[2023-03-18 21:47:29,513] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:47:29,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:47:29,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgfddc16ef-5640-4ebe-8af3-d25abc989b26/dqc_reference
[2023-03-18 21:47:30,600] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:47:30,601] [INFO] Task started: Prodigal
[2023-03-18 21:47:30,601] [INFO] Running command: cat /var/lib/cwl/stgbb33063c-0cc4-44cb-a64d-54def9440537/OceanDNA-b18643.fa | prodigal -d OceanDNA-b18643/cds.fna -a OceanDNA-b18643/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:47:37,792] [INFO] Task succeeded: Prodigal
[2023-03-18 21:47:37,793] [INFO] Task started: HMMsearch
[2023-03-18 21:47:37,793] [INFO] Running command: hmmsearch --tblout OceanDNA-b18643/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfddc16ef-5640-4ebe-8af3-d25abc989b26/dqc_reference/reference_markers.hmm OceanDNA-b18643/protein.faa > /dev/null
[2023-03-18 21:47:37,949] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:47:37,949] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbb33063c-0cc4-44cb-a64d-54def9440537/OceanDNA-b18643.fa]
[2023-03-18 21:47:38,148] [INFO] Query marker FASTA was written to OceanDNA-b18643/markers.fasta
[2023-03-18 21:47:38,148] [INFO] Task started: Blastn
[2023-03-18 21:47:38,148] [INFO] Running command: blastn -query OceanDNA-b18643/markers.fasta -db /var/lib/cwl/stgfddc16ef-5640-4ebe-8af3-d25abc989b26/dqc_reference/reference_markers.fasta -out OceanDNA-b18643/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:47:38,607] [INFO] Task succeeded: Blastn
[2023-03-18 21:47:38,681] [INFO] Selected 11 target genomes.
[2023-03-18 21:47:38,681] [INFO] Target genome list was writen to OceanDNA-b18643/target_genomes.txt
[2023-03-18 21:47:38,688] [INFO] Task started: fastANI
[2023-03-18 21:47:38,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb33063c-0cc4-44cb-a64d-54def9440537/OceanDNA-b18643.fa --refList OceanDNA-b18643/target_genomes.txt --output OceanDNA-b18643/fastani_result.tsv --threads 1
[2023-03-18 21:47:42,591] [INFO] Task succeeded: fastANI
[2023-03-18 21:47:42,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfddc16ef-5640-4ebe-8af3-d25abc989b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:47:42,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfddc16ef-5640-4ebe-8af3-d25abc989b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:47:42,592] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:47:42,592] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:47:42,592] [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
--------------------------------------------------------------------------------
[2023-03-18 21:47:42,621] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18643/tc_result.tsv
[2023-03-18 21:47:42,666] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:47:42,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:47:42,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfddc16ef-5640-4ebe-8af3-d25abc989b26/dqc_reference/checkm_data
[2023-03-18 21:47:42,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:47:42,690] [INFO] Task started: CheckM
[2023-03-18 21:47:42,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18643/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18643/checkm_input OceanDNA-b18643/checkm_result
[2023-03-18 21:48:05,955] [INFO] Task succeeded: CheckM
[2023-03-18 21:48:05,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.31%
Contamintation: 3.47%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-18 21:48:05,958] [INFO] ===== Completeness check finished =====
[2023-03-18 21:48:05,958] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:48:05,958] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18643/markers.fasta)
[2023-03-18 21:48:05,960] [INFO] Task started: Blastn
[2023-03-18 21:48:05,961] [INFO] Running command: blastn -query OceanDNA-b18643/markers.fasta -db /var/lib/cwl/stgfddc16ef-5640-4ebe-8af3-d25abc989b26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18643/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:48:06,387] [INFO] Task succeeded: Blastn
[2023-03-18 21:48:06,388] [INFO] Selected 13 target genomes.
[2023-03-18 21:48:06,388] [INFO] Target genome list was writen to OceanDNA-b18643/target_genomes_gtdb.txt
[2023-03-18 21:48:06,403] [INFO] Task started: fastANI
[2023-03-18 21:48:06,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb33063c-0cc4-44cb-a64d-54def9440537/OceanDNA-b18643.fa --refList OceanDNA-b18643/target_genomes_gtdb.txt --output OceanDNA-b18643/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:48:10,451] [INFO] Task succeeded: fastANI
[2023-03-18 21:48:10,454] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:48:10,454] [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_002701785.1	s__GCA-002701945 sp002701785	81.9137	354	479	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	97.49	97.49	0.87	0.87	2	-
GCA_004321715.1	s__GCA-002701945 sp004321715	80.7471	256	479	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701945.1	s__GCA-002701945 sp002701945	80.2155	264	479	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:48:10,455] [INFO] GTDB search result was written to OceanDNA-b18643/result_gtdb.tsv
[2023-03-18 21:48:10,455] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:48:10,455] [INFO] DFAST_QC result json was written to OceanDNA-b18643/dqc_result.json
[2023-03-18 21:48:10,455] [INFO] DFAST_QC completed!
[2023-03-18 21:48:10,455] [INFO] Total running time: 0h0m41s