[2023-03-18 00:13:25,309] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:13:25,309] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:13:25,309] [INFO] DQC Reference Directory: /var/lib/cwl/stgac4aa58a-4353-4ee6-9355-5bad82e0fe82/dqc_reference
[2023-03-18 00:13:26,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:13:26,449] [INFO] Task started: Prodigal
[2023-03-18 00:13:26,449] [INFO] Running command: cat /var/lib/cwl/stg3820d220-7a6a-41b6-b3ff-1b5b5d17b52c/OceanDNA-b28110.fa | prodigal -d OceanDNA-b28110/cds.fna -a OceanDNA-b28110/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:13:51,765] [INFO] Task succeeded: Prodigal
[2023-03-18 00:13:51,766] [INFO] Task started: HMMsearch
[2023-03-18 00:13:51,766] [INFO] Running command: hmmsearch --tblout OceanDNA-b28110/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac4aa58a-4353-4ee6-9355-5bad82e0fe82/dqc_reference/reference_markers.hmm OceanDNA-b28110/protein.faa > /dev/null
[2023-03-18 00:13:51,971] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:13:51,971] [INFO] Found 6/6 markers.
[2023-03-18 00:13:51,995] [INFO] Query marker FASTA was written to OceanDNA-b28110/markers.fasta
[2023-03-18 00:13:51,996] [INFO] Task started: Blastn
[2023-03-18 00:13:51,996] [INFO] Running command: blastn -query OceanDNA-b28110/markers.fasta -db /var/lib/cwl/stgac4aa58a-4353-4ee6-9355-5bad82e0fe82/dqc_reference/reference_markers.fasta -out OceanDNA-b28110/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:13:52,640] [INFO] Task succeeded: Blastn
[2023-03-18 00:13:52,641] [INFO] Selected 14 target genomes.
[2023-03-18 00:13:52,641] [INFO] Target genome list was writen to OceanDNA-b28110/target_genomes.txt
[2023-03-18 00:13:52,649] [INFO] Task started: fastANI
[2023-03-18 00:13:52,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg3820d220-7a6a-41b6-b3ff-1b5b5d17b52c/OceanDNA-b28110.fa --refList OceanDNA-b28110/target_genomes.txt --output OceanDNA-b28110/fastani_result.tsv --threads 1
[2023-03-18 00:14:02,442] [INFO] Task succeeded: fastANI
[2023-03-18 00:14:02,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac4aa58a-4353-4ee6-9355-5bad82e0fe82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:14:02,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac4aa58a-4353-4ee6-9355-5bad82e0fe82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:14:02,451] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:14:02,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:14:02,451] [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
Celeribacter baekdonensis	strain=DSM 27375	GCA_900102315.1	875171	875171	type	True	90.327	1035	1270	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	79.1461	647	1270	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	78.8403	614	1270	95	below_threshold
Celeribacter halophilus	strain=CGMCC 1.8891	GCA_900114135.1	576117	576117	type	True	78.8028	491	1270	95	below_threshold
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	78.7867	579	1270	95	below_threshold
Celeribacter halophilus	strain=ZXM137	GCA_001550085.1	576117	576117	type	True	78.7722	496	1270	95	below_threshold
Celeribacter halophilus	strain=DSM 26270	GCA_003254175.1	576117	576117	type	True	78.7241	500	1270	95	below_threshold
Celeribacter marinus	strain=IMCC12053	GCA_001308265.1	1397108	1397108	type	True	77.9059	316	1270	95	below_threshold
Aquimixticola soesokkakensis	strain=CECT 8620	GCA_900172375.1	1519096	1519096	type	True	77.5756	300	1270	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.0049	114	1270	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.4344	130	1270	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.2166	108	1270	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.2132	142	1270	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.9112	143	1270	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:14:02,452] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28110/tc_result.tsv
[2023-03-18 00:14:02,452] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:14:02,452] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:14:02,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac4aa58a-4353-4ee6-9355-5bad82e0fe82/dqc_reference/checkm_data
[2023-03-18 00:14:02,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:14:02,458] [INFO] Task started: CheckM
[2023-03-18 00:14:02,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28110/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28110/checkm_input OceanDNA-b28110/checkm_result
[2023-03-18 00:15:06,554] [INFO] Task succeeded: CheckM
[2023-03-18 00:15:06,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:15:06,558] [INFO] ===== Completeness check finished =====
[2023-03-18 00:15:06,558] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:15:06,558] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28110/markers.fasta)
[2023-03-18 00:15:06,559] [INFO] Task started: Blastn
[2023-03-18 00:15:06,559] [INFO] Running command: blastn -query OceanDNA-b28110/markers.fasta -db /var/lib/cwl/stgac4aa58a-4353-4ee6-9355-5bad82e0fe82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28110/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:07,655] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:07,657] [INFO] Selected 8 target genomes.
[2023-03-18 00:15:07,657] [INFO] Target genome list was writen to OceanDNA-b28110/target_genomes_gtdb.txt
[2023-03-18 00:15:07,665] [INFO] Task started: fastANI
[2023-03-18 00:15:07,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg3820d220-7a6a-41b6-b3ff-1b5b5d17b52c/OceanDNA-b28110.fa --refList OceanDNA-b28110/target_genomes_gtdb.txt --output OceanDNA-b28110/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:15:15,449] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:15,455] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:15:15,455] [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_003047105.1	s__Celeribacter baekdonensis_B	98.6084	1199	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000299875.1	s__Celeribacter baekdonensis_A	90.7663	1051	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	99.07	99.01	0.95	0.93	3	-
GCF_900102315.1	s__Celeribacter baekdonensis	90.327	1035	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.81	97.75	0.91	0.89	8	-
GCF_011806455.1	s__Celeribacter sp011806455	79.7915	649	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCF_001550095.1	s__Celeribacter ethanolicus	79.1341	648	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_900113955.1	s__Celeribacter neptunius	78.8475	613	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114135.1	s__Celeribacter halophilus	78.7984	492	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.37	95.14	0.95	0.87	4	-
GCF_003050785.1	s__Celeribacter persicus	78.7822	579	1270	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:15:15,456] [INFO] GTDB search result was written to OceanDNA-b28110/result_gtdb.tsv
[2023-03-18 00:15:15,457] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:15:15,459] [INFO] DFAST_QC result json was written to OceanDNA-b28110/dqc_result.json
[2023-03-18 00:15:15,459] [INFO] DFAST_QC completed!
[2023-03-18 00:15:15,459] [INFO] Total running time: 0h1m50s