[2023-03-16 19:29:06,161] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:29:06,162] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:29:06,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e896d17-87af-4853-88c4-feaf0d3bd07c/dqc_reference
[2023-03-16 19:29:07,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:29:07,311] [INFO] Task started: Prodigal
[2023-03-16 19:29:07,311] [INFO] Running command: cat /var/lib/cwl/stg9dc582bf-b363-4f59-8d0d-77e58c8edca1/OceanDNA-b24330.fa | prodigal -d OceanDNA-b24330/cds.fna -a OceanDNA-b24330/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:29:16,117] [INFO] Task succeeded: Prodigal
[2023-03-16 19:29:16,117] [INFO] Task started: HMMsearch
[2023-03-16 19:29:16,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b24330/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e896d17-87af-4853-88c4-feaf0d3bd07c/dqc_reference/reference_markers.hmm OceanDNA-b24330/protein.faa > /dev/null
[2023-03-16 19:29:16,478] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:29:16,479] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9dc582bf-b363-4f59-8d0d-77e58c8edca1/OceanDNA-b24330.fa]
[2023-03-16 19:29:16,507] [INFO] Query marker FASTA was written to OceanDNA-b24330/markers.fasta
[2023-03-16 19:29:16,508] [INFO] Task started: Blastn
[2023-03-16 19:29:16,508] [INFO] Running command: blastn -query OceanDNA-b24330/markers.fasta -db /var/lib/cwl/stg4e896d17-87af-4853-88c4-feaf0d3bd07c/dqc_reference/reference_markers.fasta -out OceanDNA-b24330/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:29:17,597] [INFO] Task succeeded: Blastn
[2023-03-16 19:29:17,599] [INFO] Selected 21 target genomes.
[2023-03-16 19:29:17,599] [INFO] Target genome list was writen to OceanDNA-b24330/target_genomes.txt
[2023-03-16 19:29:17,618] [INFO] Task started: fastANI
[2023-03-16 19:29:17,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc582bf-b363-4f59-8d0d-77e58c8edca1/OceanDNA-b24330.fa --refList OceanDNA-b24330/target_genomes.txt --output OceanDNA-b24330/fastani_result.tsv --threads 1
[2023-03-16 19:29:30,348] [INFO] Task succeeded: fastANI
[2023-03-16 19:29:30,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e896d17-87af-4853-88c4-feaf0d3bd07c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:29:30,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e896d17-87af-4853-88c4-feaf0d3bd07c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:29:30,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:29:30,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:29:30,349] [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
--------------------------------------------------------------------------------
[2023-03-16 19:29:30,349] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24330/tc_result.tsv
[2023-03-16 19:29:30,349] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:29:30,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:29:30,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e896d17-87af-4853-88c4-feaf0d3bd07c/dqc_reference/checkm_data
[2023-03-16 19:29:30,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:29:30,516] [INFO] Task started: CheckM
[2023-03-16 19:29:30,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24330/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24330/checkm_input OceanDNA-b24330/checkm_result
[2023-03-16 19:30:00,541] [INFO] Task succeeded: CheckM
[2023-03-16 19:30:00,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:30:00,546] [INFO] ===== Completeness check finished =====
[2023-03-16 19:30:00,546] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:30:00,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24330/markers.fasta)
[2023-03-16 19:30:00,547] [INFO] Task started: Blastn
[2023-03-16 19:30:00,547] [INFO] Running command: blastn -query OceanDNA-b24330/markers.fasta -db /var/lib/cwl/stg4e896d17-87af-4853-88c4-feaf0d3bd07c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24330/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:30:01,354] [INFO] Task succeeded: Blastn
[2023-03-16 19:30:01,355] [INFO] Selected 14 target genomes.
[2023-03-16 19:30:01,356] [INFO] Target genome list was writen to OceanDNA-b24330/target_genomes_gtdb.txt
[2023-03-16 19:30:01,364] [INFO] Task started: fastANI
[2023-03-16 19:30:01,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dc582bf-b363-4f59-8d0d-77e58c8edca1/OceanDNA-b24330.fa --refList OceanDNA-b24330/target_genomes_gtdb.txt --output OceanDNA-b24330/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:30:05,333] [INFO] Task succeeded: fastANI
[2023-03-16 19:30:05,341] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:30:05,342] [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_018657885.1	s__AG-337-I02 sp018657885	99.0519	373	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.38	99.29	0.88	0.87	3	conclusive
GCA_902511405.1	s__AG-337-I02 sp902511405	80.3079	176	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512325.1	s__AG-337-I02 sp902512325	80.2511	220	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592345.1	s__AG-337-I02 sp902592345	80.1781	208	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596365.1	s__AG-337-I02 sp902596365	80.0451	191	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902567135.1	s__AG-337-I02 sp902567135	79.9803	198	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601455.1	s__AG-337-I02 sp902601455	79.5916	255	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586695.1	s__AG-337-I02 sp902586695	79.5872	205	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591485.1	s__AG-337-I02 sp902591485	78.917	209	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	97.00	97.00	0.77	0.77	2	-
GCA_902595425.1	s__AG-337-I02 sp902595425	78.9074	225	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595855.1	s__AG-337-I02 sp902595855	78.7014	218	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594815.1	s__AG-337-I02 sp902594815	78.6364	192	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561355.1	s__AG-337-I02 sp902561355	77.9462	138	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518985.1	s__AG-337-I02 sp902518985	76.9108	89	481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:30:05,342] [INFO] GTDB search result was written to OceanDNA-b24330/result_gtdb.tsv
[2023-03-16 19:30:05,342] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:30:05,345] [INFO] DFAST_QC result json was written to OceanDNA-b24330/dqc_result.json
[2023-03-16 19:30:05,345] [INFO] DFAST_QC completed!
[2023-03-16 19:30:05,345] [INFO] Total running time: 0h0m59s