[2023-03-14 14:05:20,209] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:05:20,209] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:05:20,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ba03543-6897-4630-bc9e-8b8e6bd144e2/dqc_reference
[2023-03-14 14:05:21,285] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:05:21,285] [INFO] Task started: Prodigal
[2023-03-14 14:05:21,285] [INFO] Running command: cat /var/lib/cwl/stgce9e726d-a995-4742-92ae-7fb7575e7b20/OceanDNA-b30041.fa | prodigal -d OceanDNA-b30041/cds.fna -a OceanDNA-b30041/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:05:33,866] [INFO] Task succeeded: Prodigal
[2023-03-14 14:05:33,866] [INFO] Task started: HMMsearch
[2023-03-14 14:05:33,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b30041/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ba03543-6897-4630-bc9e-8b8e6bd144e2/dqc_reference/reference_markers.hmm OceanDNA-b30041/protein.faa > /dev/null
[2023-03-14 14:05:34,040] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:05:34,041] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgce9e726d-a995-4742-92ae-7fb7575e7b20/OceanDNA-b30041.fa]
[2023-03-14 14:05:34,059] [INFO] Query marker FASTA was written to OceanDNA-b30041/markers.fasta
[2023-03-14 14:05:34,059] [INFO] Task started: Blastn
[2023-03-14 14:05:34,060] [INFO] Running command: blastn -query OceanDNA-b30041/markers.fasta -db /var/lib/cwl/stg7ba03543-6897-4630-bc9e-8b8e6bd144e2/dqc_reference/reference_markers.fasta -out OceanDNA-b30041/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:05:34,668] [INFO] Task succeeded: Blastn
[2023-03-14 14:05:34,669] [INFO] Selected 16 target genomes.
[2023-03-14 14:05:34,669] [INFO] Target genome list was writen to OceanDNA-b30041/target_genomes.txt
[2023-03-14 14:05:34,677] [INFO] Task started: fastANI
[2023-03-14 14:05:34,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgce9e726d-a995-4742-92ae-7fb7575e7b20/OceanDNA-b30041.fa --refList OceanDNA-b30041/target_genomes.txt --output OceanDNA-b30041/fastani_result.tsv --threads 1
[2023-03-14 14:05:44,414] [INFO] Task succeeded: fastANI
[2023-03-14 14:05:44,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ba03543-6897-4630-bc9e-8b8e6bd144e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:05:44,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ba03543-6897-4630-bc9e-8b8e6bd144e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:05:44,425] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:05:44,425] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:05:44,425] [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
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	79.3546	390	604	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	78.9926	343	604	95	below_threshold
Pseudorhodobacter aquimaris	strain=KCTC 23043	GCA_001202025.1	687412	687412	type	True	78.6462	269	604	95	below_threshold
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	78.5988	294	604	95	below_threshold
Pseudorhodobacter antarcticus	strain=CGMCC 1.10836	GCA_900110135.1	1077947	1077947	type	True	78.4165	313	604	95	below_threshold
Pseudorhodobacter antarcticus	strain=KCTC 23700	GCA_001202015.1	1077947	1077947	type	True	78.3849	311	604	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.6454	245	604	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.4451	204	604	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.071	192	604	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.0283	195	604	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.8829	162	604	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.8829	162	604	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.793	177	604	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.7401	145	604	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.2638	93	604	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	76.0748	93	604	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:05:44,425] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30041/tc_result.tsv
[2023-03-14 14:05:44,425] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:05:44,425] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:05:44,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ba03543-6897-4630-bc9e-8b8e6bd144e2/dqc_reference/checkm_data
[2023-03-14 14:05:44,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:05:44,430] [INFO] Task started: CheckM
[2023-03-14 14:05:44,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30041/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30041/checkm_input OceanDNA-b30041/checkm_result
[2023-03-14 14:06:32,902] [INFO] Task succeeded: CheckM
[2023-03-14 14:06:32,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.88%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:06:32,905] [INFO] ===== Completeness check finished =====
[2023-03-14 14:06:32,905] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:06:32,905] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30041/markers.fasta)
[2023-03-14 14:06:32,906] [INFO] Task started: Blastn
[2023-03-14 14:06:32,906] [INFO] Running command: blastn -query OceanDNA-b30041/markers.fasta -db /var/lib/cwl/stg7ba03543-6897-4630-bc9e-8b8e6bd144e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30041/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:06:33,938] [INFO] Task succeeded: Blastn
[2023-03-14 14:06:33,938] [INFO] Selected 13 target genomes.
[2023-03-14 14:06:33,938] [INFO] Target genome list was writen to OceanDNA-b30041/target_genomes_gtdb.txt
[2023-03-14 14:06:33,949] [INFO] Task started: fastANI
[2023-03-14 14:06:33,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgce9e726d-a995-4742-92ae-7fb7575e7b20/OceanDNA-b30041.fa --refList OceanDNA-b30041/target_genomes_gtdb.txt --output OceanDNA-b30041/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:06:44,133] [INFO] Task succeeded: fastANI
[2023-03-14 14:06:44,141] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:06:44,141] [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_003991405.1	s__Pseudorhodobacter sp003991405	81.083	452	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420745.1	s__Pseudorhodobacter ferrugineus	79.3482	390	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001202035.1	s__Pseudorhodobacter wandonensis	78.9926	343	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001202025.1	s__Pseudorhodobacter aquimaris	78.6462	269	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005234135.1	s__Pseudorhodobacter turbinis	78.6129	293	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110135.1	s__Pseudorhodobacter antarcticus	78.4165	313	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCA_018798885.1	s__Gemmobacter sp018798885	77.6454	245	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016792925.1	s__Gemmobacter sp016792925	77.4986	173	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	77.4451	204	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	77.0268	149	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCA_016869835.1	s__KMS-5 sp016869835	76.8297	153	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004015795.1	s__Falsirhodobacter deserti	76.279	93	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054285.1	s__Litoreibacter ponti	76.0748	93	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:06:44,142] [INFO] GTDB search result was written to OceanDNA-b30041/result_gtdb.tsv
[2023-03-14 14:06:44,142] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:06:44,143] [INFO] DFAST_QC result json was written to OceanDNA-b30041/dqc_result.json
[2023-03-14 14:06:44,143] [INFO] DFAST_QC completed!
[2023-03-14 14:06:44,143] [INFO] Total running time: 0h1m24s