[2023-03-17 05:01:06,442] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,442] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c7fd0b8-6b16-4387-99c6-966bdcb76f56/dqc_reference
[2023-03-17 05:01:07,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:07,999] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,000] [INFO] Running command: cat /var/lib/cwl/stgb76e1751-012e-4b13-97ca-46ae7e05bbe0/OceanDNA-b37525.fa | prodigal -d OceanDNA-b37525/cds.fna -a OceanDNA-b37525/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:27,388] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:27,388] [INFO] Task started: HMMsearch
[2023-03-17 05:01:27,388] [INFO] Running command: hmmsearch --tblout OceanDNA-b37525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c7fd0b8-6b16-4387-99c6-966bdcb76f56/dqc_reference/reference_markers.hmm OceanDNA-b37525/protein.faa > /dev/null
[2023-03-17 05:01:27,590] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:27,591] [INFO] Found 6/6 markers.
[2023-03-17 05:01:27,609] [INFO] Query marker FASTA was written to OceanDNA-b37525/markers.fasta
[2023-03-17 05:01:27,610] [INFO] Task started: Blastn
[2023-03-17 05:01:27,610] [INFO] Running command: blastn -query OceanDNA-b37525/markers.fasta -db /var/lib/cwl/stg2c7fd0b8-6b16-4387-99c6-966bdcb76f56/dqc_reference/reference_markers.fasta -out OceanDNA-b37525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:28,328] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:28,329] [INFO] Selected 26 target genomes.
[2023-03-17 05:01:28,329] [INFO] Target genome list was writen to OceanDNA-b37525/target_genomes.txt
[2023-03-17 05:01:28,341] [INFO] Task started: fastANI
[2023-03-17 05:01:28,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgb76e1751-012e-4b13-97ca-46ae7e05bbe0/OceanDNA-b37525.fa --refList OceanDNA-b37525/target_genomes.txt --output OceanDNA-b37525/fastani_result.tsv --threads 1
[2023-03-17 05:01:44,758] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:44,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c7fd0b8-6b16-4387-99c6-966bdcb76f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:44,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c7fd0b8-6b16-4387-99c6-966bdcb76f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:44,773] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:44,773] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:01:44,773] [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	78.0572	243	1038	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.6542	209	1038	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.5895	234	1038	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.3418	197	1038	95	below_threshold
Congregibacter litoralis	strain=KT71	GCA_000153125.2	393662	393662	type	True	77.2864	255	1038	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.1827	167	1038	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	77.1391	225	1038	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.0736	179	1038	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.9121	180	1038	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.8975	183	1038	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.8061	120	1038	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.8009	118	1038	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.7656	118	1038	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.4602	107	1038	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3749	113	1038	95	below_threshold
Halomonas fontilapidosi	strain=CECT 7341	GCA_014192285.1	616675	616675	type	True	76.3272	84	1038	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.2151	87	1038	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.1799	90	1038	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	76.1636	95	1038	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	76.1207	111	1038	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.0794	65	1038	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.0782	65	1038	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	76.0164	96	1038	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.993	73	1038	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	75.9884	95	1038	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	75.9071	114	1038	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:01:44,773] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37525/tc_result.tsv
[2023-03-17 05:01:44,773] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:44,773] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:44,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c7fd0b8-6b16-4387-99c6-966bdcb76f56/dqc_reference/checkm_data
[2023-03-17 05:01:44,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:44,778] [INFO] Task started: CheckM
[2023-03-17 05:01:44,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37525/checkm_input OceanDNA-b37525/checkm_result
[2023-03-17 05:02:33,541] [INFO] Task succeeded: CheckM
[2023-03-17 05:02:33,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:02:33,544] [INFO] ===== Completeness check finished =====
[2023-03-17 05:02:33,544] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:02:33,544] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37525/markers.fasta)
[2023-03-17 05:02:33,545] [INFO] Task started: Blastn
[2023-03-17 05:02:33,545] [INFO] Running command: blastn -query OceanDNA-b37525/markers.fasta -db /var/lib/cwl/stg2c7fd0b8-6b16-4387-99c6-966bdcb76f56/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:02:34,836] [INFO] Task succeeded: Blastn
[2023-03-17 05:02:34,837] [INFO] Selected 22 target genomes.
[2023-03-17 05:02:34,837] [INFO] Target genome list was writen to OceanDNA-b37525/target_genomes_gtdb.txt
[2023-03-17 05:02:35,135] [INFO] Task started: fastANI
[2023-03-17 05:02:35,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgb76e1751-012e-4b13-97ca-46ae7e05bbe0/OceanDNA-b37525.fa --refList OceanDNA-b37525/target_genomes_gtdb.txt --output OceanDNA-b37525/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:02:50,640] [INFO] Task succeeded: fastANI
[2023-03-17 05:02:50,653] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:02:50,653] [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	78.0424	244	1038	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	77.7504	226	1038	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	77.6542	209	1038	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	77.6021	233	1038	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	77.5897	211	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_002428935.1	s__Congregibacter sp002428935	77.5315	206	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	77.5174	232	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_003457605.1	s__Halioglobus sediminis	77.3418	197	1038	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	77.319	166	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153125.2	s__Congregibacter litoralis	77.2762	256	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764025.1	s__Pseudohaliea rubra	77.1506	224	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	77.0736	179	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.8837	184	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_000158155.1	s__Congregibacter sp000158155	76.8377	185	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	76.8061	120	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCA_002416125.1	s__Haliea sp002416125	76.7856	171	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_017589465.1	s__Pseudomonas sp017589465	76.2574	114	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	76.1773	98	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_018417595.1	s__Pseudomonas_E entomophila_C	76.1396	107	1038	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_900099785.1	s__Pseudomonas panipatensis	76.1356	110	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016518545.1	s__Pseudomonas_E sp016518545	76.0068	89	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900106975.1	s__Pseudomonas_O kuykendallii	75.9203	113	1038	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-17 05:02:50,653] [INFO] GTDB search result was written to OceanDNA-b37525/result_gtdb.tsv
[2023-03-17 05:02:50,653] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:02:50,656] [INFO] DFAST_QC result json was written to OceanDNA-b37525/dqc_result.json
[2023-03-17 05:02:50,656] [INFO] DFAST_QC completed!
[2023-03-17 05:02:50,656] [INFO] Total running time: 0h1m44s