[2023-03-18 00:21:54,210] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:54,211] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:54,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9b3bf65-f6b7-4238-8f82-a50c4741ab14/dqc_reference
[2023-03-18 00:21:55,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:55,650] [INFO] Task started: Prodigal
[2023-03-18 00:21:55,651] [INFO] Running command: cat /var/lib/cwl/stgfae90dd1-0354-420a-bfb2-ec470eba2dc9/OceanDNA-b41218.fa | prodigal -d OceanDNA-b41218/cds.fna -a OceanDNA-b41218/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:19,138] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:19,138] [INFO] Task started: HMMsearch
[2023-03-18 00:22:19,138] [INFO] Running command: hmmsearch --tblout OceanDNA-b41218/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9b3bf65-f6b7-4238-8f82-a50c4741ab14/dqc_reference/reference_markers.hmm OceanDNA-b41218/protein.faa > /dev/null
[2023-03-18 00:22:19,359] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:19,359] [INFO] Found 6/6 markers.
[2023-03-18 00:22:19,385] [INFO] Query marker FASTA was written to OceanDNA-b41218/markers.fasta
[2023-03-18 00:22:19,385] [INFO] Task started: Blastn
[2023-03-18 00:22:19,386] [INFO] Running command: blastn -query OceanDNA-b41218/markers.fasta -db /var/lib/cwl/stgc9b3bf65-f6b7-4238-8f82-a50c4741ab14/dqc_reference/reference_markers.fasta -out OceanDNA-b41218/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:20,284] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:20,285] [INFO] Selected 13 target genomes.
[2023-03-18 00:22:20,286] [INFO] Target genome list was writen to OceanDNA-b41218/target_genomes.txt
[2023-03-18 00:22:20,291] [INFO] Task started: fastANI
[2023-03-18 00:22:20,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae90dd1-0354-420a-bfb2-ec470eba2dc9/OceanDNA-b41218.fa --refList OceanDNA-b41218/target_genomes.txt --output OceanDNA-b41218/fastani_result.tsv --threads 1
[2023-03-18 00:22:33,328] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:33,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9b3bf65-f6b7-4238-8f82-a50c4741ab14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:33,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9b3bf65-f6b7-4238-8f82-a50c4741ab14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:33,338] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:33,338] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:22:33,338] [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 peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	91.9809	1115	1246	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	91.9709	1125	1246	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	83.9648	919	1246	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	82.6317	796	1246	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	82.4798	820	1246	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	82.4623	805	1246	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.3105	879	1246	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.9835	772	1246	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.6547	826	1246	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.4699	743	1246	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	81.1595	769	1246	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.9831	714	1246	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.8288	683	1246	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:22:33,338] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41218/tc_result.tsv
[2023-03-18 00:22:33,338] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:33,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:33,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9b3bf65-f6b7-4238-8f82-a50c4741ab14/dqc_reference/checkm_data
[2023-03-18 00:22:33,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:33,345] [INFO] Task started: CheckM
[2023-03-18 00:22:33,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41218/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41218/checkm_input OceanDNA-b41218/checkm_result
[2023-03-18 00:23:31,407] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:31,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:31,409] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:31,410] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:31,410] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41218/markers.fasta)
[2023-03-18 00:23:31,411] [INFO] Task started: Blastn
[2023-03-18 00:23:31,411] [INFO] Running command: blastn -query OceanDNA-b41218/markers.fasta -db /var/lib/cwl/stgc9b3bf65-f6b7-4238-8f82-a50c4741ab14/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41218/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:33,104] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:33,104] [INFO] Selected 14 target genomes.
[2023-03-18 00:23:33,104] [INFO] Target genome list was writen to OceanDNA-b41218/target_genomes_gtdb.txt
[2023-03-18 00:23:33,119] [INFO] Task started: fastANI
[2023-03-18 00:23:33,119] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae90dd1-0354-420a-bfb2-ec470eba2dc9/OceanDNA-b41218.fa --refList OceanDNA-b41218/target_genomes_gtdb.txt --output OceanDNA-b41218/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:46,831] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:46,839] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:46,839] [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_900099645.1	s__Pseudomonas_E peli	91.9709	1125	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCA_002840155.1	s__Pseudomonas_E sp002840155	90.3057	1116	1246	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_900105355.1	s__Pseudomonas_E anguilliseptica	89.4369	1055	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	88.0251	983	1246	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_003060885.1	s__Pseudomonas_E sp003060885	87.4875	1009	1246	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_018816095.1	s__Pseudomonas_E sp018816095	85.3973	856	1246	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_004920405.1	s__Pseudomonas_E leptonychotis	85.0871	1025	1246	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_001465025.1	s__Pseudomonas_E sp001465025	84.1506	838	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.96	95.96	0.61	0.61	2	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	83.7328	900	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	83.3189	834	1246	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_900100495.1	s__Pseudomonas_E benzenivorans	82.3161	878	1246	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	81.8693	756	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	81.4775	709	1246	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_000761545.1	s__Pseudomonas_E sp000761545	81.1459	725	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:46,840] [INFO] GTDB search result was written to OceanDNA-b41218/result_gtdb.tsv
[2023-03-18 00:23:46,840] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:46,841] [INFO] DFAST_QC result json was written to OceanDNA-b41218/dqc_result.json
[2023-03-18 00:23:46,841] [INFO] DFAST_QC completed!
[2023-03-18 00:23:46,841] [INFO] Total running time: 0h1m53s