21cd822/OceanDNA-b37592.fa --refList OceanDNA-b37592/target_genomes_gtdb.txt --output OceanDNA-b37592/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:50:21,608] [INFO] Task succeeded: fastANI
[2023-03-15 09:50:21,620] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:50:21,620] [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_003402235.1	s__Parahaliea mediterranea	77.0958	222	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.0208	193	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646415.1	s__Halioglobus sp003646415	77.0206	146	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.0051	222	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	76.9434	214	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	76.9025	184	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	76.8744	193	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	76.8652	197	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	76.864	192	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.8552	180	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.8377	212	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002416125.1	s__Haliea sp002416125	76.7766	161	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_010669285.1	s__Kineobactrum salinum	76.7305	154	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000156295.1	s__Halioglobus sp000156295	76.7171	94	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.94	98.78	0.94	0.91	6	-
GCA_002414665.1	s__Haliea sp002414665	76.7086	148	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCF_001983995.1	s__Halioglobus japonicus	76.691	163	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_009388985.1	s__Halioglobus maricola	76.6619	129	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705825.1	s__Halioglobus japonicus_A	76.6439	155	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.6342	159	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480565.1	s__Halioglobus sp905480565	76.5278	62	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764025.1	s__Pseudohaliea rubra	75.7498	92	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:50:21,620] [INFO] GTDB search result was written to OceanDNA-b37592/result_gtdb.tsv
[2023-03-15 09:50:21,620] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:50:21,622] [INFO] DFAST_QC result json was written to OceanDNA-b37592/dqc_result.json
[2023-03-15 09:50:21,622] [INFO] DFAST_QC completed!
[2023-03-15 09:50:21,623] [INFO] Total running time: 0h2m5s