[2023-03-16 04:05:20,414] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,414] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg77426f68-3a76-488d-975c-2b421d888fde/dqc_reference
[2023-03-16 04:05:22,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,126] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,126] [INFO] Running command: cat /var/lib/cwl/stge1a74ddc-229f-4650-ac51-4b83363b4824/OceanDNA-b32050.fa | prodigal -d OceanDNA-b32050/cds.fna -a OceanDNA-b32050/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:37,891] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:37,891] [INFO] Task started: HMMsearch
[2023-03-16 04:05:37,891] [INFO] Running command: hmmsearch --tblout OceanDNA-b32050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77426f68-3a76-488d-975c-2b421d888fde/dqc_reference/reference_markers.hmm OceanDNA-b32050/protein.faa > /dev/null
[2023-03-16 04:05:38,093] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:38,094] [INFO] Found 6/6 markers.
[2023-03-16 04:05:38,114] [INFO] Query marker FASTA was written to OceanDNA-b32050/markers.fasta
[2023-03-16 04:05:38,114] [INFO] Task started: Blastn
[2023-03-16 04:05:38,114] [INFO] Running command: blastn -query OceanDNA-b32050/markers.fasta -db /var/lib/cwl/stg77426f68-3a76-488d-975c-2b421d888fde/dqc_reference/reference_markers.fasta -out OceanDNA-b32050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:38,836] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:38,837] [INFO] Selected 23 target genomes.
[2023-03-16 04:05:38,837] [INFO] Target genome list was writen to OceanDNA-b32050/target_genomes.txt
[2023-03-16 04:05:38,849] [INFO] Task started: fastANI
[2023-03-16 04:05:38,849] [INFO] Running command: fastANI --query /var/lib/cwl/stge1a74ddc-229f-4650-ac51-4b83363b4824/OceanDNA-b32050.fa --refList OceanDNA-b32050/target_genomes.txt --output OceanDNA-b32050/fastani_result.tsv --threads 1
[2023-03-16 04:05:55,766] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:55,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77426f68-3a76-488d-975c-2b421d888fde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:55,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77426f68-3a76-488d-975c-2b421d888fde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:55,778] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:55,779] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:55,779] [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
Sphingobium algorifonticola	strain=TLA-22	GCA_004005485.1	2008318	2008318	type	True	80.4224	445	833	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	78.8345	322	833	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	78.6973	319	833	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	78.6108	323	833	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	78.5632	319	833	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.511	311	833	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	78.5095	307	833	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	78.461	304	833	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	78.1647	282	833	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_000632125.2	76947	76947	type	True	78.1327	255	833	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	78.1228	285	833	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	77.973	279	833	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	77.789	224	833	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.2025	180	833	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	77.0741	140	833	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.0227	181	833	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	76.926	162	833	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	76.8444	197	833	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	76.553	159	833	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	76.5519	103	833	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	76.5161	123	833	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:55,779] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32050/tc_result.tsv
[2023-03-16 04:05:55,779] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:55,779] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:55,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77426f68-3a76-488d-975c-2b421d888fde/dqc_reference/checkm_data
[2023-03-16 04:05:55,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:55,784] [INFO] Task started: CheckM
[2023-03-16 04:05:55,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32050/checkm_input OceanDNA-b32050/checkm_result
[2023-03-16 04:06:37,172] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:37,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:37,175] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:37,176] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:37,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32050/markers.fasta)
[2023-03-16 04:06:37,176] [INFO] Task started: Blastn
[2023-03-16 04:06:37,176] [INFO] Running command: blastn -query OceanDNA-b32050/markers.fasta -db /var/lib/cwl/stg77426f68-3a76-488d-975c-2b421d888fde/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:38,467] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:38,468] [INFO] Selected 22 target genomes.
[2023-03-16 04:06:38,468] [INFO] Target genome list was writen to OceanDNA-b32050/target_genomes_gtdb.txt
[2023-03-16 04:06:38,492] [INFO] Task started: fastANI
[2023-03-16 04:06:38,493] [INFO] Running command: fastANI --query /var/lib/cwl/stge1a74ddc-229f-4650-ac51-4b83363b4824/OceanDNA-b32050.fa --refList OceanDNA-b32050/target_genomes_gtdb.txt --output OceanDNA-b32050/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:54,567] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:54,580] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:54,580] [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_002953135.1	s__Sphingobium sp002953135	80.4868	419	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005485.1	s__Sphingobium algorifonticola	80.4361	444	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	78.8281	322	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
GCF_012927105.1	s__Sphingobium psychrophilum	78.6851	320	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591655.1	s__Sphingobium sp003591655	78.598	324	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019097845.1	s__Sphingobium sp019097845	78.5899	323	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109095.1	s__Sphingobium sp900109095	78.5826	294	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710155.1	s__Sphingobium limneticum	78.576	318	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_000315525.1	s__Sphingobium yanoikuyae	78.5102	311	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_004152865.1	s__Sphingobium cupriresistens	78.4524	304	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCA_016463275.1	s__Sphingobium sp016463275	78.4196	240	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445065.1	s__Sphingobium quisquiliarum	78.3381	260	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_000281715.1	s__Sphingobium sp000281715	78.1996	284	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445105.1	s__Sphingobium lactosutens	78.1542	282	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_001563285.1	s__Sphingobium sp001563285	78.0194	236	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598335.1	s__Sphingobium abikonense	77.9611	280	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_018603885.1	s__Sphingobium sp018603885	77.2744	199	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	77.1563	156	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720115.1	s__Sphingorhabdus_B sp016720115	76.9735	138	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.85	99.81	0.95	0.95	3	-
GCF_002198665.1	s__Novosphingobium sp002198665	76.5936	115	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827305.1	s__Croceibacterium xixiisoli	76.5319	122	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970445.1	s__Sandarakinorhabdus sp018970445	76.2262	93	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:54,580] [INFO] GTDB search result was written to OceanDNA-b32050/result_gtdb.tsv
[2023-03-16 04:06:54,580] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:54,583] [INFO] DFAST_QC result json was written to OceanDNA-b32050/dqc_result.json
[2023-03-16 04:06:54,583] [INFO] DFAST_QC completed!
[2023-03-16 04:06:54,583] [INFO] Total running time: 0h1m34s