[2023-03-16 17:36:12,637] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:36:12,637] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:36:12,637] [INFO] DQC Reference Directory: /var/lib/cwl/stgb57cc6a7-4701-4f64-9e0e-fa234b8ff517/dqc_reference
[2023-03-16 17:36:13,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:36:13,760] [INFO] Task started: Prodigal
[2023-03-16 17:36:13,761] [INFO] Running command: cat /var/lib/cwl/stg4b01a5a8-021a-47b8-bce3-0589b9c0ec5d/OceanDNA-b32030.fa | prodigal -d OceanDNA-b32030/cds.fna -a OceanDNA-b32030/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:36:29,816] [INFO] Task succeeded: Prodigal
[2023-03-16 17:36:29,816] [INFO] Task started: HMMsearch
[2023-03-16 17:36:29,816] [INFO] Running command: hmmsearch --tblout OceanDNA-b32030/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb57cc6a7-4701-4f64-9e0e-fa234b8ff517/dqc_reference/reference_markers.hmm OceanDNA-b32030/protein.faa > /dev/null
[2023-03-16 17:36:29,997] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:36:29,997] [INFO] Found 6/6 markers.
[2023-03-16 17:36:30,012] [INFO] Query marker FASTA was written to OceanDNA-b32030/markers.fasta
[2023-03-16 17:36:30,013] [INFO] Task started: Blastn
[2023-03-16 17:36:30,013] [INFO] Running command: blastn -query OceanDNA-b32030/markers.fasta -db /var/lib/cwl/stgb57cc6a7-4701-4f64-9e0e-fa234b8ff517/dqc_reference/reference_markers.fasta -out OceanDNA-b32030/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:36:30,725] [INFO] Task succeeded: Blastn
[2023-03-16 17:36:30,726] [INFO] Selected 26 target genomes.
[2023-03-16 17:36:30,726] [INFO] Target genome list was writen to OceanDNA-b32030/target_genomes.txt
[2023-03-16 17:36:30,807] [INFO] Task started: fastANI
[2023-03-16 17:36:30,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b01a5a8-021a-47b8-bce3-0589b9c0ec5d/OceanDNA-b32030.fa --refList OceanDNA-b32030/target_genomes.txt --output OceanDNA-b32030/fastani_result.tsv --threads 1
[2023-03-16 17:36:46,485] [INFO] Task succeeded: fastANI
[2023-03-16 17:36:46,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb57cc6a7-4701-4f64-9e0e-fa234b8ff517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:36:46,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb57cc6a7-4701-4f64-9e0e-fa234b8ff517/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:36:46,500] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:36:46,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:36:46,500] [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
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	77.9583	245	857	95	below_threshold
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	77.9537	244	857	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	77.0073	117	857	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	77.0026	128	857	95	below_threshold
Sphingobium fluviale	strain=CHR27	GCA_004122115.1	2506423	2506423	type	True	76.9927	72	857	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	76.9264	85	857	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	76.9221	86	857	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	76.8756	100	857	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	76.8583	143	857	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	76.8512	101	857	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	76.8321	88	857	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	76.7295	127	857	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	76.7008	121	857	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	76.6947	103	857	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	76.6713	114	857	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	76.5995	151	857	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	76.5748	131	857	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.55	99	857	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	76.5218	96	857	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.4772	118	857	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	76.427	106	857	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	76.3841	68	857	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	76.3558	95	857	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	76.3097	79	857	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.2349	58	857	95	below_threshold
Novosphingobium acidiphilum	strain=DSM 19966	GCA_000429005.1	505248	505248	type	True	76.1439	81	857	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:36:46,500] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32030/tc_result.tsv
[2023-03-16 17:36:46,500] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:36:46,500] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:36:46,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb57cc6a7-4701-4f64-9e0e-fa234b8ff517/dqc_reference/checkm_data
[2023-03-16 17:36:46,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:36:46,742] [INFO] Task started: CheckM
[2023-03-16 17:36:46,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32030/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32030/checkm_input OceanDNA-b32030/checkm_result
[2023-03-16 17:37:34,514] [INFO] Task succeeded: CheckM
[2023-03-16 17:37:34,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:37:34,517] [INFO] ===== Completeness check finished =====
[2023-03-16 17:37:34,517] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:37:34,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32030/markers.fasta)
[2023-03-16 17:37:34,519] [INFO] Task started: Blastn
[2023-03-16 17:37:34,519] [INFO] Running command: blastn -query OceanDNA-b32030/markers.fasta -db /var/lib/cwl/stgb57cc6a7-4701-4f64-9e0e-fa234b8ff517/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32030/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:37:37,629] [INFO] Task succeeded: Blastn
[2023-03-16 17:37:37,630] [INFO] Selected 19 target genomes.
[2023-03-16 17:37:37,630] [INFO] Target genome list was writen to OceanDNA-b32030/target_genomes_gtdb.txt
[2023-03-16 17:37:37,646] [INFO] Task started: fastANI
[2023-03-16 17:37:37,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b01a5a8-021a-47b8-bce3-0589b9c0ec5d/OceanDNA-b32030.fa --refList OceanDNA-b32030/target_genomes_gtdb.txt --output OceanDNA-b32030/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:37:54,646] [INFO] Task succeeded: fastANI
[2023-03-16 17:37:54,656] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:37:54,657] [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_002375465.1	s__Pacificimonas sp002375465	99.9869	854	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019204005.1	s__Pacificimonas sp019204005	78.26	282	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342165.1	s__Pacificimonas flava	77.9592	245	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002211145.1	s__Pacificimonas flava_A	77.6429	198	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122115.1	s__Sphingobium fluviale	76.9927	72	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	76.868	122	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890385.1	s__Tardibacter chloracetimidivorans	76.8593	87	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tardibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	76.8583	143	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	76.8517	101	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002344055.1	s__Allosphingosinicella sp002344055	76.7558	97	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346325.1	s__Sphingomonas japonica	76.7318	102	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004005865.1	s__Rhizorhabdus crocodyli	76.681	123	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421785.1	s__Sphingomonas sp001421785	76.6717	101	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650735.1	s__Sphingomonas sp001650735	76.5944	116	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	76.524	96	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114095.1	s__Sphingomonas sp900114095	76.4772	114	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	76.2075	59	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429005.1	s__Novosphingobium acidiphilum	76.1439	81	857	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.82	98.58	0.89	0.82	13	-
--------------------------------------------------------------------------------
[2023-03-16 17:37:54,657] [INFO] GTDB search result was written to OceanDNA-b32030/result_gtdb.tsv
[2023-03-16 17:37:54,657] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:37:54,659] [INFO] DFAST_QC result json was written to OceanDNA-b32030/dqc_result.json
[2023-03-16 17:37:54,659] [INFO] DFAST_QC completed!
[2023-03-16 17:37:54,659] [INFO] Total running time: 0h1m42s