[2023-03-18 02:27:37,207] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,207] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg002d672d-b362-4051-a19f-0c6dc60702a9/dqc_reference
[2023-03-18 02:27:38,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,483] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,484] [INFO] Running command: cat /var/lib/cwl/stg1a9ac6ac-34a9-4b9b-9d34-0c54ea48c76f/OceanDNA-b32913.fa | prodigal -d OceanDNA-b32913/cds.fna -a OceanDNA-b32913/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:27:47,944] [INFO] Task succeeded: Prodigal
[2023-03-18 02:27:47,944] [INFO] Task started: HMMsearch
[2023-03-18 02:27:47,944] [INFO] Running command: hmmsearch --tblout OceanDNA-b32913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg002d672d-b362-4051-a19f-0c6dc60702a9/dqc_reference/reference_markers.hmm OceanDNA-b32913/protein.faa > /dev/null
[2023-03-18 02:27:48,104] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:27:48,105] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1a9ac6ac-34a9-4b9b-9d34-0c54ea48c76f/OceanDNA-b32913.fa]
[2023-03-18 02:27:48,121] [INFO] Query marker FASTA was written to OceanDNA-b32913/markers.fasta
[2023-03-18 02:27:48,122] [INFO] Task started: Blastn
[2023-03-18 02:27:48,122] [INFO] Running command: blastn -query OceanDNA-b32913/markers.fasta -db /var/lib/cwl/stg002d672d-b362-4051-a19f-0c6dc60702a9/dqc_reference/reference_markers.fasta -out OceanDNA-b32913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:27:48,749] [INFO] Task succeeded: Blastn
[2023-03-18 02:27:48,750] [INFO] Selected 25 target genomes.
[2023-03-18 02:27:48,750] [INFO] Target genome list was writen to OceanDNA-b32913/target_genomes.txt
[2023-03-18 02:27:48,759] [INFO] Task started: fastANI
[2023-03-18 02:27:48,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9ac6ac-34a9-4b9b-9d34-0c54ea48c76f/OceanDNA-b32913.fa --refList OceanDNA-b32913/target_genomes.txt --output OceanDNA-b32913/fastani_result.tsv --threads 1
[2023-03-18 02:28:07,673] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:07,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg002d672d-b362-4051-a19f-0c6dc60702a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:07,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg002d672d-b362-4051-a19f-0c6dc60702a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:07,680] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:07,681] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:07,681] [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
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.4939	61	443	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.3689	53	443	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.305	78	443	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.2656	81	443	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.9005	58	443	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.8832	60	443	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.5579	57	443	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.3461	71	443	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.3186	66	443	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.3186	66	443	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:07,681] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32913/tc_result.tsv
[2023-03-18 02:28:07,681] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:07,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:07,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg002d672d-b362-4051-a19f-0c6dc60702a9/dqc_reference/checkm_data
[2023-03-18 02:28:07,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:07,685] [INFO] Task started: CheckM
[2023-03-18 02:28:07,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32913/checkm_input OceanDNA-b32913/checkm_result
[2023-03-18 02:28:35,778] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:35,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:35,780] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:35,780] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:35,781] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32913/markers.fasta)
[2023-03-18 02:28:35,781] [INFO] Task started: Blastn
[2023-03-18 02:28:35,781] [INFO] Running command: blastn -query OceanDNA-b32913/markers.fasta -db /var/lib/cwl/stg002d672d-b362-4051-a19f-0c6dc60702a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:36,847] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:36,848] [INFO] Selected 16 target genomes.
[2023-03-18 02:28:36,848] [INFO] Target genome list was writen to OceanDNA-b32913/target_genomes_gtdb.txt
[2023-03-18 02:28:36,865] [INFO] Task started: fastANI
[2023-03-18 02:28:36,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9ac6ac-34a9-4b9b-9d34-0c54ea48c76f/OceanDNA-b32913.fa --refList OceanDNA-b32913/target_genomes_gtdb.txt --output OceanDNA-b32913/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:48,444] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:48,451] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:28:48,451] [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_002937555.1	s__PTKB01 sp002937555	80.0185	223	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666805.1	s__PTKB01 sp018666805	79.7868	306	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_002717225.1	s__PTKB01 sp002717225	78.4231	195	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523425.1	s__WTGU01 sp011523425	77.6871	131	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.3689	53	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.2046	67	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.1099	99	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	76.0346	51	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195145.1	s__JACQAF01 sp016195145	75.9616	54	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012971745.1	s__ORNL1 sp012971745	75.9397	55	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__ORNL1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	75.1815	64	443	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:48,452] [INFO] GTDB search result was written to OceanDNA-b32913/result_gtdb.tsv
[2023-03-18 02:28:48,452] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:48,453] [INFO] DFAST_QC result json was written to OceanDNA-b32913/dqc_result.json
[2023-03-18 02:28:48,453] [INFO] DFAST_QC completed!
[2023-03-18 02:28:48,453] [INFO] Total running time: 0h1m11s