[2023-03-15 22:15:27,637] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:15:27,643] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:15:27,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg45af4e78-3f79-40d5-aee6-6fe617adc420/dqc_reference
[2023-03-15 22:15:29,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:15:29,361] [INFO] Task started: Prodigal
[2023-03-15 22:15:29,361] [INFO] Running command: cat /var/lib/cwl/stgc6c561de-70e0-4b71-8ea9-b91c020d2711/OceanDNA-b18470.fa | prodigal -d OceanDNA-b18470/cds.fna -a OceanDNA-b18470/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:15:35,444] [INFO] Task succeeded: Prodigal
[2023-03-15 22:15:35,445] [INFO] Task started: HMMsearch
[2023-03-15 22:15:35,445] [INFO] Running command: hmmsearch --tblout OceanDNA-b18470/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45af4e78-3f79-40d5-aee6-6fe617adc420/dqc_reference/reference_markers.hmm OceanDNA-b18470/protein.faa > /dev/null
[2023-03-15 22:15:35,579] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:15:35,580] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc6c561de-70e0-4b71-8ea9-b91c020d2711/OceanDNA-b18470.fa]
[2023-03-15 22:15:35,635] [INFO] Query marker FASTA was written to OceanDNA-b18470/markers.fasta
[2023-03-15 22:15:35,636] [INFO] Task started: Blastn
[2023-03-15 22:15:35,637] [INFO] Running command: blastn -query OceanDNA-b18470/markers.fasta -db /var/lib/cwl/stg45af4e78-3f79-40d5-aee6-6fe617adc420/dqc_reference/reference_markers.fasta -out OceanDNA-b18470/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:15:36,668] [INFO] Task succeeded: Blastn
[2023-03-15 22:15:36,686] [INFO] Selected 7 target genomes.
[2023-03-15 22:15:36,687] [INFO] Target genome list was writen to OceanDNA-b18470/target_genomes.txt
[2023-03-15 22:15:36,691] [INFO] Task started: fastANI
[2023-03-15 22:15:36,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6c561de-70e0-4b71-8ea9-b91c020d2711/OceanDNA-b18470.fa --refList OceanDNA-b18470/target_genomes.txt --output OceanDNA-b18470/fastani_result.tsv --threads 1
[2023-03-15 22:15:39,753] [INFO] Task succeeded: fastANI
[2023-03-15 22:15:39,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45af4e78-3f79-40d5-aee6-6fe617adc420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:15:39,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45af4e78-3f79-40d5-aee6-6fe617adc420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:15:39,754] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:15:39,754] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:15:39,754] [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 22:15:39,757] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18470/tc_result.tsv
[2023-03-15 22:15:39,759] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:15:39,759] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:15:39,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45af4e78-3f79-40d5-aee6-6fe617adc420/dqc_reference/checkm_data
[2023-03-15 22:15:39,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:15:39,767] [INFO] Task started: CheckM
[2023-03-15 22:15:39,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18470/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18470/checkm_input OceanDNA-b18470/checkm_result
[2023-03-15 22:16:00,633] [INFO] Task succeeded: CheckM
[2023-03-15 22:16:00,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:16:00,708] [INFO] ===== Completeness check finished =====
[2023-03-15 22:16:00,708] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:16:00,708] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18470/markers.fasta)
[2023-03-15 22:16:00,709] [INFO] Task started: Blastn
[2023-03-15 22:16:00,709] [INFO] Running command: blastn -query OceanDNA-b18470/markers.fasta -db /var/lib/cwl/stg45af4e78-3f79-40d5-aee6-6fe617adc420/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18470/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:16:01,265] [INFO] Task succeeded: Blastn
[2023-03-15 22:16:01,271] [INFO] Selected 14 target genomes.
[2023-03-15 22:16:01,271] [INFO] Target genome list was writen to OceanDNA-b18470/target_genomes_gtdb.txt
[2023-03-15 22:16:01,381] [INFO] Task started: fastANI
[2023-03-15 22:16:01,381] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6c561de-70e0-4b71-8ea9-b91c020d2711/OceanDNA-b18470.fa --refList OceanDNA-b18470/target_genomes_gtdb.txt --output OceanDNA-b18470/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:16:06,768] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:06,771] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:16:06,771] [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_002170005.2	s__TMED144 sp002170005	99.2778	342	378	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED144	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902615915.1	s__TMED144 sp902615915	91.6593	318	378	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED144	95.0	95.39	95.39	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:16:06,773] [INFO] GTDB search result was written to OceanDNA-b18470/result_gtdb.tsv
[2023-03-15 22:16:06,775] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:16:06,778] [INFO] DFAST_QC result json was written to OceanDNA-b18470/dqc_result.json
[2023-03-15 22:16:06,778] [INFO] DFAST_QC completed!
[2023-03-15 22:16:06,778] [INFO] Total running time: 0h0m39s