[2023-03-19 04:11:06,935] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,935] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a29cb5b-81c0-4275-b46b-27d33fb5f748/dqc_reference
[2023-03-19 04:11:08,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stg79eeb5d5-ecd0-4c75-ba30-6742c120532f/OceanDNA-b28282.fa | prodigal -d OceanDNA-b28282/cds.fna -a OceanDNA-b28282/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:16,798] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:16,798] [INFO] Task started: HMMsearch
[2023-03-19 04:11:16,798] [INFO] Running command: hmmsearch --tblout OceanDNA-b28282/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a29cb5b-81c0-4275-b46b-27d33fb5f748/dqc_reference/reference_markers.hmm OceanDNA-b28282/protein.faa > /dev/null
[2023-03-19 04:11:16,974] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:16,974] [INFO] Found 6/6 markers.
[2023-03-19 04:11:16,988] [INFO] Query marker FASTA was written to OceanDNA-b28282/markers.fasta
[2023-03-19 04:11:16,988] [INFO] Task started: Blastn
[2023-03-19 04:11:16,988] [INFO] Running command: blastn -query OceanDNA-b28282/markers.fasta -db /var/lib/cwl/stg5a29cb5b-81c0-4275-b46b-27d33fb5f748/dqc_reference/reference_markers.fasta -out OceanDNA-b28282/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:17,552] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:17,553] [INFO] Selected 19 target genomes.
[2023-03-19 04:11:17,553] [INFO] Target genome list was writen to OceanDNA-b28282/target_genomes.txt
[2023-03-19 04:11:17,565] [INFO] Task started: fastANI
[2023-03-19 04:11:17,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg79eeb5d5-ecd0-4c75-ba30-6742c120532f/OceanDNA-b28282.fa --refList OceanDNA-b28282/target_genomes.txt --output OceanDNA-b28282/fastani_result.tsv --threads 1
[2023-03-19 04:11:28,644] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:28,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a29cb5b-81c0-4275-b46b-27d33fb5f748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:28,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a29cb5b-81c0-4275-b46b-27d33fb5f748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:28,645] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:28,645] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:11:28,645] [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
--------------------------------------------------------------------------------
[2023-03-19 04:11:28,645] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28282/tc_result.tsv
[2023-03-19 04:11:28,645] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:28,645] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:28,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a29cb5b-81c0-4275-b46b-27d33fb5f748/dqc_reference/checkm_data
[2023-03-19 04:11:28,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:28,651] [INFO] Task started: CheckM
[2023-03-19 04:11:28,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28282/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28282/checkm_input OceanDNA-b28282/checkm_result
[2023-03-19 04:11:53,729] [INFO] Task succeeded: CheckM
[2023-03-19 04:11:53,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:11:53,732] [INFO] ===== Completeness check finished =====
[2023-03-19 04:11:53,732] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:11:53,732] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28282/markers.fasta)
[2023-03-19 04:11:53,732] [INFO] Task started: Blastn
[2023-03-19 04:11:53,732] [INFO] Running command: blastn -query OceanDNA-b28282/markers.fasta -db /var/lib/cwl/stg5a29cb5b-81c0-4275-b46b-27d33fb5f748/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28282/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:54,656] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:54,657] [INFO] Selected 17 target genomes.
[2023-03-19 04:11:54,657] [INFO] Target genome list was writen to OceanDNA-b28282/target_genomes_gtdb.txt
[2023-03-19 04:11:54,766] [INFO] Task started: fastANI
[2023-03-19 04:11:54,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg79eeb5d5-ecd0-4c75-ba30-6742c120532f/OceanDNA-b28282.fa --refList OceanDNA-b28282/target_genomes_gtdb.txt --output OceanDNA-b28282/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:00,977] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:00,986] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:12:00,986] [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_003331935.1	s__CACIJG01 sp003331935	99.3128	423	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902524845.1	s__CACIJG01 sp902524845	83.5058	334	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537415.1	s__CACIJG01 sp902537415	81.9231	267	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531755.1	s__CACIJG01 sp902531755	81.6154	238	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611475.1	s__CACIJG01 sp902611475	81.5102	252	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576905.1	s__CACIJG01 sp902576905	81.4866	303	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524655.1	s__CACIJG01 sp902524655	81.3032	234	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537215.1	s__CACIJG01 sp902537215	81.2177	326	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596985.1	s__CACIJG01 sp902596985	81.1556	272	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560505.1	s__CACIJG01 sp902560505	81.131	208	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902581005.1	s__CACIJG01 sp902581005	81.1169	248	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556405.1	s__CACIJG01 sp902556405	81.0905	319	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902584635.1	s__CACIJG01 sp902584635	80.9007	272	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574225.1	s__CACIJG01 sp902574225	80.8005	329	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703515.1	s__CACIJG01 sp002703515	79.506	167	499	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:00,986] [INFO] GTDB search result was written to OceanDNA-b28282/result_gtdb.tsv
[2023-03-19 04:12:00,986] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:00,987] [INFO] DFAST_QC result json was written to OceanDNA-b28282/dqc_result.json
[2023-03-19 04:12:00,988] [INFO] DFAST_QC completed!
[2023-03-19 04:12:00,988] [INFO] Total running time: 0h0m54s