[2023-03-19 04:11:06,931] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c1b9d7f-a6bd-4259-9724-94a09db61d10/dqc_reference
[2023-03-19 04:11:08,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stgbca0f698-5b38-4838-aa3e-b2849c68babd/OceanDNA-b37609.fa | prodigal -d OceanDNA-b37609/cds.fna -a OceanDNA-b37609/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:34,241] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:34,241] [INFO] Task started: HMMsearch
[2023-03-19 04:11:34,241] [INFO] Running command: hmmsearch --tblout OceanDNA-b37609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c1b9d7f-a6bd-4259-9724-94a09db61d10/dqc_reference/reference_markers.hmm OceanDNA-b37609/protein.faa > /dev/null
[2023-03-19 04:11:34,485] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:34,486] [INFO] Found 6/6 markers.
[2023-03-19 04:11:34,519] [INFO] Query marker FASTA was written to OceanDNA-b37609/markers.fasta
[2023-03-19 04:11:34,519] [INFO] Task started: Blastn
[2023-03-19 04:11:34,519] [INFO] Running command: blastn -query OceanDNA-b37609/markers.fasta -db /var/lib/cwl/stg7c1b9d7f-a6bd-4259-9724-94a09db61d10/dqc_reference/reference_markers.fasta -out OceanDNA-b37609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:35,225] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:35,226] [INFO] Selected 27 target genomes.
[2023-03-19 04:11:35,226] [INFO] Target genome list was writen to OceanDNA-b37609/target_genomes.txt
[2023-03-19 04:11:35,242] [INFO] Task started: fastANI
[2023-03-19 04:11:35,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca0f698-5b38-4838-aa3e-b2849c68babd/OceanDNA-b37609.fa --refList OceanDNA-b37609/target_genomes.txt --output OceanDNA-b37609/fastani_result.tsv --threads 1
[2023-03-19 04:11:52,540] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:52,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c1b9d7f-a6bd-4259-9724-94a09db61d10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:52,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c1b9d7f-a6bd-4259-9724-94a09db61d10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:52,551] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:52,551] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:52,551] [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	77.197	247	1339	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.0511	240	1339	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	77.003	171	1339	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.9838	234	1339	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.8839	209	1339	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.8544	185	1339	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	76.8099	180	1339	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.8082	162	1339	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	76.7702	93	1339	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	76.633	136	1339	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.5191	125	1339	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.515	121	1339	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	76.0058	50	1339	95	below_threshold
Kushneria sinocarnis	strain=DSM 23229	GCA_003633775.1	595502	595502	type	True	75.5963	52	1339	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	75.558	65	1339	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	75.4317	65	1339	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:52,551] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37609/tc_result.tsv
[2023-03-19 04:11:52,551] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:52,551] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:52,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c1b9d7f-a6bd-4259-9724-94a09db61d10/dqc_reference/checkm_data
[2023-03-19 04:11:52,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:52,585] [INFO] Task started: CheckM
[2023-03-19 04:11:52,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37609/checkm_input OceanDNA-b37609/checkm_result
[2023-03-19 04:12:54,334] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:54,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:54,337] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:54,337] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:54,337] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37609/markers.fasta)
[2023-03-19 04:12:54,338] [INFO] Task started: Blastn
[2023-03-19 04:12:54,338] [INFO] Running command: blastn -query OceanDNA-b37609/markers.fasta -db /var/lib/cwl/stg7c1b9d7f-a6bd-4259-9724-94a09db61d10/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:55,546] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:55,547] [INFO] Selected 23 target genomes.
[2023-03-19 04:12:55,547] [INFO] Target genome list was writen to OceanDNA-b37609/target_genomes_gtdb.txt
[2023-03-19 04:12:55,582] [INFO] Task started: fastANI
[2023-03-19 04:12:55,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca0f698-5b38-4838-aa3e-b2849c68babd/OceanDNA-b37609.fa --refList OceanDNA-b37609/target_genomes_gtdb.txt --output OceanDNA-b37609/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:13:11,976] [INFO] Task succeeded: fastANI
[2023-03-19 04:13:11,987] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:13:11,987] [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_002699145.1	s__Halioglobus sp002699145	77.6733	455	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.3083	235	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	77.1962	245	1339	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	77.1652	233	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.039	239	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	77.0202	185	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_003719295.1	s__Haliea alexandrii	77.008	169	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	76.9942	233	1339	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	76.8685	207	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	76.826	177	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCA_009937575.1	s__Halioglobus sp009937575	76.7911	204	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416125.1	s__Haliea sp002416125	76.7265	164	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCA_016704305.1	s__Halioglobus sp016704305	76.6706	252	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCF_008370495.1	s__Halioglobus sp008370495	76.6366	182	1339	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	76.6185	135	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCA_002414665.1	s__Haliea sp002414665	76.6044	153	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.476	125	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003633775.1	s__Kushneria sinocarnis	75.5963	52	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712065.1	s__Pseudomonas_E chengduensis_A	75.5905	67	1339	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7107	97.25	97.17	0.91	0.89	9	-
--------------------------------------------------------------------------------
[2023-03-19 04:13:11,987] [INFO] GTDB search result was written to OceanDNA-b37609/result_gtdb.tsv
[2023-03-19 04:13:11,988] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:13:11,989] [INFO] DFAST_QC result json was written to OceanDNA-b37609/dqc_result.json
[2023-03-19 04:13:11,990] [INFO] DFAST_QC completed!
[2023-03-19 04:13:11,990] [INFO] Total running time: 0h2m5s