[2023-03-18 02:27:59,035] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:59,036] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:59,036] [INFO] DQC Reference Directory: /var/lib/cwl/stge9f41484-1d07-4ad8-827a-abc22788f677/dqc_reference
[2023-03-18 02:28:00,129] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:28:00,130] [INFO] Task started: Prodigal
[2023-03-18 02:28:00,131] [INFO] Running command: cat /var/lib/cwl/stg18b8bf5d-5148-4ae2-929e-c2fe19f2557b/OceanDNA-b32136.fa | prodigal -d OceanDNA-b32136/cds.fna -a OceanDNA-b32136/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:10,134] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:10,135] [INFO] Task started: HMMsearch
[2023-03-18 02:28:10,135] [INFO] Running command: hmmsearch --tblout OceanDNA-b32136/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9f41484-1d07-4ad8-827a-abc22788f677/dqc_reference/reference_markers.hmm OceanDNA-b32136/protein.faa > /dev/null
[2023-03-18 02:28:10,291] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:10,291] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg18b8bf5d-5148-4ae2-929e-c2fe19f2557b/OceanDNA-b32136.fa]
[2023-03-18 02:28:10,309] [INFO] Query marker FASTA was written to OceanDNA-b32136/markers.fasta
[2023-03-18 02:28:10,309] [INFO] Task started: Blastn
[2023-03-18 02:28:10,309] [INFO] Running command: blastn -query OceanDNA-b32136/markers.fasta -db /var/lib/cwl/stge9f41484-1d07-4ad8-827a-abc22788f677/dqc_reference/reference_markers.fasta -out OceanDNA-b32136/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:10,918] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:10,919] [INFO] Selected 19 target genomes.
[2023-03-18 02:28:10,919] [INFO] Target genome list was writen to OceanDNA-b32136/target_genomes.txt
[2023-03-18 02:28:10,929] [INFO] Task started: fastANI
[2023-03-18 02:28:10,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b8bf5d-5148-4ae2-929e-c2fe19f2557b/OceanDNA-b32136.fa --refList OceanDNA-b32136/target_genomes.txt --output OceanDNA-b32136/fastani_result.tsv --threads 1
[2023-03-18 02:28:22,470] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:22,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9f41484-1d07-4ad8-827a-abc22788f677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:22,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9f41484-1d07-4ad8-827a-abc22788f677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:22,481] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:22,481] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:22,481] [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 ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	79.5755	233	483	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	79.499	228	483	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	79.4176	233	483	95	below_threshold
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	79.3111	246	483	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	79.1938	241	483	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	79.1575	253	483	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	79.0852	232	483	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	78.8926	236	483	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	78.6807	180	483	95	below_threshold
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	78.3813	209	483	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	78.3807	202	483	95	below_threshold
Sphingomonas faeni	strain=MA-olki	GCA_003053745.1	185950	185950	type	True	78.372	222	483	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	78.249	190	483	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	78.1944	186	483	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	78.0839	161	483	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	77.9159	179	483	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.9143	161	483	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	77.8973	180	483	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.5322	170	483	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:22,481] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32136/tc_result.tsv
[2023-03-18 02:28:22,481] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:22,481] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:22,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9f41484-1d07-4ad8-827a-abc22788f677/dqc_reference/checkm_data
[2023-03-18 02:28:22,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:22,486] [INFO] Task started: CheckM
[2023-03-18 02:28:22,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32136/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32136/checkm_input OceanDNA-b32136/checkm_result
[2023-03-18 02:28:51,774] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:51,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.24%
Contamintation: 3.82%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 02:28:51,777] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:51,777] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:51,777] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32136/markers.fasta)
[2023-03-18 02:28:51,777] [INFO] Task started: Blastn
[2023-03-18 02:28:51,778] [INFO] Running command: blastn -query OceanDNA-b32136/markers.fasta -db /var/lib/cwl/stge9f41484-1d07-4ad8-827a-abc22788f677/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32136/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:52,712] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:52,818] [INFO] Selected 17 target genomes.
[2023-03-18 02:28:52,818] [INFO] Target genome list was writen to OceanDNA-b32136/target_genomes_gtdb.txt
[2023-03-18 02:28:52,836] [INFO] Task started: fastANI
[2023-03-18 02:28:52,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b8bf5d-5148-4ae2-929e-c2fe19f2557b/OceanDNA-b32136.fa --refList OceanDNA-b32136/target_genomes_gtdb.txt --output OceanDNA-b32136/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:03,459] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:03,468] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:29:03,469] [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_006438955.1	s__Sphingomonas oligophenolica	81.314	306	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	79.563	234	483	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	79.4066	249	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050705.1	s__Sphingomonas aurantiaca	79.3111	246	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.29	95.02	0.87	0.86	4	-
GCF_014196115.1	s__Sphingomonas aquatilis	79.1938	241	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCF_003046295.1	s__Sphingomonas aerolata	79.0901	233	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.52	96.36	0.90	0.73	15	-
GCA_003075315.1	s__Sphingomonas sp003075315	78.9856	251	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_902506455.1	s__Sphingomonas sp902506455	78.8769	169	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427505.1	s__Sphingomonas sp016427505	78.7879	206	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	78.69	210	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_007859635.1	s__Sphingomonas panacisoli	78.6807	180	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421745.1	s__Sphingomonas sp001421745	78.673	214	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001717955.1	s__Sphingomonas panacis	78.2489	190	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003171655.1	s__Sphingomonas portus	78.1057	160	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000419605.1	s__Sphingomonas phyllosphaerae_B	78.1016	170	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	77.9143	161	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	77.8939	172	483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:03,469] [INFO] GTDB search result was written to OceanDNA-b32136/result_gtdb.tsv
[2023-03-18 02:29:03,469] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:03,471] [INFO] DFAST_QC result json was written to OceanDNA-b32136/dqc_result.json
[2023-03-18 02:29:03,471] [INFO] DFAST_QC completed!
[2023-03-18 02:29:03,471] [INFO] Total running time: 0h1m4s