[2023-03-17 02:31:12,850] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,850] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,851] [INFO] DQC Reference Directory: /var/lib/cwl/stga1dbdd58-b877-48d4-9990-ec8a68a9951c/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stg9aa73c11-5ca0-46cf-9939-32aa6503e6fd/OceanDNA-b13613.fa | prodigal -d OceanDNA-b13613/cds.fna -a OceanDNA-b13613/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:20,752] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:20,752] [INFO] Task started: HMMsearch
[2023-03-17 02:31:20,752] [INFO] Running command: hmmsearch --tblout OceanDNA-b13613/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1dbdd58-b877-48d4-9990-ec8a68a9951c/dqc_reference/reference_markers.hmm OceanDNA-b13613/protein.faa > /dev/null
[2023-03-17 02:31:20,894] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:20,894] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9aa73c11-5ca0-46cf-9939-32aa6503e6fd/OceanDNA-b13613.fa]
[2023-03-17 02:31:20,904] [INFO] Query marker FASTA was written to OceanDNA-b13613/markers.fasta
[2023-03-17 02:31:20,904] [INFO] Task started: Blastn
[2023-03-17 02:31:20,904] [INFO] Running command: blastn -query OceanDNA-b13613/markers.fasta -db /var/lib/cwl/stga1dbdd58-b877-48d4-9990-ec8a68a9951c/dqc_reference/reference_markers.fasta -out OceanDNA-b13613/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:21,387] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:21,387] [INFO] Selected 16 target genomes.
[2023-03-17 02:31:21,388] [INFO] Target genome list was writen to OceanDNA-b13613/target_genomes.txt
[2023-03-17 02:31:21,396] [INFO] Task started: fastANI
[2023-03-17 02:31:21,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa73c11-5ca0-46cf-9939-32aa6503e6fd/OceanDNA-b13613.fa --refList OceanDNA-b13613/target_genomes.txt --output OceanDNA-b13613/fastani_result.tsv --threads 1
[2023-03-17 02:31:27,696] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:27,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1dbdd58-b877-48d4-9990-ec8a68a9951c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:27,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1dbdd58-b877-48d4-9990-ec8a68a9951c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:27,697] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:27,697] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:27,697] [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 02:31:27,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13613/tc_result.tsv
[2023-03-17 02:31:27,697] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:27,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:27,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1dbdd58-b877-48d4-9990-ec8a68a9951c/dqc_reference/checkm_data
[2023-03-17 02:31:27,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:27,705] [INFO] Task started: CheckM
[2023-03-17 02:31:27,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13613/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13613/checkm_input OceanDNA-b13613/checkm_result
[2023-03-17 02:31:49,102] [INFO] Task succeeded: CheckM
[2023-03-17 02:31:49,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.09%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-17 02:31:49,104] [INFO] ===== Completeness check finished =====
[2023-03-17 02:31:49,104] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:31:49,104] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13613/markers.fasta)
[2023-03-17 02:31:49,104] [INFO] Task started: Blastn
[2023-03-17 02:31:49,104] [INFO] Running command: blastn -query OceanDNA-b13613/markers.fasta -db /var/lib/cwl/stga1dbdd58-b877-48d4-9990-ec8a68a9951c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13613/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:49,750] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:49,751] [INFO] Selected 17 target genomes.
[2023-03-17 02:31:49,751] [INFO] Target genome list was writen to OceanDNA-b13613/target_genomes_gtdb.txt
[2023-03-17 02:31:50,144] [INFO] Task started: fastANI
[2023-03-17 02:31:50,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa73c11-5ca0-46cf-9939-32aa6503e6fd/OceanDNA-b13613.fa --refList OceanDNA-b13613/target_genomes_gtdb.txt --output OceanDNA-b13613/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:31:55,384] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:55,389] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:31:55,389] [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_002688105.1	s__GCA-2688105 sp002688105	99.6942	334	381	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__GCA-2688105;g__GCA-2688105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004376105.1	s__E44-bin46 sp004376105	77.5485	85	381	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__E44-bin46;g__E44-bin46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016783245.1	s__BS750m-G39 sp016783245	77.2779	70	381	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__BS750m-G39;g__BS750m-G39	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011170285.1	s__W498 sp011170285	77.1126	77	381	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__W498;g__W498	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011191875.1	s__W498 sp011191875	76.8384	83	381	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__W498;g__W498	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011192075.1	s__S120 sp011192075	76.8134	72	381	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__S120;g__S120	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004376435.1	s__SOJS01 sp004376435	76.2824	56	381	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__SOJS01;g__SOJS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:31:55,389] [INFO] GTDB search result was written to OceanDNA-b13613/result_gtdb.tsv
[2023-03-17 02:31:55,389] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:31:55,390] [INFO] DFAST_QC result json was written to OceanDNA-b13613/dqc_result.json
[2023-03-17 02:31:55,390] [INFO] DFAST_QC completed!
[2023-03-17 02:31:55,390] [INFO] Total running time: 0h0m43s