[2023-03-15 21:52:12,175] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:52:12,175] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:52:12,175] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4c3127b-9741-46c5-84bc-d12ca3b12772/dqc_reference
[2023-03-15 21:52:15,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:52:15,416] [INFO] Task started: Prodigal
[2023-03-15 21:52:15,416] [INFO] Running command: cat /var/lib/cwl/stge161900d-de8c-4cc7-b646-4f96f205aade/OceanDNA-b20044.fa | prodigal -d OceanDNA-b20044/cds.fna -a OceanDNA-b20044/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:52:21,573] [INFO] Task succeeded: Prodigal
[2023-03-15 21:52:21,573] [INFO] Task started: HMMsearch
[2023-03-15 21:52:21,574] [INFO] Running command: hmmsearch --tblout OceanDNA-b20044/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4c3127b-9741-46c5-84bc-d12ca3b12772/dqc_reference/reference_markers.hmm OceanDNA-b20044/protein.faa > /dev/null
[2023-03-15 21:52:21,740] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:52:21,741] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge161900d-de8c-4cc7-b646-4f96f205aade/OceanDNA-b20044.fa]
[2023-03-15 21:52:21,754] [INFO] Query marker FASTA was written to OceanDNA-b20044/markers.fasta
[2023-03-15 21:52:21,755] [INFO] Task started: Blastn
[2023-03-15 21:52:21,755] [INFO] Running command: blastn -query OceanDNA-b20044/markers.fasta -db /var/lib/cwl/stgc4c3127b-9741-46c5-84bc-d12ca3b12772/dqc_reference/reference_markers.fasta -out OceanDNA-b20044/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:52:22,440] [INFO] Task succeeded: Blastn
[2023-03-15 21:52:22,441] [INFO] Selected 15 target genomes.
[2023-03-15 21:52:22,441] [INFO] Target genome list was writen to OceanDNA-b20044/target_genomes.txt
[2023-03-15 21:52:22,454] [INFO] Task started: fastANI
[2023-03-15 21:52:22,454] [INFO] Running command: fastANI --query /var/lib/cwl/stge161900d-de8c-4cc7-b646-4f96f205aade/OceanDNA-b20044.fa --refList OceanDNA-b20044/target_genomes.txt --output OceanDNA-b20044/fastani_result.tsv --threads 1
[2023-03-15 21:52:28,955] [INFO] Task succeeded: fastANI
[2023-03-15 21:52:28,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4c3127b-9741-46c5-84bc-d12ca3b12772/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:52:28,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4c3127b-9741-46c5-84bc-d12ca3b12772/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:52:28,955] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:52:28,955] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:52:28,955] [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 21:52:29,343] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20044/tc_result.tsv
[2023-03-15 21:52:29,343] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:52:29,343] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:52:29,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4c3127b-9741-46c5-84bc-d12ca3b12772/dqc_reference/checkm_data
[2023-03-15 21:52:29,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:52:29,423] [INFO] Task started: CheckM
[2023-03-15 21:52:29,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20044/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20044/checkm_input OceanDNA-b20044/checkm_result
[2023-03-15 21:52:53,822] [INFO] Task succeeded: CheckM
[2023-03-15 21:52:53,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.23%
Contamintation: 11.63%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-15 21:52:53,863] [INFO] ===== Completeness check finished =====
[2023-03-15 21:52:53,863] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:52:53,863] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20044/markers.fasta)
[2023-03-15 21:52:53,865] [INFO] Task started: Blastn
[2023-03-15 21:52:53,865] [INFO] Running command: blastn -query OceanDNA-b20044/markers.fasta -db /var/lib/cwl/stgc4c3127b-9741-46c5-84bc-d12ca3b12772/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20044/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:52:54,784] [INFO] Task succeeded: Blastn
[2023-03-15 21:52:54,789] [INFO] Selected 21 target genomes.
[2023-03-15 21:52:54,789] [INFO] Target genome list was writen to OceanDNA-b20044/target_genomes_gtdb.txt
[2023-03-15 21:52:55,086] [INFO] Task started: fastANI
[2023-03-15 21:52:55,086] [INFO] Running command: fastANI --query /var/lib/cwl/stge161900d-de8c-4cc7-b646-4f96f205aade/OceanDNA-b20044.fa --refList OceanDNA-b20044/target_genomes_gtdb.txt --output OceanDNA-b20044/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:53:02,433] [INFO] Task succeeded: fastANI
[2023-03-15 21:53:02,435] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:53:02,435] [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_002713885.1	s__TMED80 sp002713885	93.2108	210	353	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169695.1	s__TMED80 sp002169695	77.533	80	353	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:53:02,438] [INFO] GTDB search result was written to OceanDNA-b20044/result_gtdb.tsv
[2023-03-15 21:53:02,443] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:53:02,447] [INFO] DFAST_QC result json was written to OceanDNA-b20044/dqc_result.json
[2023-03-15 21:53:02,447] [INFO] DFAST_QC completed!
[2023-03-15 21:53:02,447] [INFO] Total running time: 0h0m50s