[2023-03-15 05:00:03,357] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:00:03,357] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:00:03,357] [INFO] DQC Reference Directory: /var/lib/cwl/stg953a769e-4e4c-4b52-9f0b-550ffac0bf40/dqc_reference
[2023-03-15 05:00:04,468] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:00:04,468] [INFO] Task started: Prodigal
[2023-03-15 05:00:04,469] [INFO] Running command: cat /var/lib/cwl/stgb0598213-af07-4beb-9f81-746fed37df6e/OceanDNA-b3549.fa | prodigal -d OceanDNA-b3549/cds.fna -a OceanDNA-b3549/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:00:22,774] [INFO] Task succeeded: Prodigal
[2023-03-15 05:00:22,774] [INFO] Task started: HMMsearch
[2023-03-15 05:00:22,774] [INFO] Running command: hmmsearch --tblout OceanDNA-b3549/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg953a769e-4e4c-4b52-9f0b-550ffac0bf40/dqc_reference/reference_markers.hmm OceanDNA-b3549/protein.faa > /dev/null
[2023-03-15 05:00:22,975] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:00:22,976] [INFO] Found 6/6 markers.
[2023-03-15 05:00:23,014] [INFO] Query marker FASTA was written to OceanDNA-b3549/markers.fasta
[2023-03-15 05:00:23,016] [INFO] Task started: Blastn
[2023-03-15 05:00:23,016] [INFO] Running command: blastn -query OceanDNA-b3549/markers.fasta -db /var/lib/cwl/stg953a769e-4e4c-4b52-9f0b-550ffac0bf40/dqc_reference/reference_markers.fasta -out OceanDNA-b3549/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:23,550] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:23,556] [INFO] Selected 23 target genomes.
[2023-03-15 05:00:23,556] [INFO] Target genome list was writen to OceanDNA-b3549/target_genomes.txt
[2023-03-15 05:00:23,569] [INFO] Task started: fastANI
[2023-03-15 05:00:23,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0598213-af07-4beb-9f81-746fed37df6e/OceanDNA-b3549.fa --refList OceanDNA-b3549/target_genomes.txt --output OceanDNA-b3549/fastani_result.tsv --threads 1
[2023-03-15 05:00:36,082] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:36,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg953a769e-4e4c-4b52-9f0b-550ffac0bf40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:00:36,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg953a769e-4e4c-4b52-9f0b-550ffac0bf40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:00:36,083] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:00:36,083] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:00:36,083] [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 05:00:36,085] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3549/tc_result.tsv
[2023-03-15 05:00:36,089] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:00:36,089] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:00:36,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg953a769e-4e4c-4b52-9f0b-550ffac0bf40/dqc_reference/checkm_data
[2023-03-15 05:00:36,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:00:36,124] [INFO] Task started: CheckM
[2023-03-15 05:00:36,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3549/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3549/checkm_input OceanDNA-b3549/checkm_result
[2023-03-15 05:01:23,739] [INFO] Task succeeded: CheckM
[2023-03-15 05:01:23,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:01:23,771] [INFO] ===== Completeness check finished =====
[2023-03-15 05:01:23,772] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:01:23,772] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3549/markers.fasta)
[2023-03-15 05:01:23,773] [INFO] Task started: Blastn
[2023-03-15 05:01:23,773] [INFO] Running command: blastn -query OceanDNA-b3549/markers.fasta -db /var/lib/cwl/stg953a769e-4e4c-4b52-9f0b-550ffac0bf40/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3549/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:01:24,508] [INFO] Task succeeded: Blastn
[2023-03-15 05:01:24,516] [INFO] Selected 25 target genomes.
[2023-03-15 05:01:24,517] [INFO] Target genome list was writen to OceanDNA-b3549/target_genomes_gtdb.txt
[2023-03-15 05:01:24,738] [INFO] Task started: fastANI
[2023-03-15 05:01:24,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0598213-af07-4beb-9f81-746fed37df6e/OceanDNA-b3549.fa --refList OceanDNA-b3549/target_genomes_gtdb.txt --output OceanDNA-b3549/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:01:39,316] [INFO] Task succeeded: fastANI
[2023-03-15 05:01:39,321] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:01:39,321] [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_002686705.1	s__GCA-002708315 sp002686705	99.8277	730	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002708315.1	s__GCA-002708315 sp002708315	78.0187	73	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018661505.1	s__GCA-002708315 sp018661505	77.6365	89	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.95	99.92	0.97	0.96	16	-
GCA_014382445.1	s__GCA-002708315 sp014382445	77.6306	304	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.88	99.88	0.96	0.96	2	-
GCA_013203805.1	s__GCA-002708315 sp013203805	76.563	195	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845105.1	s__GCA-002708315 sp016845105	76.5097	170	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:01:39,324] [INFO] GTDB search result was written to OceanDNA-b3549/result_gtdb.tsv
[2023-03-15 05:01:39,329] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:01:39,333] [INFO] DFAST_QC result json was written to OceanDNA-b3549/dqc_result.json
[2023-03-15 05:01:39,333] [INFO] DFAST_QC completed!
[2023-03-15 05:01:39,333] [INFO] Total running time: 0h1m36s