[2023-03-16 09:13:21,233] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:13:21,248] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:13:21,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b56cccb-9177-4ce1-bcf2-62481bc296c4/dqc_reference
[2023-03-16 09:13:22,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:13:22,472] [INFO] Task started: Prodigal
[2023-03-16 09:13:22,473] [INFO] Running command: cat /var/lib/cwl/stgb65e6d8e-7225-4ef1-9c21-d618c1e1cc4a/OceanDNA-b37602.fa | prodigal -d OceanDNA-b37602/cds.fna -a OceanDNA-b37602/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:13:51,151] [INFO] Task succeeded: Prodigal
[2023-03-16 09:13:51,151] [INFO] Task started: HMMsearch
[2023-03-16 09:13:51,151] [INFO] Running command: hmmsearch --tblout OceanDNA-b37602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b56cccb-9177-4ce1-bcf2-62481bc296c4/dqc_reference/reference_markers.hmm OceanDNA-b37602/protein.faa > /dev/null
[2023-03-16 09:13:51,387] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:13:51,387] [INFO] Found 6/6 markers.
[2023-03-16 09:13:51,514] [INFO] Query marker FASTA was written to OceanDNA-b37602/markers.fasta
[2023-03-16 09:13:51,515] [INFO] Task started: Blastn
[2023-03-16 09:13:51,515] [INFO] Running command: blastn -query OceanDNA-b37602/markers.fasta -db /var/lib/cwl/stg9b56cccb-9177-4ce1-bcf2-62481bc296c4/dqc_reference/reference_markers.fasta -out OceanDNA-b37602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:13:52,181] [INFO] Task succeeded: Blastn
[2023-03-16 09:13:52,210] [INFO] Selected 26 target genomes.
[2023-03-16 09:13:52,210] [INFO] Target genome list was writen to OceanDNA-b37602/target_genomes.txt
[2023-03-16 09:13:52,221] [INFO] Task started: fastANI
[2023-03-16 09:13:52,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgb65e6d8e-7225-4ef1-9c21-d618c1e1cc4a/OceanDNA-b37602.fa --refList OceanDNA-b37602/target_genomes.txt --output OceanDNA-b37602/fastani_result.tsv --threads 1
[2023-03-16 09:14:08,699] [INFO] Task succeeded: fastANI
[2023-03-16 09:14:08,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b56cccb-9177-4ce1-bcf2-62481bc296c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:14:08,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b56cccb-9177-4ce1-bcf2-62481bc296c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:14:08,710] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:14:08,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:14:08,710] [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	78.2925	219	1529	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.1472	139	1529	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.1199	199	1529	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.0734	135	1529	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	77.0702	140	1529	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.0461	181	1529	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.9521	208	1529	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.9286	160	1529	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.8744	137	1529	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	76.7361	137	1529	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.6756	138	1529	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	76.6326	144	1529	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	75.8921	60	1529	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	75.7516	53	1529	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.2972	52	1529	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.2903	51	1529	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.1006	50	1529	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	75.0542	53	1529	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:14:08,723] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37602/tc_result.tsv
[2023-03-16 09:14:08,737] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:14:08,737] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:14:08,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b56cccb-9177-4ce1-bcf2-62481bc296c4/dqc_reference/checkm_data
[2023-03-16 09:14:08,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:14:08,763] [INFO] Task started: CheckM
[2023-03-16 09:14:08,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37602/checkm_input OceanDNA-b37602/checkm_result
[2023-03-16 09:15:17,769] [INFO] Task succeeded: CheckM
[2023-03-16 09:15:17,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:15:17,833] [INFO] ===== Completeness check finished =====
[2023-03-16 09:15:17,833] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:15:17,833] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37602/markers.fasta)
[2023-03-16 09:15:17,835] [INFO] Task started: Blastn
[2023-03-16 09:15:17,835] [INFO] Running command: blastn -query OceanDNA-b37602/markers.fasta -db /var/lib/cwl/stg9b56cccb-9177-4ce1-bcf2-62481bc296c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:15:18,895] [INFO] Task succeeded: Blastn
[2023-03-16 09:15:18,910] [INFO] Selected 23 target genomes.
[2023-03-16 09:15:18,911] [INFO] Target genome list was writen to OceanDNA-b37602/target_genomes_gtdb.txt
[2023-03-16 09:15:18,958] [INFO] Task started: fastANI
[2023-03-16 09:15:18,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgb65e6d8e-7225-4ef1-9c21-d618c1e1cc4a/OceanDNA-b37602.fa --refList OceanDNA-b37602/target_genomes_gtdb.txt --output OceanDNA-b37602/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:15:34,469] [INFO] Task succeeded: fastANI
[2023-03-16 09:15:34,480] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:15:34,481] [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	78.2925	219	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.4002	215	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646415.1	s__Halioglobus sp003646415	77.2075	150	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	77.1493	138	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCA_004354085.1	s__Halioglobus sp004354085	77.1214	198	1529	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	77.093	214	1529	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	77.0461	181	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705825.1	s__Halioglobus japonicus_A	77.0214	156	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000156295.1	s__Halioglobus sp000156295	76.9718	95	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.94	98.78	0.94	0.91	6	-
GCF_008064635.1	s__Parahaliea aestuarii	76.9643	207	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	76.9286	160	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.8828	167	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009388985.1	s__Halioglobus maricola	76.8607	137	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704305.1	s__Halioglobus sp016704305	76.8591	178	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.7738	220	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.748	180	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	76.7361	137	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCA_002862985.1	s__Halioglobus sp002862985	76.7134	64	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719295.1	s__Haliea alexandrii	76.6746	137	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.6729	200	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_000423125.1	s__Haliea salexigens	76.6313	143	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
--------------------------------------------------------------------------------
[2023-03-16 09:15:34,486] [INFO] GTDB search result was written to OceanDNA-b37602/result_gtdb.tsv
[2023-03-16 09:15:34,493] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:15:34,500] [INFO] DFAST_QC result json was written to OceanDNA-b37602/dqc_result.json
[2023-03-16 09:15:34,500] [INFO] DFAST_QC completed!
[2023-03-16 09:15:34,500] [INFO] Total running time: 0h2m13s