[2023-03-17 14:23:21,354] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:23:21,354] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:23:21,354] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd371eff-4a09-4e2f-9639-9635dda00a32/dqc_reference
[2023-03-17 14:23:23,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:23:23,907] [INFO] Task started: Prodigal
[2023-03-17 14:23:23,907] [INFO] Running command: cat /var/lib/cwl/stg8e07aada-6ab7-4ef0-993c-0ba1ad37efe3/OceanDNA-b41512.fa | prodigal -d OceanDNA-b41512/cds.fna -a OceanDNA-b41512/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:23:50,355] [INFO] Task succeeded: Prodigal
[2023-03-17 14:23:50,355] [INFO] Task started: HMMsearch
[2023-03-17 14:23:50,355] [INFO] Running command: hmmsearch --tblout OceanDNA-b41512/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd371eff-4a09-4e2f-9639-9635dda00a32/dqc_reference/reference_markers.hmm OceanDNA-b41512/protein.faa > /dev/null
[2023-03-17 14:23:50,741] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:23:50,741] [INFO] Found 6/6 markers.
[2023-03-17 14:23:50,776] [INFO] Query marker FASTA was written to OceanDNA-b41512/markers.fasta
[2023-03-17 14:23:50,777] [INFO] Task started: Blastn
[2023-03-17 14:23:50,777] [INFO] Running command: blastn -query OceanDNA-b41512/markers.fasta -db /var/lib/cwl/stgcd371eff-4a09-4e2f-9639-9635dda00a32/dqc_reference/reference_markers.fasta -out OceanDNA-b41512/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:23:51,859] [INFO] Task succeeded: Blastn
[2023-03-17 14:23:51,860] [INFO] Selected 33 target genomes.
[2023-03-17 14:23:51,860] [INFO] Target genome list was writen to OceanDNA-b41512/target_genomes.txt
[2023-03-17 14:23:51,878] [INFO] Task started: fastANI
[2023-03-17 14:23:51,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e07aada-6ab7-4ef0-993c-0ba1ad37efe3/OceanDNA-b41512.fa --refList OceanDNA-b41512/target_genomes.txt --output OceanDNA-b41512/fastani_result.tsv --threads 1
[2023-03-17 14:24:16,568] [INFO] Task succeeded: fastANI
[2023-03-17 14:24:16,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd371eff-4a09-4e2f-9639-9635dda00a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:24:16,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd371eff-4a09-4e2f-9639-9635dda00a32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:24:16,576] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:24:16,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 14:24:16,577] [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
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	78.1292	345	1348	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.3456	113	1348	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	76.5781	104	1348	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.5596	104	1348	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	76.4873	117	1348	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.1928	58	1348	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.1928	58	1348	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.1927	58	1348	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	75.9651	56	1348	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	75.9373	57	1348	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.5158	53	1348	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.4705	62	1348	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 14:24:16,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41512/tc_result.tsv
[2023-03-17 14:24:16,577] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:24:16,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:24:16,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd371eff-4a09-4e2f-9639-9635dda00a32/dqc_reference/checkm_data
[2023-03-17 14:24:16,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:24:16,600] [INFO] Task started: CheckM
[2023-03-17 14:24:16,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41512/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41512/checkm_input OceanDNA-b41512/checkm_result
[2023-03-17 14:25:21,769] [INFO] Task succeeded: CheckM
[2023-03-17 14:25:21,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 14:25:21,773] [INFO] ===== Completeness check finished =====
[2023-03-17 14:25:21,773] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:25:21,773] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41512/markers.fasta)
[2023-03-17 14:25:21,775] [INFO] Task started: Blastn
[2023-03-17 14:25:21,775] [INFO] Running command: blastn -query OceanDNA-b41512/markers.fasta -db /var/lib/cwl/stgcd371eff-4a09-4e2f-9639-9635dda00a32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41512/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:25:24,563] [INFO] Task succeeded: Blastn
[2023-03-17 14:25:24,564] [INFO] Selected 23 target genomes.
[2023-03-17 14:25:24,564] [INFO] Target genome list was writen to OceanDNA-b41512/target_genomes_gtdb.txt
[2023-03-17 14:25:24,675] [INFO] Task started: fastANI
[2023-03-17 14:25:24,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e07aada-6ab7-4ef0-993c-0ba1ad37efe3/OceanDNA-b41512.fa --refList OceanDNA-b41512/target_genomes_gtdb.txt --output OceanDNA-b41512/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:25:50,506] [INFO] Task succeeded: fastANI
[2023-03-17 14:25:50,514] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 14:25:50,514] [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_002415025.1	s__Litorivivens sp002415025	98.3173	1138	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	99.88	99.82	0.96	0.94	3	conclusive
GCF_014191715.1	s__Litorivivens lipolytica	78.134	345	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710725.1	s__Litorivivens sp002710725	77.9293	290	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016132545.1	s__CSC3-9 sp016132545	77.3453	113	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422345.1	s__Spongiibacter marinus_A	77.0403	92	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420325.1	s__Spongiibacter tropicus	76.4719	118	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCA_002692965.1	s__NZNC01 sp002692965	76.2773	57	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_018067195.1	s__Marortus sp018067195	76.2715	64	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	76.1671	59	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_004745945.1	s__Halioglobus sp004745945	75.987	68	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	75.8764	57	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471665.1	s__Ketobacter sp002471665	75.7264	55	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	75.6932	57	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:25:50,515] [INFO] GTDB search result was written to OceanDNA-b41512/result_gtdb.tsv
[2023-03-17 14:25:50,515] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:25:50,516] [INFO] DFAST_QC result json was written to OceanDNA-b41512/dqc_result.json
[2023-03-17 14:25:50,517] [INFO] DFAST_QC completed!
[2023-03-17 14:25:50,517] [INFO] Total running time: 0h2m29s