[2023-03-15 18:12:37,907] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:12:37,909] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:12:37,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c5fae18-a39a-4bfa-986b-3ccb8fbb2ff8/dqc_reference
[2023-03-15 18:12:39,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:12:39,782] [INFO] Task started: Prodigal
[2023-03-15 18:12:39,782] [INFO] Running command: cat /var/lib/cwl/stg240ac285-3fc7-41e3-b0b2-e4e4e5025784/OceanDNA-b16578.fa | prodigal -d OceanDNA-b16578/cds.fna -a OceanDNA-b16578/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:12:47,238] [INFO] Task succeeded: Prodigal
[2023-03-15 18:12:47,239] [INFO] Task started: HMMsearch
[2023-03-15 18:12:47,239] [INFO] Running command: hmmsearch --tblout OceanDNA-b16578/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c5fae18-a39a-4bfa-986b-3ccb8fbb2ff8/dqc_reference/reference_markers.hmm OceanDNA-b16578/protein.faa > /dev/null
[2023-03-15 18:12:47,362] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:12:47,362] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg240ac285-3fc7-41e3-b0b2-e4e4e5025784/OceanDNA-b16578.fa]
[2023-03-15 18:12:47,374] [INFO] Query marker FASTA was written to OceanDNA-b16578/markers.fasta
[2023-03-15 18:12:47,374] [INFO] Task started: Blastn
[2023-03-15 18:12:47,374] [INFO] Running command: blastn -query OceanDNA-b16578/markers.fasta -db /var/lib/cwl/stg8c5fae18-a39a-4bfa-986b-3ccb8fbb2ff8/dqc_reference/reference_markers.fasta -out OceanDNA-b16578/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:12:47,923] [INFO] Task succeeded: Blastn
[2023-03-15 18:12:47,923] [INFO] Selected 24 target genomes.
[2023-03-15 18:12:47,924] [INFO] Target genome list was writen to OceanDNA-b16578/target_genomes.txt
[2023-03-15 18:12:48,164] [INFO] Task started: fastANI
[2023-03-15 18:12:48,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg240ac285-3fc7-41e3-b0b2-e4e4e5025784/OceanDNA-b16578.fa --refList OceanDNA-b16578/target_genomes.txt --output OceanDNA-b16578/fastani_result.tsv --threads 1
[2023-03-15 18:13:06,366] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:06,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c5fae18-a39a-4bfa-986b-3ccb8fbb2ff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:13:06,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c5fae18-a39a-4bfa-986b-3ccb8fbb2ff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:13:06,367] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:13:06,367] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:13:06,367] [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 18:13:06,367] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16578/tc_result.tsv
[2023-03-15 18:13:06,367] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:13:06,367] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:13:06,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c5fae18-a39a-4bfa-986b-3ccb8fbb2ff8/dqc_reference/checkm_data
[2023-03-15 18:13:06,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:13:06,374] [INFO] Task started: CheckM
[2023-03-15 18:13:06,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16578/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16578/checkm_input OceanDNA-b16578/checkm_result
[2023-03-15 18:13:31,841] [INFO] Task succeeded: CheckM
[2023-03-15 18:13:31,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.76%
Contamintation: 7.09%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 18:13:31,844] [INFO] ===== Completeness check finished =====
[2023-03-15 18:13:31,844] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:13:31,844] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16578/markers.fasta)
[2023-03-15 18:13:31,844] [INFO] Task started: Blastn
[2023-03-15 18:13:31,844] [INFO] Running command: blastn -query OceanDNA-b16578/markers.fasta -db /var/lib/cwl/stg8c5fae18-a39a-4bfa-986b-3ccb8fbb2ff8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16578/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:13:32,317] [INFO] Task succeeded: Blastn
[2023-03-15 18:13:32,318] [INFO] Selected 8 target genomes.
[2023-03-15 18:13:32,318] [INFO] Target genome list was writen to OceanDNA-b16578/target_genomes_gtdb.txt
[2023-03-15 18:13:32,450] [INFO] Task started: fastANI
[2023-03-15 18:13:32,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg240ac285-3fc7-41e3-b0b2-e4e4e5025784/OceanDNA-b16578.fa --refList OceanDNA-b16578/target_genomes_gtdb.txt --output OceanDNA-b16578/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:13:34,955] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:34,961] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:13:34,961] [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_000012625.1	s__Synechococcus_E sp000012625	97.1798	60	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	conclusive
GCF_014279895.1	s__Synechococcus_E sp002724845	92.1416	58	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCF_000161795.2	s__Synechococcus_E sp000161795	91.9617	58	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911515.1	s__Synechococcus_E sp013911515	90.3021	56	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737595.1	s__Synechococcus_E sp000737595	89.0169	59	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779825.1	s__Synechococcus_E sp016779825	88.4343	53	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209165.1	s__Synechococcus_E sp003209165	87.7997	54	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900474185.1	s__Synechococcus_E sp900474185	85.36	59	60	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.68	95.24	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-15 18:13:34,961] [INFO] GTDB search result was written to OceanDNA-b16578/result_gtdb.tsv
[2023-03-15 18:13:34,961] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:13:34,962] [INFO] DFAST_QC result json was written to OceanDNA-b16578/dqc_result.json
[2023-03-15 18:13:34,962] [INFO] DFAST_QC completed!
[2023-03-15 18:13:34,962] [INFO] Total running time: 0h0m57s