[2023-03-14 12:13:42,663] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:13:42,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:13:42,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg8eb052c6-b937-46bb-b742-645c69d849af/dqc_reference
[2023-03-14 12:13:44,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:13:44,621] [INFO] Task started: Prodigal
[2023-03-14 12:13:44,621] [INFO] Running command: cat /var/lib/cwl/stge0a5163c-9ea5-420a-add2-b7e27b7419da/OceanDNA-a1744.fa | prodigal -d OceanDNA-a1744/cds.fna -a OceanDNA-a1744/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:13:51,767] [INFO] Task succeeded: Prodigal
[2023-03-14 12:13:51,767] [INFO] Task started: HMMsearch
[2023-03-14 12:13:51,767] [INFO] Running command: hmmsearch --tblout OceanDNA-a1744/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8eb052c6-b937-46bb-b742-645c69d849af/dqc_reference/reference_markers.hmm OceanDNA-a1744/protein.faa > /dev/null
[2023-03-14 12:13:51,902] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:13:51,902] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge0a5163c-9ea5-420a-add2-b7e27b7419da/OceanDNA-a1744.fa]
[2023-03-14 12:13:51,910] [INFO] Query marker FASTA was written to OceanDNA-a1744/markers.fasta
[2023-03-14 12:13:51,911] [INFO] Task started: Blastn
[2023-03-14 12:13:51,911] [INFO] Running command: blastn -query OceanDNA-a1744/markers.fasta -db /var/lib/cwl/stg8eb052c6-b937-46bb-b742-645c69d849af/dqc_reference/reference_markers.fasta -out OceanDNA-a1744/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:13:52,335] [INFO] Task succeeded: Blastn
[2023-03-14 12:13:52,335] [INFO] Selected 5 target genomes.
[2023-03-14 12:13:52,336] [INFO] Target genome list was writen to OceanDNA-a1744/target_genomes.txt
[2023-03-14 12:13:52,339] [INFO] Task started: fastANI
[2023-03-14 12:13:52,339] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a5163c-9ea5-420a-add2-b7e27b7419da/OceanDNA-a1744.fa --refList OceanDNA-a1744/target_genomes.txt --output OceanDNA-a1744/fastani_result.tsv --threads 1
[2023-03-14 12:13:55,331] [INFO] Task succeeded: fastANI
[2023-03-14 12:13:55,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8eb052c6-b937-46bb-b742-645c69d849af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:13:55,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8eb052c6-b937-46bb-b742-645c69d849af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:13:55,332] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:13:55,332] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:13:55,332] [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
--------------------------------------------------------------------------------
[2023-03-14 12:13:55,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1744/tc_result.tsv
[2023-03-14 12:13:55,332] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:13:55,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:13:55,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8eb052c6-b937-46bb-b742-645c69d849af/dqc_reference/checkm_data
[2023-03-14 12:13:55,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:13:55,338] [INFO] Task started: CheckM
[2023-03-14 12:13:55,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1744/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1744/checkm_input OceanDNA-a1744/checkm_result
[2023-03-14 12:14:18,576] [INFO] Task succeeded: CheckM
[2023-03-14 12:14:18,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.59%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:14:18,579] [INFO] ===== Completeness check finished =====
[2023-03-14 12:14:18,579] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:14:18,579] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1744/markers.fasta)
[2023-03-14 12:14:18,580] [INFO] Task started: Blastn
[2023-03-14 12:14:18,580] [INFO] Running command: blastn -query OceanDNA-a1744/markers.fasta -db /var/lib/cwl/stg8eb052c6-b937-46bb-b742-645c69d849af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1744/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:14:19,012] [INFO] Task succeeded: Blastn
[2023-03-14 12:14:19,013] [INFO] Selected 11 target genomes.
[2023-03-14 12:14:19,013] [INFO] Target genome list was writen to OceanDNA-a1744/target_genomes_gtdb.txt
[2023-03-14 12:14:19,022] [INFO] Task started: fastANI
[2023-03-14 12:14:19,022] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a5163c-9ea5-420a-add2-b7e27b7419da/OceanDNA-a1744.fa --refList OceanDNA-a1744/target_genomes_gtdb.txt --output OceanDNA-a1744/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:14:23,447] [INFO] Task succeeded: fastANI
[2023-03-14 12:14:23,451] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:14:23,451] [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_002731905.1	s__UBA8886 sp002731905	84.6277	181	257	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003193815.1	s__UBA8886 sp003193815	84.319	116	257	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731655.1	s__UBA8886 sp002731655	83.8064	144	257	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	95.77	95.71	0.74	0.71	4	-
GCA_002509165.1	s__UBA8886 sp002509165	83.7196	183	257	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA8886	95.0	99.54	99.45	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-14 12:14:23,451] [INFO] GTDB search result was written to OceanDNA-a1744/result_gtdb.tsv
[2023-03-14 12:14:23,451] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:14:23,452] [INFO] DFAST_QC result json was written to OceanDNA-a1744/dqc_result.json
[2023-03-14 12:14:23,452] [INFO] DFAST_QC completed!
[2023-03-14 12:14:23,452] [INFO] Total running time: 0h0m41s