[2023-03-15 15:18:22,043] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,044] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f9b7969-7ec1-40ee-b3c3-ede8db0afb04/dqc_reference
[2023-03-15 15:18:23,164] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,164] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,165] [INFO] Running command: cat /var/lib/cwl/stg114ec8c6-b7f6-4859-8f5a-7b21075d85ef/OceanDNA-b31535.fa | prodigal -d OceanDNA-b31535/cds.fna -a OceanDNA-b31535/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:45,608] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:45,609] [INFO] Task started: HMMsearch
[2023-03-15 15:18:45,609] [INFO] Running command: hmmsearch --tblout OceanDNA-b31535/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f9b7969-7ec1-40ee-b3c3-ede8db0afb04/dqc_reference/reference_markers.hmm OceanDNA-b31535/protein.faa > /dev/null
[2023-03-15 15:18:45,840] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:45,841] [INFO] Found 6/6 markers.
[2023-03-15 15:18:45,871] [INFO] Query marker FASTA was written to OceanDNA-b31535/markers.fasta
[2023-03-15 15:18:45,873] [INFO] Task started: Blastn
[2023-03-15 15:18:45,874] [INFO] Running command: blastn -query OceanDNA-b31535/markers.fasta -db /var/lib/cwl/stg6f9b7969-7ec1-40ee-b3c3-ede8db0afb04/dqc_reference/reference_markers.fasta -out OceanDNA-b31535/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:46,703] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:46,706] [INFO] Selected 24 target genomes.
[2023-03-15 15:18:46,706] [INFO] Target genome list was writen to OceanDNA-b31535/target_genomes.txt
[2023-03-15 15:18:46,722] [INFO] Task started: fastANI
[2023-03-15 15:18:46,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg114ec8c6-b7f6-4859-8f5a-7b21075d85ef/OceanDNA-b31535.fa --refList OceanDNA-b31535/target_genomes.txt --output OceanDNA-b31535/fastani_result.tsv --threads 1
[2023-03-15 15:19:03,339] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:03,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f9b7969-7ec1-40ee-b3c3-ede8db0afb04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:19:03,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f9b7969-7ec1-40ee-b3c3-ede8db0afb04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:19:03,354] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:19:03,354] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:19:03,354] [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
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	92.1696	895	1199	95	below_threshold
Sphingosinicella soli	strain=DSM 17328	GCA_014199685.1	333708	333708	type	True	86.944	772	1199	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	77.6162	322	1199	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	77.5463	290	1199	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	77.462	293	1199	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.4229	204	1199	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	77.3583	287	1199	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.3406	301	1199	95	below_threshold
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	77.2762	195	1199	95	below_threshold
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	77.248	197	1199	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.2086	217	1199	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.193	211	1199	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	77.1775	169	1199	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.166	287	1199	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	77.1626	273	1199	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	77.1565	137	1199	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.1529	253	1199	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	77.1499	201	1199	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.0419	259	1199	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	76.9935	187	1199	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	76.9433	264	1199	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.9031	248	1199	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	76.8887	257	1199	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	76.8726	150	1199	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:19:03,357] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31535/tc_result.tsv
[2023-03-15 15:19:03,360] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:19:03,360] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:19:03,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f9b7969-7ec1-40ee-b3c3-ede8db0afb04/dqc_reference/checkm_data
[2023-03-15 15:19:03,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:19:03,399] [INFO] Task started: CheckM
[2023-03-15 15:19:03,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31535/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31535/checkm_input OceanDNA-b31535/checkm_result
[2023-03-15 15:20:00,048] [INFO] Task succeeded: CheckM
[2023-03-15 15:20:00,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:20:00,063] [INFO] ===== Completeness check finished =====
[2023-03-15 15:20:00,063] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:20:00,063] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31535/markers.fasta)
[2023-03-15 15:20:00,064] [INFO] Task started: Blastn
[2023-03-15 15:20:00,064] [INFO] Running command: blastn -query OceanDNA-b31535/markers.fasta -db /var/lib/cwl/stg6f9b7969-7ec1-40ee-b3c3-ede8db0afb04/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31535/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:20:01,670] [INFO] Task succeeded: Blastn
[2023-03-15 15:20:01,672] [INFO] Selected 12 target genomes.
[2023-03-15 15:20:01,673] [INFO] Target genome list was writen to OceanDNA-b31535/target_genomes_gtdb.txt
[2023-03-15 15:20:01,679] [INFO] Task started: fastANI
[2023-03-15 15:20:01,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg114ec8c6-b7f6-4859-8f5a-7b21075d85ef/OceanDNA-b31535.fa --refList OceanDNA-b31535/target_genomes_gtdb.txt --output OceanDNA-b31535/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:20:10,386] [INFO] Task succeeded: fastANI
[2023-03-15 15:20:10,394] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:20:10,394] [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_003634215.1	s__Sphingosinicella microcystinivorans	92.1778	894	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_013911755.1	s__Sphingosinicella sp013911755	91.2809	887	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793845.1	s__Sphingosinicella sp016793845	89.6315	693	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199685.1	s__Sphingosinicella soli	86.9562	771	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871605.1	s__Sphingomonas_N sp903871605	77.5283	246	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003550065.1	s__Sphingomonas caeni	77.5257	261	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188185.1	s__Sphingopyxis indica	77.4695	258	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	77.4234	203	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018982925.1	s__Glacieibacterium sp018982925	77.1419	245	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	77.1329	276	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	76.953	190	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019204005.1	s__Pacificimonas sp019204005	76.333	142	1199	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:20:10,396] [INFO] GTDB search result was written to OceanDNA-b31535/result_gtdb.tsv
[2023-03-15 15:20:10,396] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:20:10,399] [INFO] DFAST_QC result json was written to OceanDNA-b31535/dqc_result.json
[2023-03-15 15:20:10,399] [INFO] DFAST_QC completed!
[2023-03-15 15:20:10,399] [INFO] Total running time: 0h1m48s