[2023-03-15 19:02:29,954] [INFO] DFAST_QC pipeline started.
[2023-03-15 19:02:29,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 19:02:29,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d6ef103-77d3-4408-aaa4-022d7ecc7c2a/dqc_reference
[2023-03-15 19:02:32,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 19:02:32,598] [INFO] Task started: Prodigal
[2023-03-15 19:02:32,599] [INFO] Running command: cat /var/lib/cwl/stg903f637a-7dfb-4112-be75-84ba9ae8ff85/OceanDNA-b5769.fa | prodigal -d OceanDNA-b5769/cds.fna -a OceanDNA-b5769/protein.faa -g 11 -q > /dev/null
[2023-03-15 19:02:41,058] [INFO] Task succeeded: Prodigal
[2023-03-15 19:02:41,058] [INFO] Task started: HMMsearch
[2023-03-15 19:02:41,058] [INFO] Running command: hmmsearch --tblout OceanDNA-b5769/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d6ef103-77d3-4408-aaa4-022d7ecc7c2a/dqc_reference/reference_markers.hmm OceanDNA-b5769/protein.faa > /dev/null
[2023-03-15 19:02:41,210] [INFO] Task succeeded: HMMsearch
[2023-03-15 19:02:41,211] [INFO] Found 6/6 markers.
[2023-03-15 19:02:41,221] [INFO] Query marker FASTA was written to OceanDNA-b5769/markers.fasta
[2023-03-15 19:02:41,222] [INFO] Task started: Blastn
[2023-03-15 19:02:41,222] [INFO] Running command: blastn -query OceanDNA-b5769/markers.fasta -db /var/lib/cwl/stg7d6ef103-77d3-4408-aaa4-022d7ecc7c2a/dqc_reference/reference_markers.fasta -out OceanDNA-b5769/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:02:41,748] [INFO] Task succeeded: Blastn
[2023-03-15 19:02:41,749] [INFO] Selected 26 target genomes.
[2023-03-15 19:02:41,749] [INFO] Target genome list was writen to OceanDNA-b5769/target_genomes.txt
[2023-03-15 19:02:41,766] [INFO] Task started: fastANI
[2023-03-15 19:02:41,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg903f637a-7dfb-4112-be75-84ba9ae8ff85/OceanDNA-b5769.fa --refList OceanDNA-b5769/target_genomes.txt --output OceanDNA-b5769/fastani_result.tsv --threads 1
[2023-03-15 19:02:56,680] [INFO] Task succeeded: fastANI
[2023-03-15 19:02:56,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d6ef103-77d3-4408-aaa4-022d7ecc7c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 19:02:56,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d6ef103-77d3-4408-aaa4-022d7ecc7c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 19:02:56,681] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 19:02:56,681] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 19:02:56,681] [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 19:02:56,681] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5769/tc_result.tsv
[2023-03-15 19:02:56,681] [INFO] ===== Taxonomy check completed =====
[2023-03-15 19:02:56,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 19:02:56,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d6ef103-77d3-4408-aaa4-022d7ecc7c2a/dqc_reference/checkm_data
[2023-03-15 19:02:56,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 19:02:56,687] [INFO] Task started: CheckM
[2023-03-15 19:02:56,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5769/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5769/checkm_input OceanDNA-b5769/checkm_result
[2023-03-15 19:03:23,087] [INFO] Task succeeded: CheckM
[2023-03-15 19:03:23,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 19:03:23,089] [INFO] ===== Completeness check finished =====
[2023-03-15 19:03:23,089] [INFO] ===== Start GTDB Search =====
[2023-03-15 19:03:23,090] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5769/markers.fasta)
[2023-03-15 19:03:23,090] [INFO] Task started: Blastn
[2023-03-15 19:03:23,090] [INFO] Running command: blastn -query OceanDNA-b5769/markers.fasta -db /var/lib/cwl/stg7d6ef103-77d3-4408-aaa4-022d7ecc7c2a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5769/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:03:23,832] [INFO] Task succeeded: Blastn
[2023-03-15 19:03:23,833] [INFO] Selected 7 target genomes.
[2023-03-15 19:03:23,833] [INFO] Target genome list was writen to OceanDNA-b5769/target_genomes_gtdb.txt
[2023-03-15 19:03:24,234] [INFO] Task started: fastANI
[2023-03-15 19:03:24,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg903f637a-7dfb-4112-be75-84ba9ae8ff85/OceanDNA-b5769.fa --refList OceanDNA-b5769/target_genomes_gtdb.txt --output OceanDNA-b5769/fastani_result_gtdb.tsv --threads 1
[2023-03-15 19:03:26,435] [INFO] Task succeeded: fastANI
[2023-03-15 19:03:26,440] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 19:03:26,440] [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_003385605.1	s__UBA10364 sp003385605	99.2231	288	292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	conclusive
GCA_011525035.1	s__UBA10364 sp011525035	94.8507	281	292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430755.1	s__UBA10364 sp002430755	91.5895	207	292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911625.1	s__UBA10364 sp013911625	90.0814	161	292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269745.1	s__UBA10364 sp012269745	86.0645	237	292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	84.7248	184	292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545085.1	s__UBA10364 sp003545085	83.431	193	292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 19:03:26,440] [INFO] GTDB search result was written to OceanDNA-b5769/result_gtdb.tsv
[2023-03-15 19:03:26,440] [INFO] ===== GTDB Search completed =====
[2023-03-15 19:03:26,441] [INFO] DFAST_QC result json was written to OceanDNA-b5769/dqc_result.json
[2023-03-15 19:03:26,441] [INFO] DFAST_QC completed!
[2023-03-15 19:03:26,441] [INFO] Total running time: 0h0m56s