[2023-03-14 13:55:26,880] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:55:26,880] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:55:26,880] [INFO] DQC Reference Directory: /var/lib/cwl/stgb71c77c0-d597-450b-aef6-58194a6fe5fc/dqc_reference
[2023-03-14 13:55:29,659] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:55:29,669] [INFO] Task started: Prodigal
[2023-03-14 13:55:29,670] [INFO] Running command: cat /var/lib/cwl/stg37429388-5076-466e-864d-f23b8643a85d/OceanDNA-b11604.fa | prodigal -d OceanDNA-b11604/cds.fna -a OceanDNA-b11604/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:55:41,554] [INFO] Task succeeded: Prodigal
[2023-03-14 13:55:41,554] [INFO] Task started: HMMsearch
[2023-03-14 13:55:41,554] [INFO] Running command: hmmsearch --tblout OceanDNA-b11604/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb71c77c0-d597-450b-aef6-58194a6fe5fc/dqc_reference/reference_markers.hmm OceanDNA-b11604/protein.faa > /dev/null
[2023-03-14 13:55:41,761] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:55:41,762] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg37429388-5076-466e-864d-f23b8643a85d/OceanDNA-b11604.fa]
[2023-03-14 13:55:41,772] [INFO] Query marker FASTA was written to OceanDNA-b11604/markers.fasta
[2023-03-14 13:55:41,776] [INFO] Task started: Blastn
[2023-03-14 13:55:41,777] [INFO] Running command: blastn -query OceanDNA-b11604/markers.fasta -db /var/lib/cwl/stgb71c77c0-d597-450b-aef6-58194a6fe5fc/dqc_reference/reference_markers.fasta -out OceanDNA-b11604/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:55:42,289] [INFO] Task succeeded: Blastn
[2023-03-14 13:55:42,290] [INFO] Selected 23 target genomes.
[2023-03-14 13:55:42,290] [INFO] Target genome list was writen to OceanDNA-b11604/target_genomes.txt
[2023-03-14 13:55:42,304] [INFO] Task started: fastANI
[2023-03-14 13:55:42,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg37429388-5076-466e-864d-f23b8643a85d/OceanDNA-b11604.fa --refList OceanDNA-b11604/target_genomes.txt --output OceanDNA-b11604/fastani_result.tsv --threads 1
[2023-03-14 13:55:57,621] [INFO] Task succeeded: fastANI
[2023-03-14 13:55:57,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb71c77c0-d597-450b-aef6-58194a6fe5fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:55:57,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb71c77c0-d597-450b-aef6-58194a6fe5fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:55:57,622] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:55:57,622] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:55:57,622] [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 13:55:57,622] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11604/tc_result.tsv
[2023-03-14 13:55:57,622] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:55:57,622] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:55:57,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb71c77c0-d597-450b-aef6-58194a6fe5fc/dqc_reference/checkm_data
[2023-03-14 13:55:57,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:55:57,629] [INFO] Task started: CheckM
[2023-03-14 13:55:57,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11604/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11604/checkm_input OceanDNA-b11604/checkm_result
[2023-03-14 13:56:31,955] [INFO] Task succeeded: CheckM
[2023-03-14 13:56:31,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:56:31,957] [INFO] ===== Completeness check finished =====
[2023-03-14 13:56:31,957] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:56:31,957] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11604/markers.fasta)
[2023-03-14 13:56:31,958] [INFO] Task started: Blastn
[2023-03-14 13:56:31,958] [INFO] Running command: blastn -query OceanDNA-b11604/markers.fasta -db /var/lib/cwl/stgb71c77c0-d597-450b-aef6-58194a6fe5fc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11604/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:56:32,678] [INFO] Task succeeded: Blastn
[2023-03-14 13:56:32,679] [INFO] Selected 25 target genomes.
[2023-03-14 13:56:32,679] [INFO] Target genome list was writen to OceanDNA-b11604/target_genomes_gtdb.txt
[2023-03-14 13:56:32,694] [INFO] Task started: fastANI
[2023-03-14 13:56:32,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg37429388-5076-466e-864d-f23b8643a85d/OceanDNA-b11604.fa --refList OceanDNA-b11604/target_genomes_gtdb.txt --output OceanDNA-b11604/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:56:42,607] [INFO] Task succeeded: fastANI
[2023-03-14 13:56:42,609] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:56:42,610] [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_002863085.1	s__GCA-2863085 sp002863085	96.6971	290	385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2863085	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002714185.1	s__SP256 sp002714185	76.0407	68	385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:56:42,610] [INFO] GTDB search result was written to OceanDNA-b11604/result_gtdb.tsv
[2023-03-14 13:56:42,610] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:56:42,610] [INFO] DFAST_QC result json was written to OceanDNA-b11604/dqc_result.json
[2023-03-14 13:56:42,611] [INFO] DFAST_QC completed!
[2023-03-14 13:56:42,611] [INFO] Total running time: 0h1m16s