[2023-03-18 01:54:19,443] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:19,443] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:19,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgb98917bf-630e-453e-83ac-e2470828e4f7/dqc_reference
[2023-03-18 01:54:20,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:20,602] [INFO] Task started: Prodigal
[2023-03-18 01:54:20,602] [INFO] Running command: cat /var/lib/cwl/stg72a42beb-e9d8-4c22-a9da-2635f3202c2c/OceanDNA-b32135.fa | prodigal -d OceanDNA-b32135/cds.fna -a OceanDNA-b32135/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:36,859] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:36,859] [INFO] Task started: HMMsearch
[2023-03-18 01:54:36,859] [INFO] Running command: hmmsearch --tblout OceanDNA-b32135/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb98917bf-630e-453e-83ac-e2470828e4f7/dqc_reference/reference_markers.hmm OceanDNA-b32135/protein.faa > /dev/null
[2023-03-18 01:54:37,056] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:37,056] [INFO] Found 6/6 markers.
[2023-03-18 01:54:37,079] [INFO] Query marker FASTA was written to OceanDNA-b32135/markers.fasta
[2023-03-18 01:54:37,080] [INFO] Task started: Blastn
[2023-03-18 01:54:37,080] [INFO] Running command: blastn -query OceanDNA-b32135/markers.fasta -db /var/lib/cwl/stgb98917bf-630e-453e-83ac-e2470828e4f7/dqc_reference/reference_markers.fasta -out OceanDNA-b32135/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:37,874] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:37,875] [INFO] Selected 16 target genomes.
[2023-03-18 01:54:37,875] [INFO] Target genome list was writen to OceanDNA-b32135/target_genomes.txt
[2023-03-18 01:54:37,884] [INFO] Task started: fastANI
[2023-03-18 01:54:37,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a42beb-e9d8-4c22-a9da-2635f3202c2c/OceanDNA-b32135.fa --refList OceanDNA-b32135/target_genomes.txt --output OceanDNA-b32135/fastani_result.tsv --threads 1
[2023-03-18 01:54:49,780] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:49,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb98917bf-630e-453e-83ac-e2470828e4f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:49,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb98917bf-630e-453e-83ac-e2470828e4f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:49,790] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:49,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:54:49,790] [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
Stakelama pacifica	strain=DSM 25059	GCA_004361835.1	517720	517720	type	True	83.6648	612	884	95	below_threshold
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	83.613	616	884	95	below_threshold
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	82.6261	579	884	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	79.8018	424	884	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	79.2301	387	884	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.408	370	884	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	78.4036	337	884	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.3498	315	884	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.0534	344	884	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	77.9427	311	884	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.9256	315	884	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	77.8457	317	884	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	77.7542	348	884	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	77.465	250	884	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	77.3058	253	884	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.2162	282	884	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:54:49,790] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32135/tc_result.tsv
[2023-03-18 01:54:49,791] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:49,791] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:49,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb98917bf-630e-453e-83ac-e2470828e4f7/dqc_reference/checkm_data
[2023-03-18 01:54:49,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:49,805] [INFO] Task started: CheckM
[2023-03-18 01:54:49,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32135/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32135/checkm_input OceanDNA-b32135/checkm_result
[2023-03-18 01:55:32,389] [INFO] Task succeeded: CheckM
[2023-03-18 01:55:32,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:55:32,419] [INFO] ===== Completeness check finished =====
[2023-03-18 01:55:32,419] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:55:32,419] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32135/markers.fasta)
[2023-03-18 01:55:32,420] [INFO] Task started: Blastn
[2023-03-18 01:55:32,420] [INFO] Running command: blastn -query OceanDNA-b32135/markers.fasta -db /var/lib/cwl/stgb98917bf-630e-453e-83ac-e2470828e4f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32135/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:55:33,936] [INFO] Task succeeded: Blastn
[2023-03-18 01:55:33,938] [INFO] Selected 22 target genomes.
[2023-03-18 01:55:33,938] [INFO] Target genome list was writen to OceanDNA-b32135/target_genomes_gtdb.txt
[2023-03-18 01:55:33,951] [INFO] Task started: fastANI
[2023-03-18 01:55:33,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg72a42beb-e9d8-4c22-a9da-2635f3202c2c/OceanDNA-b32135.fa --refList OceanDNA-b32135/target_genomes_gtdb.txt --output OceanDNA-b32135/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:55:49,453] [INFO] Task succeeded: fastANI
[2023-03-18 01:55:49,465] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:55:49,465] [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_004361835.1	s__Sphingomonas pacifica	83.6499	613	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.75	97.51	0.88	0.77	3	-
GCA_018122655.1	s__Sphingomonas sp018122655	81.0251	476	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199335.1	s__Sphingomonas sediminis	79.8018	424	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707985.1	s__Sphingomonas sp002707985	79.2777	364	884	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	79.241	386	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	78.4999	364	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	78.4538	339	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_007833215.1	s__Sphingomonas sp007833215	78.4187	369	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	78.3821	353	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144715.1	s__Sphingomonas sp005144715	78.3375	316	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001619955.1	s__Sphingomonas hankookensis	78.2299	357	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.49	99.35	0.90	0.87	3	-
GCF_013409985.1	s__Sphingomonas melonis_A	78.2145	345	884	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	78.1365	358	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014171475.1	s__Sphingomonas alpina_A	78.078	336	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	77.9996	331	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199625.1	s__Sphingomonas abaci	77.9427	311	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083435.1	s__Sphingomonas sp002083435	77.8385	282	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716975.1	s__Sphingomonas trueperi_A	77.8309	351	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.23	95.23	0.88	0.88	2	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	77.825	319	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745215.1	s__Sphingomonas sp017745215	77.7702	326	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498785.1	s__Sphingomonas sp902498785	77.7444	306	884	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	77.3187	252	884	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 01:55:49,466] [INFO] GTDB search result was written to OceanDNA-b32135/result_gtdb.tsv
[2023-03-18 01:55:49,466] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:55:49,468] [INFO] DFAST_QC result json was written to OceanDNA-b32135/dqc_result.json
[2023-03-18 01:55:49,468] [INFO] DFAST_QC completed!
[2023-03-18 01:55:49,468] [INFO] Total running time: 0h1m30s