[2023-03-18 08:55:50,616] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,616] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c025ed8-73fb-4fb5-91f8-840a4069ea4e/dqc_reference
[2023-03-18 08:55:51,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,912] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,912] [INFO] Running command: cat /var/lib/cwl/stg31ebd940-b4fd-4b89-b6d8-58325e7f8e23/OceanDNA-b27193.fa | prodigal -d OceanDNA-b27193/cds.fna -a OceanDNA-b27193/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:57,603] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:57,603] [INFO] Task started: HMMsearch
[2023-03-18 08:55:57,603] [INFO] Running command: hmmsearch --tblout OceanDNA-b27193/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c025ed8-73fb-4fb5-91f8-840a4069ea4e/dqc_reference/reference_markers.hmm OceanDNA-b27193/protein.faa > /dev/null
[2023-03-18 08:55:57,764] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:57,765] [INFO] Found 6/6 markers.
[2023-03-18 08:55:57,775] [INFO] Query marker FASTA was written to OceanDNA-b27193/markers.fasta
[2023-03-18 08:55:57,776] [INFO] Task started: Blastn
[2023-03-18 08:55:57,777] [INFO] Running command: blastn -query OceanDNA-b27193/markers.fasta -db /var/lib/cwl/stg2c025ed8-73fb-4fb5-91f8-840a4069ea4e/dqc_reference/reference_markers.fasta -out OceanDNA-b27193/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:55:58,408] [INFO] Task succeeded: Blastn
[2023-03-18 08:55:58,409] [INFO] Selected 22 target genomes.
[2023-03-18 08:55:58,409] [INFO] Target genome list was writen to OceanDNA-b27193/target_genomes.txt
[2023-03-18 08:55:58,425] [INFO] Task started: fastANI
[2023-03-18 08:55:58,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ebd940-b4fd-4b89-b6d8-58325e7f8e23/OceanDNA-b27193.fa --refList OceanDNA-b27193/target_genomes.txt --output OceanDNA-b27193/fastani_result.tsv --threads 1
[2023-03-18 08:56:08,385] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:08,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c025ed8-73fb-4fb5-91f8-840a4069ea4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:08,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c025ed8-73fb-4fb5-91f8-840a4069ea4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:08,386] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:08,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:56:08,386] [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
--------------------------------------------------------------------------------
[2023-03-18 08:56:08,386] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27193/tc_result.tsv
[2023-03-18 08:56:08,386] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:08,386] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:08,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c025ed8-73fb-4fb5-91f8-840a4069ea4e/dqc_reference/checkm_data
[2023-03-18 08:56:08,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:08,393] [INFO] Task started: CheckM
[2023-03-18 08:56:08,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27193/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27193/checkm_input OceanDNA-b27193/checkm_result
[2023-03-18 08:56:28,107] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:28,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:28,110] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:28,111] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:28,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27193/markers.fasta)
[2023-03-18 08:56:28,112] [INFO] Task started: Blastn
[2023-03-18 08:56:28,112] [INFO] Running command: blastn -query OceanDNA-b27193/markers.fasta -db /var/lib/cwl/stg2c025ed8-73fb-4fb5-91f8-840a4069ea4e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27193/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:29,047] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:29,048] [INFO] Selected 15 target genomes.
[2023-03-18 08:56:29,048] [INFO] Target genome list was writen to OceanDNA-b27193/target_genomes_gtdb.txt
[2023-03-18 08:56:29,076] [INFO] Task started: fastANI
[2023-03-18 08:56:29,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ebd940-b4fd-4b89-b6d8-58325e7f8e23/OceanDNA-b27193.fa --refList OceanDNA-b27193/target_genomes_gtdb.txt --output OceanDNA-b27193/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:32,429] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:32,436] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:56:32,436] [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_018658685.1	s__MED-G09 sp018658685	98.4458	272	359	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	conclusive
GCA_002704345.1	s__MED-G09 sp002704345	86.5185	251	359	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	-
GCA_905182015.1	s__MED-G09 sp905182015	78.7836	205	359	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_003279705.1	s__MED-G09 sp003279705	78.1039	123	359	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_902626605.1	s__MED-G09 sp902626605	77.6309	138	359	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_002170885.2	s__MED-G09 sp002170885	77.5801	86	359	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	77.4544	152	359	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_002683015.1	s__MED-G09 sp002683015	77.4191	84	359	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	77.2768	78	359	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	77.2019	97	359	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_002728335.1	s__AG-430-B22 sp002728335	76.4841	51	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	97.53	96.38	0.78	0.71	4	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:32,437] [INFO] GTDB search result was written to OceanDNA-b27193/result_gtdb.tsv
[2023-03-18 08:56:32,437] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:32,438] [INFO] DFAST_QC result json was written to OceanDNA-b27193/dqc_result.json
[2023-03-18 08:56:32,438] [INFO] DFAST_QC completed!
[2023-03-18 08:56:32,438] [INFO] Total running time: 0h0m42s