[2023-03-17 13:46:30,403] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:46:30,403] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:46:30,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg07702bf4-84b5-47c9-91c1-6cf1881b8587/dqc_reference
[2023-03-17 13:46:32,765] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:46:32,778] [INFO] Task started: Prodigal
[2023-03-17 13:46:32,778] [INFO] Running command: cat /var/lib/cwl/stg6b81c980-176e-4595-bf48-f763bdbc9694/OceanDNA-b32257.fa | prodigal -d OceanDNA-b32257/cds.fna -a OceanDNA-b32257/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:46:55,357] [INFO] Task succeeded: Prodigal
[2023-03-17 13:46:55,358] [INFO] Task started: HMMsearch
[2023-03-17 13:46:55,358] [INFO] Running command: hmmsearch --tblout OceanDNA-b32257/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07702bf4-84b5-47c9-91c1-6cf1881b8587/dqc_reference/reference_markers.hmm OceanDNA-b32257/protein.faa > /dev/null
[2023-03-17 13:46:55,573] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:46:55,574] [INFO] Found 6/6 markers.
[2023-03-17 13:46:55,593] [INFO] Query marker FASTA was written to OceanDNA-b32257/markers.fasta
[2023-03-17 13:46:55,593] [INFO] Task started: Blastn
[2023-03-17 13:46:55,593] [INFO] Running command: blastn -query OceanDNA-b32257/markers.fasta -db /var/lib/cwl/stg07702bf4-84b5-47c9-91c1-6cf1881b8587/dqc_reference/reference_markers.fasta -out OceanDNA-b32257/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:46:56,298] [INFO] Task succeeded: Blastn
[2023-03-17 13:46:56,299] [INFO] Selected 20 target genomes.
[2023-03-17 13:46:56,299] [INFO] Target genome list was writen to OceanDNA-b32257/target_genomes.txt
[2023-03-17 13:46:56,339] [INFO] Task started: fastANI
[2023-03-17 13:46:56,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b81c980-176e-4595-bf48-f763bdbc9694/OceanDNA-b32257.fa --refList OceanDNA-b32257/target_genomes.txt --output OceanDNA-b32257/fastani_result.tsv --threads 1
[2023-03-17 13:47:18,494] [INFO] Task succeeded: fastANI
[2023-03-17 13:47:18,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07702bf4-84b5-47c9-91c1-6cf1881b8587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:47:18,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07702bf4-84b5-47c9-91c1-6cf1881b8587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:47:18,506] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:47:18,506] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:47:18,506] [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	82.9356	691	997	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.5748	372	997	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.1343	372	997	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.0887	309	997	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.9516	324	997	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	77.2952	201	997	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	77.2795	171	997	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	77.1752	177	997	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.103	168	997	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	77.0768	152	997	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	76.9835	131	997	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.921	138	997	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.8217	164	997	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	76.7805	170	997	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.7711	142	997	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	76.746	140	997	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	76.7443	137	997	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.7397	133	997	95	below_threshold
Sphingomonas sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	76.5774	98	997	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	76.5772	136	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:47:18,508] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32257/tc_result.tsv
[2023-03-17 13:47:18,508] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:47:18,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:47:18,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07702bf4-84b5-47c9-91c1-6cf1881b8587/dqc_reference/checkm_data
[2023-03-17 13:47:18,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:47:18,516] [INFO] Task started: CheckM
[2023-03-17 13:47:18,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32257/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32257/checkm_input OceanDNA-b32257/checkm_result
[2023-03-17 13:48:06,215] [INFO] Task succeeded: CheckM
[2023-03-17 13:48:06,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:48:06,218] [INFO] ===== Completeness check finished =====
[2023-03-17 13:48:06,218] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:48:06,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32257/markers.fasta)
[2023-03-17 13:48:06,219] [INFO] Task started: Blastn
[2023-03-17 13:48:06,219] [INFO] Running command: blastn -query OceanDNA-b32257/markers.fasta -db /var/lib/cwl/stg07702bf4-84b5-47c9-91c1-6cf1881b8587/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32257/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:48:07,325] [INFO] Task succeeded: Blastn
[2023-03-17 13:48:07,326] [INFO] Selected 11 target genomes.
[2023-03-17 13:48:07,326] [INFO] Target genome list was writen to OceanDNA-b32257/target_genomes_gtdb.txt
[2023-03-17 13:48:07,590] [INFO] Task started: fastANI
[2023-03-17 13:48:07,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b81c980-176e-4595-bf48-f763bdbc9694/OceanDNA-b32257.fa --refList OceanDNA-b32257/target_genomes_gtdb.txt --output OceanDNA-b32257/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:48:15,437] [INFO] Task succeeded: fastANI
[2023-03-17 13:48:15,444] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:48:15,444] [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_002783865.1	s__Parasphingorhabdus sp002783865	84.4352	634	997	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	84.1485	475	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	83.696	758	997	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	83.6903	762	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204445.1	s__Parasphingorhabdus sp013204445	83.5583	459	997	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	83.0383	737	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	82.9356	691	997	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	82.772	700	997	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	82.6161	713	997	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	82.4654	551	997	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	82.2764	689	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:48:15,444] [INFO] GTDB search result was written to OceanDNA-b32257/result_gtdb.tsv
[2023-03-17 13:48:15,444] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:48:15,446] [INFO] DFAST_QC result json was written to OceanDNA-b32257/dqc_result.json
[2023-03-17 13:48:15,446] [INFO] DFAST_QC completed!
[2023-03-17 13:48:15,446] [INFO] Total running time: 0h1m45s