[2023-03-15 05:00:03,358] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:00:03,358] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:00:03,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgfea5a6a7-1c88-42eb-9fc3-8c6d920416e9/dqc_reference
[2023-03-15 05:00:04,420] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:00:04,420] [INFO] Task started: Prodigal
[2023-03-15 05:00:04,420] [INFO] Running command: cat /var/lib/cwl/stg3d42e40e-552a-4e83-bdea-18650721072e/OceanDNA-b11601.fa | prodigal -d OceanDNA-b11601/cds.fna -a OceanDNA-b11601/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:00:12,129] [INFO] Task succeeded: Prodigal
[2023-03-15 05:00:12,129] [INFO] Task started: HMMsearch
[2023-03-15 05:00:12,129] [INFO] Running command: hmmsearch --tblout OceanDNA-b11601/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfea5a6a7-1c88-42eb-9fc3-8c6d920416e9/dqc_reference/reference_markers.hmm OceanDNA-b11601/protein.faa > /dev/null
[2023-03-15 05:00:12,333] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:00:12,333] [INFO] Found 6/6 markers.
[2023-03-15 05:00:12,358] [INFO] Query marker FASTA was written to OceanDNA-b11601/markers.fasta
[2023-03-15 05:00:12,358] [INFO] Task started: Blastn
[2023-03-15 05:00:12,358] [INFO] Running command: blastn -query OceanDNA-b11601/markers.fasta -db /var/lib/cwl/stgfea5a6a7-1c88-42eb-9fc3-8c6d920416e9/dqc_reference/reference_markers.fasta -out OceanDNA-b11601/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:12,934] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:12,938] [INFO] Selected 31 target genomes.
[2023-03-15 05:00:12,938] [INFO] Target genome list was writen to OceanDNA-b11601/target_genomes.txt
[2023-03-15 05:00:12,952] [INFO] Task started: fastANI
[2023-03-15 05:00:12,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d42e40e-552a-4e83-bdea-18650721072e/OceanDNA-b11601.fa --refList OceanDNA-b11601/target_genomes.txt --output OceanDNA-b11601/fastani_result.tsv --threads 1
[2023-03-15 05:00:29,267] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:29,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfea5a6a7-1c88-42eb-9fc3-8c6d920416e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:00:29,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfea5a6a7-1c88-42eb-9fc3-8c6d920416e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:00:29,267] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:00:29,268] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:00:29,268] [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
--------------------------------------------------------------------------------
[2023-03-15 05:00:29,271] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11601/tc_result.tsv
[2023-03-15 05:00:29,274] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:00:29,274] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:00:29,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfea5a6a7-1c88-42eb-9fc3-8c6d920416e9/dqc_reference/checkm_data
[2023-03-15 05:00:29,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:00:29,338] [INFO] Task started: CheckM
[2023-03-15 05:00:29,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11601/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11601/checkm_input OceanDNA-b11601/checkm_result
[2023-03-15 05:00:53,508] [INFO] Task succeeded: CheckM
[2023-03-15 05:00:53,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:00:53,555] [INFO] ===== Completeness check finished =====
[2023-03-15 05:00:53,555] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:00:53,555] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11601/markers.fasta)
[2023-03-15 05:00:53,555] [INFO] Task started: Blastn
[2023-03-15 05:00:53,556] [INFO] Running command: blastn -query OceanDNA-b11601/markers.fasta -db /var/lib/cwl/stgfea5a6a7-1c88-42eb-9fc3-8c6d920416e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11601/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:54,503] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:54,508] [INFO] Selected 23 target genomes.
[2023-03-15 05:00:54,508] [INFO] Target genome list was writen to OceanDNA-b11601/target_genomes_gtdb.txt
[2023-03-15 05:00:54,527] [INFO] Task started: fastANI
[2023-03-15 05:00:54,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d42e40e-552a-4e83-bdea-18650721072e/OceanDNA-b11601.fa --refList OceanDNA-b11601/target_genomes_gtdb.txt --output OceanDNA-b11601/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:01:02,546] [INFO] Task succeeded: fastANI
[2023-03-15 05:01:02,552] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:01:02,552] [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_002718895.1	s__GCA-2718895 sp002718895	99.7939	347	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718895	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002714185.1	s__SP256 sp002714185	77.1753	122	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707245.1	s__GCA-002707245 sp002707245	76.9989	96	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	76.7468	93	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713285.1	s__SP256 sp002713285	76.707	104	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.6967	108	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698365.1	s__GCA-002707245 sp002698365	76.4768	84	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722215.1	s__SP256 sp002722215	76.2125	99	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:01:02,553] [INFO] GTDB search result was written to OceanDNA-b11601/result_gtdb.tsv
[2023-03-15 05:01:02,553] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:01:02,554] [INFO] DFAST_QC result json was written to OceanDNA-b11601/dqc_result.json
[2023-03-15 05:01:02,554] [INFO] DFAST_QC completed!
[2023-03-15 05:01:02,554] [INFO] Total running time: 0h0m59s