[2023-03-15 12:44:24,478] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,478] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fe88c89-a089-49be-9a0b-f50245f6cf6c/dqc_reference
[2023-03-15 12:44:26,206] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,207] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,207] [INFO] Running command: cat /var/lib/cwl/stg391f1c38-7a9f-4fe5-aa00-b921d7f37696/OceanDNA-b27315.fa | prodigal -d OceanDNA-b27315/cds.fna -a OceanDNA-b27315/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:33,016] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:33,016] [INFO] Task started: HMMsearch
[2023-03-15 12:44:33,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b27315/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fe88c89-a089-49be-9a0b-f50245f6cf6c/dqc_reference/reference_markers.hmm OceanDNA-b27315/protein.faa > /dev/null
[2023-03-15 12:44:33,202] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:33,203] [INFO] Found 6/6 markers.
[2023-03-15 12:44:33,213] [INFO] Query marker FASTA was written to OceanDNA-b27315/markers.fasta
[2023-03-15 12:44:33,214] [INFO] Task started: Blastn
[2023-03-15 12:44:33,214] [INFO] Running command: blastn -query OceanDNA-b27315/markers.fasta -db /var/lib/cwl/stg1fe88c89-a089-49be-9a0b-f50245f6cf6c/dqc_reference/reference_markers.fasta -out OceanDNA-b27315/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:33,771] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:33,772] [INFO] Selected 21 target genomes.
[2023-03-15 12:44:33,773] [INFO] Target genome list was writen to OceanDNA-b27315/target_genomes.txt
[2023-03-15 12:44:33,785] [INFO] Task started: fastANI
[2023-03-15 12:44:33,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg391f1c38-7a9f-4fe5-aa00-b921d7f37696/OceanDNA-b27315.fa --refList OceanDNA-b27315/target_genomes.txt --output OceanDNA-b27315/fastani_result.tsv --threads 1
[2023-03-15 12:44:41,242] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:41,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fe88c89-a089-49be-9a0b-f50245f6cf6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:41,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fe88c89-a089-49be-9a0b-f50245f6cf6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:41,243] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:41,243] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:41,243] [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
--------------------------------------------------------------------------------
[2023-03-15 12:44:41,243] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27315/tc_result.tsv
[2023-03-15 12:44:41,243] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:41,243] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:41,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fe88c89-a089-49be-9a0b-f50245f6cf6c/dqc_reference/checkm_data
[2023-03-15 12:44:41,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:41,249] [INFO] Task started: CheckM
[2023-03-15 12:44:41,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27315/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27315/checkm_input OceanDNA-b27315/checkm_result
[2023-03-15 12:45:03,443] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:03,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:03,445] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:03,445] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:03,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27315/markers.fasta)
[2023-03-15 12:45:03,446] [INFO] Task started: Blastn
[2023-03-15 12:45:03,446] [INFO] Running command: blastn -query OceanDNA-b27315/markers.fasta -db /var/lib/cwl/stg1fe88c89-a089-49be-9a0b-f50245f6cf6c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27315/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:04,385] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:04,386] [INFO] Selected 19 target genomes.
[2023-03-15 12:45:04,386] [INFO] Target genome list was writen to OceanDNA-b27315/target_genomes_gtdb.txt
[2023-03-15 12:45:04,515] [INFO] Task started: fastANI
[2023-03-15 12:45:04,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg391f1c38-7a9f-4fe5-aa00-b921d7f37696/OceanDNA-b27315.fa --refList OceanDNA-b27315/target_genomes_gtdb.txt --output OceanDNA-b27315/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:08,917] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:08,924] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:45:08,924] [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_002704345.1	s__MED-G09 sp002704345	99.0235	330	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.20	99.20	0.77	0.77	2	conclusive
GCA_018658685.1	s__MED-G09 sp018658685	86.4105	280	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182015.1	s__MED-G09 sp905182015	78.7298	240	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278145.1	s__MED-G09 sp003278145	78.6705	190	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	98.26	96.25	0.89	0.83	4	-
GCA_003279705.1	s__MED-G09 sp003279705	78.4498	152	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.31	98.62	0.86	0.72	3	-
GCA_002170885.2	s__MED-G09 sp002170885	77.988	94	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626605.1	s__MED-G09 sp902626605	77.9043	169	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537725.1	s__MED-G09 sp902537725	77.8245	128	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723035.1	s__MED-G09 sp002723035	77.3669	104	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209955.1	s__AG-430-B22 sp003209955	76.6577	75	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003212795.1	s__AG-430-B22 sp003212795	76.4824	79	451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.52	95.66	0.95	0.87	7	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:08,924] [INFO] GTDB search result was written to OceanDNA-b27315/result_gtdb.tsv
[2023-03-15 12:45:08,924] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:08,925] [INFO] DFAST_QC result json was written to OceanDNA-b27315/dqc_result.json
[2023-03-15 12:45:08,925] [INFO] DFAST_QC completed!
[2023-03-15 12:45:08,925] [INFO] Total running time: 0h0m44s