[2023-03-16 11:11:06,074] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:11:06,074] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:11:06,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg87be361d-4efa-4fb9-900a-ebd8ba857eeb/dqc_reference
[2023-03-16 11:11:07,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:11:07,483] [INFO] Task started: Prodigal
[2023-03-16 11:11:07,483] [INFO] Running command: cat /var/lib/cwl/stg7eee86c1-0ba0-4616-9102-c8c27bcce671/OceanDNA-b17023.fa | prodigal -d OceanDNA-b17023/cds.fna -a OceanDNA-b17023/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:11:12,206] [INFO] Task succeeded: Prodigal
[2023-03-16 11:11:12,206] [INFO] Task started: HMMsearch
[2023-03-16 11:11:12,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b17023/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87be361d-4efa-4fb9-900a-ebd8ba857eeb/dqc_reference/reference_markers.hmm OceanDNA-b17023/protein.faa > /dev/null
[2023-03-16 11:11:12,364] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:11:12,365] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7eee86c1-0ba0-4616-9102-c8c27bcce671/OceanDNA-b17023.fa]
[2023-03-16 11:11:12,372] [INFO] Query marker FASTA was written to OceanDNA-b17023/markers.fasta
[2023-03-16 11:11:12,374] [INFO] Task started: Blastn
[2023-03-16 11:11:12,374] [INFO] Running command: blastn -query OceanDNA-b17023/markers.fasta -db /var/lib/cwl/stg87be361d-4efa-4fb9-900a-ebd8ba857eeb/dqc_reference/reference_markers.fasta -out OceanDNA-b17023/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:11:13,134] [INFO] Task succeeded: Blastn
[2023-03-16 11:11:13,135] [INFO] Selected 17 target genomes.
[2023-03-16 11:11:13,135] [INFO] Target genome list was writen to OceanDNA-b17023/target_genomes.txt
[2023-03-16 11:11:13,174] [INFO] Task started: fastANI
[2023-03-16 11:11:13,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eee86c1-0ba0-4616-9102-c8c27bcce671/OceanDNA-b17023.fa --refList OceanDNA-b17023/target_genomes.txt --output OceanDNA-b17023/fastani_result.tsv --threads 1
[2023-03-16 11:11:23,160] [INFO] Task succeeded: fastANI
[2023-03-16 11:11:23,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87be361d-4efa-4fb9-900a-ebd8ba857eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:11:23,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87be361d-4efa-4fb9-900a-ebd8ba857eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:11:23,160] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:11:23,161] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:11:23,161] [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 11:11:23,161] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17023/tc_result.tsv
[2023-03-16 11:11:23,163] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:11:23,164] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:11:23,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87be361d-4efa-4fb9-900a-ebd8ba857eeb/dqc_reference/checkm_data
[2023-03-16 11:11:23,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:11:23,169] [INFO] Task started: CheckM
[2023-03-16 11:11:23,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17023/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17023/checkm_input OceanDNA-b17023/checkm_result
[2023-03-16 11:11:50,473] [INFO] Task succeeded: CheckM
[2023-03-16 11:11:50,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:11:50,475] [INFO] ===== Completeness check finished =====
[2023-03-16 11:11:50,475] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:11:50,476] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17023/markers.fasta)
[2023-03-16 11:11:50,478] [INFO] Task started: Blastn
[2023-03-16 11:11:50,478] [INFO] Running command: blastn -query OceanDNA-b17023/markers.fasta -db /var/lib/cwl/stg87be361d-4efa-4fb9-900a-ebd8ba857eeb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17023/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:11:51,204] [INFO] Task succeeded: Blastn
[2023-03-16 11:11:51,205] [INFO] Selected 14 target genomes.
[2023-03-16 11:11:51,205] [INFO] Target genome list was writen to OceanDNA-b17023/target_genomes_gtdb.txt
[2023-03-16 11:11:51,214] [INFO] Task started: fastANI
[2023-03-16 11:11:51,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eee86c1-0ba0-4616-9102-c8c27bcce671/OceanDNA-b17023.fa --refList OceanDNA-b17023/target_genomes_gtdb.txt --output OceanDNA-b17023/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:11:54,117] [INFO] Task succeeded: fastANI
[2023-03-16 11:11:54,122] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:11:54,122] [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_002708105.2	s__TMED58 sp002708105	99.3378	264	305	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018654605.1	s__TMED58 sp018654605	78.4402	159	305	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	99.90	99.90	0.96	0.96	2	-
GCA_002701865.2	s__TMED58 sp002701865	78.3966	164	305	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167555.2	s__TMED58 sp002167555	78.3206	152	305	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	97.87	96.79	0.94	0.92	5	-
GCA_905181755.1	s__TMED58 sp905181755	77.6868	100	305	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701925.2	s__GCA-2701925 sp002701925	76.814	91	305	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-2701925	95.0	97.33	97.15	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2023-03-16 11:11:54,123] [INFO] GTDB search result was written to OceanDNA-b17023/result_gtdb.tsv
[2023-03-16 11:11:54,123] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:11:54,124] [INFO] DFAST_QC result json was written to OceanDNA-b17023/dqc_result.json
[2023-03-16 11:11:54,124] [INFO] DFAST_QC completed!
[2023-03-16 11:11:54,124] [INFO] Total running time: 0h0m48s