[2023-03-16 08:50:58,973] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:58,974] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:58,974] [INFO] DQC Reference Directory: /var/lib/cwl/stgd12c82f4-398f-40e2-909d-a2c28eba0bda/dqc_reference
[2023-03-16 08:51:00,135] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,135] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,135] [INFO] Running command: cat /var/lib/cwl/stg9f671a2a-4eff-4af2-b7cc-f8c960b78210/OceanDNA-b30411.fa | prodigal -d OceanDNA-b30411/cds.fna -a OceanDNA-b30411/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:14,212] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:14,213] [INFO] Task started: HMMsearch
[2023-03-16 08:51:14,213] [INFO] Running command: hmmsearch --tblout OceanDNA-b30411/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd12c82f4-398f-40e2-909d-a2c28eba0bda/dqc_reference/reference_markers.hmm OceanDNA-b30411/protein.faa > /dev/null
[2023-03-16 08:51:14,401] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:14,402] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9f671a2a-4eff-4af2-b7cc-f8c960b78210/OceanDNA-b30411.fa]
[2023-03-16 08:51:14,424] [INFO] Query marker FASTA was written to OceanDNA-b30411/markers.fasta
[2023-03-16 08:51:14,424] [INFO] Task started: Blastn
[2023-03-16 08:51:14,424] [INFO] Running command: blastn -query OceanDNA-b30411/markers.fasta -db /var/lib/cwl/stgd12c82f4-398f-40e2-909d-a2c28eba0bda/dqc_reference/reference_markers.fasta -out OceanDNA-b30411/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:15,068] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:15,069] [INFO] Selected 11 target genomes.
[2023-03-16 08:51:15,070] [INFO] Target genome list was writen to OceanDNA-b30411/target_genomes.txt
[2023-03-16 08:51:15,079] [INFO] Task started: fastANI
[2023-03-16 08:51:15,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f671a2a-4eff-4af2-b7cc-f8c960b78210/OceanDNA-b30411.fa --refList OceanDNA-b30411/target_genomes.txt --output OceanDNA-b30411/fastani_result.tsv --threads 1
[2023-03-16 08:51:23,283] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:23,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd12c82f4-398f-40e2-909d-a2c28eba0bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:23,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd12c82f4-398f-40e2-909d-a2c28eba0bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:23,291] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:23,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:51:23,292] [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
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	87.3098	653	717	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	85.4321	644	717	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	85.4125	634	717	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	83.8821	597	717	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	83.6081	564	717	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.0833	326	717	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.6556	246	717	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.2368	194	717	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.1989	183	717	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.9207	191	717	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8783	195	717	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:51:23,294] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30411/tc_result.tsv
[2023-03-16 08:51:23,295] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:23,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:23,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd12c82f4-398f-40e2-909d-a2c28eba0bda/dqc_reference/checkm_data
[2023-03-16 08:51:23,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:23,302] [INFO] Task started: CheckM
[2023-03-16 08:51:23,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30411/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30411/checkm_input OceanDNA-b30411/checkm_result
[2023-03-16 08:52:00,811] [INFO] Task succeeded: CheckM
[2023-03-16 08:52:00,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:52:00,820] [INFO] ===== Completeness check finished =====
[2023-03-16 08:52:00,820] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:52:00,820] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30411/markers.fasta)
[2023-03-16 08:52:00,821] [INFO] Task started: Blastn
[2023-03-16 08:52:00,821] [INFO] Running command: blastn -query OceanDNA-b30411/markers.fasta -db /var/lib/cwl/stgd12c82f4-398f-40e2-909d-a2c28eba0bda/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30411/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:52:01,796] [INFO] Task succeeded: Blastn
[2023-03-16 08:52:01,799] [INFO] Selected 7 target genomes.
[2023-03-16 08:52:01,799] [INFO] Target genome list was writen to OceanDNA-b30411/target_genomes_gtdb.txt
[2023-03-16 08:52:01,806] [INFO] Task started: fastANI
[2023-03-16 08:52:01,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f671a2a-4eff-4af2-b7cc-f8c960b78210/OceanDNA-b30411.fa --refList OceanDNA-b30411/target_genomes_gtdb.txt --output OceanDNA-b30411/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:52:07,208] [INFO] Task succeeded: fastANI
[2023-03-16 08:52:07,212] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:52:07,213] [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_017743885.1	s__Sulfitobacter sp001635605	96.2799	687	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	conclusive
GCF_003611275.1	s__Sulfitobacter sp001634775	89.1511	676	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_002703405.1	s__Sulfitobacter sp002703405	88.4261	587	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_900113435.1	s__Sulfitobacter dubius	87.2903	654	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_000172095.1	s__Sulfitobacter indolifex	85.3957	635	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102535.1	s__Sulfitobacter delicatus	83.8821	597	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	83.6081	564	717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:52:07,214] [INFO] GTDB search result was written to OceanDNA-b30411/result_gtdb.tsv
[2023-03-16 08:52:07,214] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:52:07,216] [INFO] DFAST_QC result json was written to OceanDNA-b30411/dqc_result.json
[2023-03-16 08:52:07,217] [INFO] DFAST_QC completed!
[2023-03-16 08:52:07,217] [INFO] Total running time: 0h1m8s