[2023-03-14 11:40:05,657] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,659] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg105fe016-8d18-4994-9253-bf94142a552f/dqc_reference
[2023-03-14 11:40:06,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,784] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,784] [INFO] Running command: cat /var/lib/cwl/stg73d07257-c3c2-48eb-8dcd-e6b041bca8fb/OceanDNA-b32147.fa | prodigal -d OceanDNA-b32147/cds.fna -a OceanDNA-b32147/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:21,272] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:21,272] [INFO] Task started: HMMsearch
[2023-03-14 11:40:21,272] [INFO] Running command: hmmsearch --tblout OceanDNA-b32147/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg105fe016-8d18-4994-9253-bf94142a552f/dqc_reference/reference_markers.hmm OceanDNA-b32147/protein.faa > /dev/null
[2023-03-14 11:40:21,457] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:21,457] [INFO] Found 6/6 markers.
[2023-03-14 11:40:21,482] [INFO] Query marker FASTA was written to OceanDNA-b32147/markers.fasta
[2023-03-14 11:40:21,483] [INFO] Task started: Blastn
[2023-03-14 11:40:21,483] [INFO] Running command: blastn -query OceanDNA-b32147/markers.fasta -db /var/lib/cwl/stg105fe016-8d18-4994-9253-bf94142a552f/dqc_reference/reference_markers.fasta -out OceanDNA-b32147/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:22,290] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:22,294] [INFO] Selected 21 target genomes.
[2023-03-14 11:40:22,294] [INFO] Target genome list was writen to OceanDNA-b32147/target_genomes.txt
[2023-03-14 11:40:22,305] [INFO] Task started: fastANI
[2023-03-14 11:40:22,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d07257-c3c2-48eb-8dcd-e6b041bca8fb/OceanDNA-b32147.fa --refList OceanDNA-b32147/target_genomes.txt --output OceanDNA-b32147/fastani_result.tsv --threads 1
[2023-03-14 11:40:37,078] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:37,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg105fe016-8d18-4994-9253-bf94142a552f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:37,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg105fe016-8d18-4994-9253-bf94142a552f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:37,091] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:37,091] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:40:37,091] [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
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	88.7657	569	740	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	85.9842	583	740	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	85.4202	563	740	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	84.9071	515	740	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	84.7869	507	740	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.431	532	740	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.2724	507	740	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	84.0806	510	740	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	83.8933	524	740	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	83.8898	505	740	95	below_threshold
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	83.8069	532	740	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	83.6746	500	740	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	83.5932	491	740	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	83.4672	507	740	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	83.0974	499	740	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.0297	505	740	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.7944	232	740	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.5479	193	740	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.1024	218	740	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	76.9975	118	740	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	76.9928	109	740	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:40:37,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32147/tc_result.tsv
[2023-03-14 11:40:37,097] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:37,097] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:37,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg105fe016-8d18-4994-9253-bf94142a552f/dqc_reference/checkm_data
[2023-03-14 11:40:37,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:37,106] [INFO] Task started: CheckM
[2023-03-14 11:40:37,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32147/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32147/checkm_input OceanDNA-b32147/checkm_result
[2023-03-14 11:41:15,626] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:15,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:15,665] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:15,666] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:15,666] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32147/markers.fasta)
[2023-03-14 11:41:15,666] [INFO] Task started: Blastn
[2023-03-14 11:41:15,666] [INFO] Running command: blastn -query OceanDNA-b32147/markers.fasta -db /var/lib/cwl/stg105fe016-8d18-4994-9253-bf94142a552f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32147/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:17,147] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:17,155] [INFO] Selected 18 target genomes.
[2023-03-14 11:41:17,155] [INFO] Target genome list was writen to OceanDNA-b32147/target_genomes_gtdb.txt
[2023-03-14 11:41:17,176] [INFO] Task started: fastANI
[2023-03-14 11:41:17,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d07257-c3c2-48eb-8dcd-e6b041bca8fb/OceanDNA-b32147.fa --refList OceanDNA-b32147/target_genomes_gtdb.txt --output OceanDNA-b32147/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:30,741] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:30,751] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:41:30,752] [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_000013985.1	s__Sphingopyxis alaskensis	88.7863	568	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609835.1	s__Sphingopyxis sp003609835	88.7435	569	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595975.1	s__Sphingopyxis sp014595975	87.8461	537	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756385.1	s__Sphingopyxis sp000756385	86.5696	576	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	86.1655	555	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468465.1	s__Sphingopyxis sp001468465	86.0948	572	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	86.0223	576	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011926545.1	s__Sphingopyxis italica	85.9884	583	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	85.9086	560	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCA_005503215.1	s__Sphingopyxis sp005503215	85.5816	553	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCA_001830555.1	s__Sphingopyxis sp001830555	85.1597	567	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468285.1	s__Sphingopyxis sp001468285	84.9953	553	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.98	0.98	2	-
GCF_015475875.1	s__Sphingopyxis solisilvae	84.9471	513	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_014207235.1	s__Sphingopyxis sp014207235	84.9151	543	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821905.1	s__Sphingopyxis sp013821905	84.8238	452	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454115.1	s__Sphingopyxis sp002454115	84.4425	528	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCA_016463225.1	s__Sphingopyxis sp016463225	83.8915	519	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704835.1	s__Sphingopyxis sp016704835	83.6414	513	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:30,755] [INFO] GTDB search result was written to OceanDNA-b32147/result_gtdb.tsv
[2023-03-14 11:41:30,756] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:30,761] [INFO] DFAST_QC result json was written to OceanDNA-b32147/dqc_result.json
[2023-03-14 11:41:30,761] [INFO] DFAST_QC completed!
[2023-03-14 11:41:30,761] [INFO] Total running time: 0h1m25s