[2023-03-17 02:03:49,451] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:49,451] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:49,451] [INFO] DQC Reference Directory: /var/lib/cwl/stg05b83a87-375b-45a6-88cb-45386c47e62e/dqc_reference
[2023-03-17 02:03:50,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:50,614] [INFO] Task started: Prodigal
[2023-03-17 02:03:50,614] [INFO] Running command: cat /var/lib/cwl/stg749ad7ea-6e28-4b4e-b57a-4762e9903ed0/OceanDNA-b16236.fa | prodigal -d OceanDNA-b16236/cds.fna -a OceanDNA-b16236/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:03:59,775] [INFO] Task succeeded: Prodigal
[2023-03-17 02:03:59,775] [INFO] Task started: HMMsearch
[2023-03-17 02:03:59,775] [INFO] Running command: hmmsearch --tblout OceanDNA-b16236/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05b83a87-375b-45a6-88cb-45386c47e62e/dqc_reference/reference_markers.hmm OceanDNA-b16236/protein.faa > /dev/null
[2023-03-17 02:03:59,932] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:03:59,932] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg749ad7ea-6e28-4b4e-b57a-4762e9903ed0/OceanDNA-b16236.fa]
[2023-03-17 02:03:59,943] [INFO] Query marker FASTA was written to OceanDNA-b16236/markers.fasta
[2023-03-17 02:03:59,943] [INFO] Task started: Blastn
[2023-03-17 02:03:59,943] [INFO] Running command: blastn -query OceanDNA-b16236/markers.fasta -db /var/lib/cwl/stg05b83a87-375b-45a6-88cb-45386c47e62e/dqc_reference/reference_markers.fasta -out OceanDNA-b16236/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:00,447] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:00,447] [INFO] Selected 16 target genomes.
[2023-03-17 02:04:00,448] [INFO] Target genome list was writen to OceanDNA-b16236/target_genomes.txt
[2023-03-17 02:04:00,457] [INFO] Task started: fastANI
[2023-03-17 02:04:00,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg749ad7ea-6e28-4b4e-b57a-4762e9903ed0/OceanDNA-b16236.fa --refList OceanDNA-b16236/target_genomes.txt --output OceanDNA-b16236/fastani_result.tsv --threads 1
[2023-03-17 02:04:07,135] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:07,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05b83a87-375b-45a6-88cb-45386c47e62e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:04:07,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05b83a87-375b-45a6-88cb-45386c47e62e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:04:07,136] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:04:07,136] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:04:07,136] [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
--------------------------------------------------------------------------------
[2023-03-17 02:04:07,136] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16236/tc_result.tsv
[2023-03-17 02:04:07,136] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:04:07,136] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:04:07,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05b83a87-375b-45a6-88cb-45386c47e62e/dqc_reference/checkm_data
[2023-03-17 02:04:07,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:04:07,141] [INFO] Task started: CheckM
[2023-03-17 02:04:07,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16236/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16236/checkm_input OceanDNA-b16236/checkm_result
[2023-03-17 02:04:35,899] [INFO] Task succeeded: CheckM
[2023-03-17 02:04:35,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:04:35,901] [INFO] ===== Completeness check finished =====
[2023-03-17 02:04:35,902] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:04:35,902] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16236/markers.fasta)
[2023-03-17 02:04:35,902] [INFO] Task started: Blastn
[2023-03-17 02:04:35,902] [INFO] Running command: blastn -query OceanDNA-b16236/markers.fasta -db /var/lib/cwl/stg05b83a87-375b-45a6-88cb-45386c47e62e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16236/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:36,651] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:36,652] [INFO] Selected 13 target genomes.
[2023-03-17 02:04:36,652] [INFO] Target genome list was writen to OceanDNA-b16236/target_genomes_gtdb.txt
[2023-03-17 02:04:36,890] [INFO] Task started: fastANI
[2023-03-17 02:04:36,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg749ad7ea-6e28-4b4e-b57a-4762e9903ed0/OceanDNA-b16236.fa --refList OceanDNA-b16236/target_genomes_gtdb.txt --output OceanDNA-b16236/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:04:41,736] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:41,739] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:04:41,739] [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_000760295.1	s__Prochlorococcus_C sp000760295	81.5934	257	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	99.99	99.99	0.99	0.99	3	-
GCA_003214855.1	s__Prochlorococcus_C sp003214855	80.905	173	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011485.1	s__Prochlorococcus_C marinus_B	80.7537	257	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_C	95.0	96.34	95.12	0.90	0.85	19	-
GCF_014279595.1	s__Synechococcus_C sp000153065	76.1267	51	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.83	99.83	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:04:41,740] [INFO] GTDB search result was written to OceanDNA-b16236/result_gtdb.tsv
[2023-03-17 02:04:41,740] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:04:41,740] [INFO] DFAST_QC result json was written to OceanDNA-b16236/dqc_result.json
[2023-03-17 02:04:41,740] [INFO] DFAST_QC completed!
[2023-03-17 02:04:41,740] [INFO] Total running time: 0h0m52s