[2023-03-15 03:56:21,757] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg44a5b0ab-422c-42bb-bf42-3c9dfd13783d/dqc_reference
[2023-03-15 03:56:23,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,405] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,405] [INFO] Running command: cat /var/lib/cwl/stgb6c05d78-4837-42ca-a229-9750a51bb1fb/OceanDNA-b20631.fa | prodigal -d OceanDNA-b20631/cds.fna -a OceanDNA-b20631/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:30,437] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:30,437] [INFO] Task started: HMMsearch
[2023-03-15 03:56:30,437] [INFO] Running command: hmmsearch --tblout OceanDNA-b20631/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44a5b0ab-422c-42bb-bf42-3c9dfd13783d/dqc_reference/reference_markers.hmm OceanDNA-b20631/protein.faa > /dev/null
[2023-03-15 03:56:30,646] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:30,646] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb6c05d78-4837-42ca-a229-9750a51bb1fb/OceanDNA-b20631.fa]
[2023-03-15 03:56:30,659] [INFO] Query marker FASTA was written to OceanDNA-b20631/markers.fasta
[2023-03-15 03:56:30,659] [INFO] Task started: Blastn
[2023-03-15 03:56:30,659] [INFO] Running command: blastn -query OceanDNA-b20631/markers.fasta -db /var/lib/cwl/stg44a5b0ab-422c-42bb-bf42-3c9dfd13783d/dqc_reference/reference_markers.fasta -out OceanDNA-b20631/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:31,247] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:31,248] [INFO] Selected 20 target genomes.
[2023-03-15 03:56:31,248] [INFO] Target genome list was writen to OceanDNA-b20631/target_genomes.txt
[2023-03-15 03:56:31,260] [INFO] Task started: fastANI
[2023-03-15 03:56:31,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6c05d78-4837-42ca-a229-9750a51bb1fb/OceanDNA-b20631.fa --refList OceanDNA-b20631/target_genomes.txt --output OceanDNA-b20631/fastani_result.tsv --threads 1
[2023-03-15 03:56:42,971] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:42,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44a5b0ab-422c-42bb-bf42-3c9dfd13783d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:42,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44a5b0ab-422c-42bb-bf42-3c9dfd13783d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:42,972] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:42,972] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:56:42,972] [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 03:56:42,972] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20631/tc_result.tsv
[2023-03-15 03:56:42,972] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:42,973] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:42,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44a5b0ab-422c-42bb-bf42-3c9dfd13783d/dqc_reference/checkm_data
[2023-03-15 03:56:42,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:42,978] [INFO] Task started: CheckM
[2023-03-15 03:56:42,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20631/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20631/checkm_input OceanDNA-b20631/checkm_result
[2023-03-15 03:57:06,276] [INFO] Task succeeded: CheckM
[2023-03-15 03:57:06,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.88%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 03:57:06,279] [INFO] ===== Completeness check finished =====
[2023-03-15 03:57:06,279] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:57:06,279] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20631/markers.fasta)
[2023-03-15 03:57:06,280] [INFO] Task started: Blastn
[2023-03-15 03:57:06,280] [INFO] Running command: blastn -query OceanDNA-b20631/markers.fasta -db /var/lib/cwl/stg44a5b0ab-422c-42bb-bf42-3c9dfd13783d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20631/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:06,938] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:06,939] [INFO] Selected 21 target genomes.
[2023-03-15 03:57:06,939] [INFO] Target genome list was writen to OceanDNA-b20631/target_genomes_gtdb.txt
[2023-03-15 03:57:06,961] [INFO] Task started: fastANI
[2023-03-15 03:57:06,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6c05d78-4837-42ca-a229-9750a51bb1fb/OceanDNA-b20631.fa --refList OceanDNA-b20631/target_genomes_gtdb.txt --output OceanDNA-b20631/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:57:13,230] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:13,233] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:57:13,233] [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_002689995.1	s__GCA-2689995 sp002689995	79.2259	302	472	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-2689995;g__GCA-2689995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381925.1	s__GCA-2689995 sp014381925	77.3656	166	472	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-2689995;g__GCA-2689995	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:57:13,234] [INFO] GTDB search result was written to OceanDNA-b20631/result_gtdb.tsv
[2023-03-15 03:57:13,234] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:57:13,234] [INFO] DFAST_QC result json was written to OceanDNA-b20631/dqc_result.json
[2023-03-15 03:57:13,235] [INFO] DFAST_QC completed!
[2023-03-15 03:57:13,235] [INFO] Total running time: 0h0m51s