[2023-03-16 01:03:15,341] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:03:15,342] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:03:15,342] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8e648f0-aaa1-4191-b069-ca7418338d9a/dqc_reference
[2023-03-16 01:03:16,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:03:16,489] [INFO] Task started: Prodigal
[2023-03-16 01:03:16,489] [INFO] Running command: cat /var/lib/cwl/stg12a19980-76fe-406a-878a-8b1129aa5b8d/OceanDNA-b26969.fa | prodigal -d OceanDNA-b26969/cds.fna -a OceanDNA-b26969/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:03:19,498] [INFO] Task succeeded: Prodigal
[2023-03-16 01:03:19,498] [INFO] Task started: HMMsearch
[2023-03-16 01:03:19,498] [INFO] Running command: hmmsearch --tblout OceanDNA-b26969/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8e648f0-aaa1-4191-b069-ca7418338d9a/dqc_reference/reference_markers.hmm OceanDNA-b26969/protein.faa > /dev/null
[2023-03-16 01:03:19,664] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:03:19,664] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg12a19980-76fe-406a-878a-8b1129aa5b8d/OceanDNA-b26969.fa]
[2023-03-16 01:03:19,672] [INFO] Query marker FASTA was written to OceanDNA-b26969/markers.fasta
[2023-03-16 01:03:19,673] [INFO] Task started: Blastn
[2023-03-16 01:03:19,673] [INFO] Running command: blastn -query OceanDNA-b26969/markers.fasta -db /var/lib/cwl/stgd8e648f0-aaa1-4191-b069-ca7418338d9a/dqc_reference/reference_markers.fasta -out OceanDNA-b26969/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:03:20,371] [INFO] Task succeeded: Blastn
[2023-03-16 01:03:20,371] [INFO] Selected 7 target genomes.
[2023-03-16 01:03:20,372] [INFO] Target genome list was writen to OceanDNA-b26969/target_genomes.txt
[2023-03-16 01:03:20,378] [INFO] Task started: fastANI
[2023-03-16 01:03:20,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a19980-76fe-406a-878a-8b1129aa5b8d/OceanDNA-b26969.fa --refList OceanDNA-b26969/target_genomes.txt --output OceanDNA-b26969/fastani_result.tsv --threads 1
[2023-03-16 01:03:24,741] [INFO] Task succeeded: fastANI
[2023-03-16 01:03:24,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8e648f0-aaa1-4191-b069-ca7418338d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:03:24,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8e648f0-aaa1-4191-b069-ca7418338d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:03:24,742] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:03:24,742] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:03:24,742] [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
--------------------------------------------------------------------------------
[2023-03-16 01:03:24,742] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26969/tc_result.tsv
[2023-03-16 01:03:24,742] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:03:24,742] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:03:24,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8e648f0-aaa1-4191-b069-ca7418338d9a/dqc_reference/checkm_data
[2023-03-16 01:03:24,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:03:24,902] [INFO] Task started: CheckM
[2023-03-16 01:03:24,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26969/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26969/checkm_input OceanDNA-b26969/checkm_result
[2023-03-16 01:03:44,982] [INFO] Task succeeded: CheckM
[2023-03-16 01:03:44,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:03:44,984] [INFO] ===== Completeness check finished =====
[2023-03-16 01:03:44,985] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:03:44,985] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26969/markers.fasta)
[2023-03-16 01:03:44,986] [INFO] Task started: Blastn
[2023-03-16 01:03:44,986] [INFO] Running command: blastn -query OceanDNA-b26969/markers.fasta -db /var/lib/cwl/stgd8e648f0-aaa1-4191-b069-ca7418338d9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26969/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:03:46,491] [INFO] Task succeeded: Blastn
[2023-03-16 01:03:46,492] [INFO] Selected 15 target genomes.
[2023-03-16 01:03:46,492] [INFO] Target genome list was writen to OceanDNA-b26969/target_genomes_gtdb.txt
[2023-03-16 01:03:47,114] [INFO] Task started: fastANI
[2023-03-16 01:03:47,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a19980-76fe-406a-878a-8b1129aa5b8d/OceanDNA-b26969.fa --refList OceanDNA-b26969/target_genomes_gtdb.txt --output OceanDNA-b26969/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:03:49,789] [INFO] Task succeeded: fastANI
[2023-03-16 01:03:49,792] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:03:49,792] [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_902533755.1	s__AG-430-B22 sp902533755	77.5399	58	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	99.48	99.48	0.87	0.87	3	-
GCA_902608415.1	s__AG-430-B22 sp902608415	77.1742	65	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726005.1	s__AG-430-B22 sp002726005	77.0543	74	185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.76	98.76	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-16 01:03:49,792] [INFO] GTDB search result was written to OceanDNA-b26969/result_gtdb.tsv
[2023-03-16 01:03:49,792] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:03:49,793] [INFO] DFAST_QC result json was written to OceanDNA-b26969/dqc_result.json
[2023-03-16 01:03:49,793] [INFO] DFAST_QC completed!
[2023-03-16 01:03:49,793] [INFO] Total running time: 0h0m34s