[2023-03-16 10:07:19,370] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:07:19,370] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:07:19,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg18cdd5c9-b742-431b-aa4f-fa130095c86e/dqc_reference
[2023-03-16 10:07:20,482] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:07:20,483] [INFO] Task started: Prodigal
[2023-03-16 10:07:20,483] [INFO] Running command: cat /var/lib/cwl/stg8e0e5547-c388-4084-ad16-81aed94c0e53/OceanDNA-b31656.fa | prodigal -d OceanDNA-b31656/cds.fna -a OceanDNA-b31656/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:07:40,316] [INFO] Task succeeded: Prodigal
[2023-03-16 10:07:40,317] [INFO] Task started: HMMsearch
[2023-03-16 10:07:40,317] [INFO] Running command: hmmsearch --tblout OceanDNA-b31656/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18cdd5c9-b742-431b-aa4f-fa130095c86e/dqc_reference/reference_markers.hmm OceanDNA-b31656/protein.faa > /dev/null
[2023-03-16 10:07:40,513] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:07:40,513] [INFO] Found 6/6 markers.
[2023-03-16 10:07:40,533] [INFO] Query marker FASTA was written to OceanDNA-b31656/markers.fasta
[2023-03-16 10:07:40,534] [INFO] Task started: Blastn
[2023-03-16 10:07:40,534] [INFO] Running command: blastn -query OceanDNA-b31656/markers.fasta -db /var/lib/cwl/stg18cdd5c9-b742-431b-aa4f-fa130095c86e/dqc_reference/reference_markers.fasta -out OceanDNA-b31656/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:07:41,336] [INFO] Task succeeded: Blastn
[2023-03-16 10:07:41,337] [INFO] Selected 12 target genomes.
[2023-03-16 10:07:41,337] [INFO] Target genome list was writen to OceanDNA-b31656/target_genomes.txt
[2023-03-16 10:07:41,347] [INFO] Task started: fastANI
[2023-03-16 10:07:41,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e0e5547-c388-4084-ad16-81aed94c0e53/OceanDNA-b31656.fa --refList OceanDNA-b31656/target_genomes.txt --output OceanDNA-b31656/fastani_result.tsv --threads 1
[2023-03-16 10:07:49,560] [INFO] Task succeeded: fastANI
[2023-03-16 10:07:49,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18cdd5c9-b742-431b-aa4f-fa130095c86e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:07:49,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18cdd5c9-b742-431b-aa4f-fa130095c86e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:07:49,568] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:07:49,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:07:49,568] [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
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	87.8932	870	1056	95	below_threshold
Croceicoccus mobilis	strain=Ery22	GCA_001661965.1	1703339	1703339	type	True	82.3002	643	1056	95	below_threshold
Croceicoccus mobilis	strain=CGMCC 1.15360	GCA_014642595.1	1703339	1703339	type	True	82.2909	655	1056	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	80.2678	480	1056	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	79.8884	445	1056	95	below_threshold
Croceicoccus naphthovorans	strain=DSM 102796	GCA_014196855.1	1348774	1348774	type	True	79.7415	444	1056	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	79.6077	481	1056	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	79.5977	501	1056	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	79.3819	495	1056	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.5436	328	1056	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.1721	328	1056	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7414	289	1056	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:07:49,569] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31656/tc_result.tsv
[2023-03-16 10:07:49,569] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:07:49,569] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:07:49,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18cdd5c9-b742-431b-aa4f-fa130095c86e/dqc_reference/checkm_data
[2023-03-16 10:07:49,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:07:49,574] [INFO] Task started: CheckM
[2023-03-16 10:07:49,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31656/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31656/checkm_input OceanDNA-b31656/checkm_result
[2023-03-16 10:08:39,071] [INFO] Task succeeded: CheckM
[2023-03-16 10:08:39,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:08:39,074] [INFO] ===== Completeness check finished =====
[2023-03-16 10:08:39,074] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:08:39,074] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31656/markers.fasta)
[2023-03-16 10:08:39,075] [INFO] Task started: Blastn
[2023-03-16 10:08:39,075] [INFO] Running command: blastn -query OceanDNA-b31656/markers.fasta -db /var/lib/cwl/stg18cdd5c9-b742-431b-aa4f-fa130095c86e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31656/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:40,464] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:40,465] [INFO] Selected 12 target genomes.
[2023-03-16 10:08:40,466] [INFO] Target genome list was writen to OceanDNA-b31656/target_genomes_gtdb.txt
[2023-03-16 10:08:40,478] [INFO] Task started: fastANI
[2023-03-16 10:08:40,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e0e5547-c388-4084-ad16-81aed94c0e53/OceanDNA-b31656.fa --refList OceanDNA-b31656/target_genomes_gtdb.txt --output OceanDNA-b31656/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:08:49,535] [INFO] Task succeeded: fastANI
[2023-03-16 10:08:49,543] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:08:49,543] [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_002694745.1	s__Croceicoccus sp002694745	99.9486	1016	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	99.91	99.91	0.91	0.91	2	conclusive
GCF_001661675.2	s__Croceicoccus marinus	87.9037	869	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	96.65	96.65	0.86	0.86	2	-
GCF_001661965.1	s__Croceicoccus mobilis	82.3181	641	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001634625.1	s__Croceicoccus bisphenolivorans	79.9007	444	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570835.1	s__Croceicoccus sediminis	79.5932	482	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398395.1	s__Croceicoccus sp018398395	79.5926	501	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661915.1	s__Croceicoccus pelagius	79.3926	494	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016745095.1	s__Croceicoccus sp016745095	79.3105	453	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.1499	330	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	78.1163	320	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCF_000281975.1	s__Novosphingobium sp000281975	78.081	353	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506425.1	s__Novosphingobium sp902506425	77.9346	341	1056	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:08:49,543] [INFO] GTDB search result was written to OceanDNA-b31656/result_gtdb.tsv
[2023-03-16 10:08:49,543] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:08:49,545] [INFO] DFAST_QC result json was written to OceanDNA-b31656/dqc_result.json
[2023-03-16 10:08:49,545] [INFO] DFAST_QC completed!
[2023-03-16 10:08:49,545] [INFO] Total running time: 0h1m30s