[2023-03-15 05:29:10,768] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,768] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg3db90183-949f-4f93-a7b0-ac24752f3253/dqc_reference
[2023-03-15 05:29:12,384] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,384] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,384] [INFO] Running command: cat /var/lib/cwl/stgd9306dde-c091-4c14-9a31-cbf189ba20fd/OceanDNA-b32215.fa | prodigal -d OceanDNA-b32215/cds.fna -a OceanDNA-b32215/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:27,559] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:27,559] [INFO] Task started: HMMsearch
[2023-03-15 05:29:27,559] [INFO] Running command: hmmsearch --tblout OceanDNA-b32215/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3db90183-949f-4f93-a7b0-ac24752f3253/dqc_reference/reference_markers.hmm OceanDNA-b32215/protein.faa > /dev/null
[2023-03-15 05:29:27,800] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:27,801] [INFO] Found 6/6 markers.
[2023-03-15 05:29:27,821] [INFO] Query marker FASTA was written to OceanDNA-b32215/markers.fasta
[2023-03-15 05:29:27,822] [INFO] Task started: Blastn
[2023-03-15 05:29:27,822] [INFO] Running command: blastn -query OceanDNA-b32215/markers.fasta -db /var/lib/cwl/stg3db90183-949f-4f93-a7b0-ac24752f3253/dqc_reference/reference_markers.fasta -out OceanDNA-b32215/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:28,721] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:28,722] [INFO] Selected 23 target genomes.
[2023-03-15 05:29:28,723] [INFO] Target genome list was writen to OceanDNA-b32215/target_genomes.txt
[2023-03-15 05:29:28,739] [INFO] Task started: fastANI
[2023-03-15 05:29:28,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9306dde-c091-4c14-9a31-cbf189ba20fd/OceanDNA-b32215.fa --refList OceanDNA-b32215/target_genomes.txt --output OceanDNA-b32215/fastani_result.tsv --threads 1
[2023-03-15 05:29:44,076] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:44,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3db90183-949f-4f93-a7b0-ac24752f3253/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:44,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3db90183-949f-4f93-a7b0-ac24752f3253/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:44,089] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:44,089] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:44,089] [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
Parasphingorhabdus flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	81.9243	517	786	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.5712	292	786	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.689	197	786	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.5884	237	786	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.5798	210	786	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	77.5082	190	786	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.2538	182	786	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	77.1316	186	786	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.0963	151	786	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.0765	154	786	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	77.0611	167	786	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.9631	168	786	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	76.8978	102	786	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	76.8911	142	786	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	76.8877	167	786	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	76.8007	143	786	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	76.7602	142	786	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	76.7453	123	786	95	below_threshold
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	76.6944	91	786	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.6737	133	786	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	76.6333	152	786	95	below_threshold
Novosphingobium lindaniclasticum	strain=LE124	GCA_000445125.1	1329895	1329895	type	True	76.5969	109	786	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	76.435	98	786	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:44,089] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32215/tc_result.tsv
[2023-03-15 05:29:44,089] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:44,090] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:44,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3db90183-949f-4f93-a7b0-ac24752f3253/dqc_reference/checkm_data
[2023-03-15 05:29:44,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:44,095] [INFO] Task started: CheckM
[2023-03-15 05:29:44,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32215/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32215/checkm_input OceanDNA-b32215/checkm_result
[2023-03-15 05:30:24,831] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:24,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:24,834] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:24,834] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:24,834] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32215/markers.fasta)
[2023-03-15 05:30:24,834] [INFO] Task started: Blastn
[2023-03-15 05:30:24,835] [INFO] Running command: blastn -query OceanDNA-b32215/markers.fasta -db /var/lib/cwl/stg3db90183-949f-4f93-a7b0-ac24752f3253/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32215/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:26,423] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:26,423] [INFO] Selected 10 target genomes.
[2023-03-15 05:30:26,424] [INFO] Target genome list was writen to OceanDNA-b32215/target_genomes_gtdb.txt
[2023-03-15 05:30:26,432] [INFO] Task started: fastANI
[2023-03-15 05:30:26,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9306dde-c091-4c14-9a31-cbf189ba20fd/OceanDNA-b32215.fa --refList OceanDNA-b32215/target_genomes_gtdb.txt --output OceanDNA-b32215/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:33,359] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:33,366] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:30:33,366] [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_002354635.1	s__Parasphingorhabdus sp002354635	85.4188	590	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776575.1	s__Parasphingorhabdus sp002776575	83.7111	592	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCA_002783865.1	s__Parasphingorhabdus sp002783865	83.6056	491	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCA_018067055.1	s__Parasphingorhabdus sp018067055	83.5556	395	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	83.3838	570	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	82.7056	547	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	82.0658	527	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	82.0611	551	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	81.931	516	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479715.1	s__Parasphingorhabdus sp905479715	81.6317	422	786	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:33,366] [INFO] GTDB search result was written to OceanDNA-b32215/result_gtdb.tsv
[2023-03-15 05:30:33,367] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:33,368] [INFO] DFAST_QC result json was written to OceanDNA-b32215/dqc_result.json
[2023-03-15 05:30:33,369] [INFO] DFAST_QC completed!
[2023-03-15 05:30:33,369] [INFO] Total running time: 0h1m23s