[2023-03-16 20:59:00,578] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:59:00,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:59:00,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgeee2994f-821c-4f66-8e52-03770e77bdfd/dqc_reference
[2023-03-16 20:59:03,790] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:59:03,791] [INFO] Task started: Prodigal
[2023-03-16 20:59:03,791] [INFO] Running command: cat /var/lib/cwl/stgd8d47a3d-a242-443c-9d33-177c92062456/OceanDNA-b32141.fa | prodigal -d OceanDNA-b32141/cds.fna -a OceanDNA-b32141/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:59:31,308] [INFO] Task succeeded: Prodigal
[2023-03-16 20:59:31,308] [INFO] Task started: HMMsearch
[2023-03-16 20:59:31,308] [INFO] Running command: hmmsearch --tblout OceanDNA-b32141/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeee2994f-821c-4f66-8e52-03770e77bdfd/dqc_reference/reference_markers.hmm OceanDNA-b32141/protein.faa > /dev/null
[2023-03-16 20:59:31,504] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:59:31,504] [INFO] Found 6/6 markers.
[2023-03-16 20:59:31,527] [INFO] Query marker FASTA was written to OceanDNA-b32141/markers.fasta
[2023-03-16 20:59:31,527] [INFO] Task started: Blastn
[2023-03-16 20:59:31,527] [INFO] Running command: blastn -query OceanDNA-b32141/markers.fasta -db /var/lib/cwl/stgeee2994f-821c-4f66-8e52-03770e77bdfd/dqc_reference/reference_markers.fasta -out OceanDNA-b32141/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:59:32,424] [INFO] Task succeeded: Blastn
[2023-03-16 20:59:32,425] [INFO] Selected 17 target genomes.
[2023-03-16 20:59:32,425] [INFO] Target genome list was writen to OceanDNA-b32141/target_genomes.txt
[2023-03-16 20:59:32,435] [INFO] Task started: fastANI
[2023-03-16 20:59:32,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d47a3d-a242-443c-9d33-177c92062456/OceanDNA-b32141.fa --refList OceanDNA-b32141/target_genomes.txt --output OceanDNA-b32141/fastani_result.tsv --threads 1
[2023-03-16 20:59:47,270] [INFO] Task succeeded: fastANI
[2023-03-16 20:59:47,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeee2994f-821c-4f66-8e52-03770e77bdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:59:47,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeee2994f-821c-4f66-8e52-03770e77bdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:59:47,281] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:59:47,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:59:47,281] [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
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	87.3971	901	1265	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	87.3682	900	1265	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	86.5994	857	1265	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	84.9572	809	1265	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	84.9513	818	1265	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	84.8674	751	1265	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	81.9038	708	1265	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	81.7331	646	1265	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	80.7188	671	1265	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.7052	692	1265	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.5741	693	1265	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	80.0679	610	1265	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	80.0247	527	1265	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.8951	630	1265	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	79.5814	580	1265	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	79.4698	617	1265	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.8783	461	1265	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:59:47,281] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32141/tc_result.tsv
[2023-03-16 20:59:47,281] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:59:47,281] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:59:47,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeee2994f-821c-4f66-8e52-03770e77bdfd/dqc_reference/checkm_data
[2023-03-16 20:59:47,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:59:47,287] [INFO] Task started: CheckM
[2023-03-16 20:59:47,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32141/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32141/checkm_input OceanDNA-b32141/checkm_result
[2023-03-16 21:00:55,754] [INFO] Task succeeded: CheckM
[2023-03-16 21:00:55,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:00:55,757] [INFO] ===== Completeness check finished =====
[2023-03-16 21:00:55,757] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:00:55,757] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32141/markers.fasta)
[2023-03-16 21:00:55,759] [INFO] Task started: Blastn
[2023-03-16 21:00:55,759] [INFO] Running command: blastn -query OceanDNA-b32141/markers.fasta -db /var/lib/cwl/stgeee2994f-821c-4f66-8e52-03770e77bdfd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32141/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:00:57,543] [INFO] Task succeeded: Blastn
[2023-03-16 21:00:57,544] [INFO] Selected 9 target genomes.
[2023-03-16 21:00:57,544] [INFO] Target genome list was writen to OceanDNA-b32141/target_genomes_gtdb.txt
[2023-03-16 21:00:57,684] [INFO] Task started: fastANI
[2023-03-16 21:00:57,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8d47a3d-a242-443c-9d33-177c92062456/OceanDNA-b32141.fa --refList OceanDNA-b32141/target_genomes_gtdb.txt --output OceanDNA-b32141/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:01:08,335] [INFO] Task succeeded: fastANI
[2023-03-16 21:01:08,341] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:01:08,341] [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_002292295.1	s__Sphingomonas sp002292295	99.9803	1164	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010450875.1	s__Sphingomonas insulae	87.3683	900	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000764535.1	s__Sphingomonas taxi	86.5341	862	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_013409985.1	s__Sphingomonas melonis_A	86.438	849	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632225.1	s__Sphingomonas sp000632225	85.6506	815	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196115.1	s__Sphingomonas aquatilis	84.9339	819	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCA_003075315.1	s__Sphingomonas sp003075315	84.8767	796	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_011761945.1	s__Sphingomonas leidyi	79.5719	582	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	79.5116	609	1265	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:01:08,341] [INFO] GTDB search result was written to OceanDNA-b32141/result_gtdb.tsv
[2023-03-16 21:01:08,345] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:01:08,347] [INFO] DFAST_QC result json was written to OceanDNA-b32141/dqc_result.json
[2023-03-16 21:01:08,347] [INFO] DFAST_QC completed!
[2023-03-16 21:01:08,347] [INFO] Total running time: 0h2m8s