[2023-03-17 05:39:41,248] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:39:41,248] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:39:41,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg1de02cba-1ad8-4bbc-9493-9efd92bdfc73/dqc_reference
[2023-03-17 05:39:42,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:39:42,366] [INFO] Task started: Prodigal
[2023-03-17 05:39:42,366] [INFO] Running command: cat /var/lib/cwl/stg11301fc1-85e1-4279-960c-6ab9ef529f3e/OceanDNA-b16886.fa | prodigal -d OceanDNA-b16886/cds.fna -a OceanDNA-b16886/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:39:47,382] [INFO] Task succeeded: Prodigal
[2023-03-17 05:39:47,383] [INFO] Task started: HMMsearch
[2023-03-17 05:39:47,383] [INFO] Running command: hmmsearch --tblout OceanDNA-b16886/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1de02cba-1ad8-4bbc-9493-9efd92bdfc73/dqc_reference/reference_markers.hmm OceanDNA-b16886/protein.faa > /dev/null
[2023-03-17 05:39:47,530] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:39:47,530] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg11301fc1-85e1-4279-960c-6ab9ef529f3e/OceanDNA-b16886.fa]
[2023-03-17 05:39:47,537] [INFO] Query marker FASTA was written to OceanDNA-b16886/markers.fasta
[2023-03-17 05:39:47,538] [INFO] Task started: Blastn
[2023-03-17 05:39:47,538] [INFO] Running command: blastn -query OceanDNA-b16886/markers.fasta -db /var/lib/cwl/stg1de02cba-1ad8-4bbc-9493-9efd92bdfc73/dqc_reference/reference_markers.fasta -out OceanDNA-b16886/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:39:48,019] [INFO] Task succeeded: Blastn
[2023-03-17 05:39:48,020] [INFO] Selected 12 target genomes.
[2023-03-17 05:39:48,020] [INFO] Target genome list was writen to OceanDNA-b16886/target_genomes.txt
[2023-03-17 05:39:48,026] [INFO] Task started: fastANI
[2023-03-17 05:39:48,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg11301fc1-85e1-4279-960c-6ab9ef529f3e/OceanDNA-b16886.fa --refList OceanDNA-b16886/target_genomes.txt --output OceanDNA-b16886/fastani_result.tsv --threads 1
[2023-03-17 05:39:51,233] [INFO] Task succeeded: fastANI
[2023-03-17 05:39:51,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1de02cba-1ad8-4bbc-9493-9efd92bdfc73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:39:51,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1de02cba-1ad8-4bbc-9493-9efd92bdfc73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:39:51,234] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:39:51,234] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:39:51,234] [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 05:39:51,234] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16886/tc_result.tsv
[2023-03-17 05:39:51,234] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:39:51,234] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:39:51,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1de02cba-1ad8-4bbc-9493-9efd92bdfc73/dqc_reference/checkm_data
[2023-03-17 05:39:51,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:39:51,295] [INFO] Task started: CheckM
[2023-03-17 05:39:51,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16886/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16886/checkm_input OceanDNA-b16886/checkm_result
[2023-03-17 05:40:10,601] [INFO] Task succeeded: CheckM
[2023-03-17 05:40:10,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:40:10,602] [INFO] ===== Completeness check finished =====
[2023-03-17 05:40:10,602] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:40:10,603] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16886/markers.fasta)
[2023-03-17 05:40:10,603] [INFO] Task started: Blastn
[2023-03-17 05:40:10,603] [INFO] Running command: blastn -query OceanDNA-b16886/markers.fasta -db /var/lib/cwl/stg1de02cba-1ad8-4bbc-9493-9efd92bdfc73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16886/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:40:11,548] [INFO] Task succeeded: Blastn
[2023-03-17 05:40:11,549] [INFO] Selected 15 target genomes.
[2023-03-17 05:40:11,549] [INFO] Target genome list was writen to OceanDNA-b16886/target_genomes_gtdb.txt
[2023-03-17 05:40:11,700] [INFO] Task started: fastANI
[2023-03-17 05:40:11,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg11301fc1-85e1-4279-960c-6ab9ef529f3e/OceanDNA-b16886.fa --refList OceanDNA-b16886/target_genomes_gtdb.txt --output OceanDNA-b16886/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:40:15,101] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:15,105] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:40:15,105] [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_002701925.2	s__GCA-2701925 sp002701925	97.035	308	329	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	conclusive
GCA_018654605.1	s__TMED58 sp018654605	78.0211	92	329	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_002167555.2	s__TMED58 sp002167555	77.9046	107	329	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	76.9979	69	329	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:40:15,105] [INFO] GTDB search result was written to OceanDNA-b16886/result_gtdb.tsv
[2023-03-17 05:40:15,105] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:40:15,106] [INFO] DFAST_QC result json was written to OceanDNA-b16886/dqc_result.json
[2023-03-17 05:40:15,106] [INFO] DFAST_QC completed!
[2023-03-17 05:40:15,106] [INFO] Total running time: 0h0m34s