[2023-03-15 19:02:30,675] [INFO] DFAST_QC pipeline started.
[2023-03-15 19:02:30,675] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 19:02:30,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ff50990-1777-4759-951c-f99aae631ad3/dqc_reference
[2023-03-15 19:02:34,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 19:02:34,957] [INFO] Task started: Prodigal
[2023-03-15 19:02:34,958] [INFO] Running command: cat /var/lib/cwl/stgb723c013-51eb-48a5-a72d-f2ae23793772/OceanDNA-b23122.fa | prodigal -d OceanDNA-b23122/cds.fna -a OceanDNA-b23122/protein.faa -g 11 -q > /dev/null
[2023-03-15 19:03:03,035] [INFO] Task succeeded: Prodigal
[2023-03-15 19:03:03,035] [INFO] Task started: HMMsearch
[2023-03-15 19:03:03,036] [INFO] Running command: hmmsearch --tblout OceanDNA-b23122/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ff50990-1777-4759-951c-f99aae631ad3/dqc_reference/reference_markers.hmm OceanDNA-b23122/protein.faa > /dev/null
[2023-03-15 19:03:03,285] [INFO] Task succeeded: HMMsearch
[2023-03-15 19:03:03,286] [INFO] Found 6/6 markers.
[2023-03-15 19:03:03,321] [INFO] Query marker FASTA was written to OceanDNA-b23122/markers.fasta
[2023-03-15 19:03:03,322] [INFO] Task started: Blastn
[2023-03-15 19:03:03,322] [INFO] Running command: blastn -query OceanDNA-b23122/markers.fasta -db /var/lib/cwl/stg3ff50990-1777-4759-951c-f99aae631ad3/dqc_reference/reference_markers.fasta -out OceanDNA-b23122/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:03:03,877] [INFO] Task succeeded: Blastn
[2023-03-15 19:03:03,878] [INFO] Selected 20 target genomes.
[2023-03-15 19:03:03,878] [INFO] Target genome list was writen to OceanDNA-b23122/target_genomes.txt
[2023-03-15 19:03:03,930] [INFO] Task started: fastANI
[2023-03-15 19:03:03,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgb723c013-51eb-48a5-a72d-f2ae23793772/OceanDNA-b23122.fa --refList OceanDNA-b23122/target_genomes.txt --output OceanDNA-b23122/fastani_result.tsv --threads 1
[2023-03-15 19:03:20,119] [INFO] Task succeeded: fastANI
[2023-03-15 19:03:20,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ff50990-1777-4759-951c-f99aae631ad3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 19:03:20,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ff50990-1777-4759-951c-f99aae631ad3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 19:03:20,124] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 19:03:20,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 19:03:20,124] [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
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.7475	55	1518	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 19:03:20,124] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23122/tc_result.tsv
[2023-03-15 19:03:20,124] [INFO] ===== Taxonomy check completed =====
[2023-03-15 19:03:20,124] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 19:03:20,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ff50990-1777-4759-951c-f99aae631ad3/dqc_reference/checkm_data
[2023-03-15 19:03:20,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 19:03:20,134] [INFO] Task started: CheckM
[2023-03-15 19:03:20,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23122/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23122/checkm_input OceanDNA-b23122/checkm_result
[2023-03-15 19:04:28,358] [INFO] Task succeeded: CheckM
[2023-03-15 19:04:28,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 19:04:28,362] [INFO] ===== Completeness check finished =====
[2023-03-15 19:04:28,362] [INFO] ===== Start GTDB Search =====
[2023-03-15 19:04:28,363] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23122/markers.fasta)
[2023-03-15 19:04:28,366] [INFO] Task started: Blastn
[2023-03-15 19:04:28,367] [INFO] Running command: blastn -query OceanDNA-b23122/markers.fasta -db /var/lib/cwl/stg3ff50990-1777-4759-951c-f99aae631ad3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23122/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 19:04:29,194] [INFO] Task succeeded: Blastn
[2023-03-15 19:04:29,195] [INFO] Selected 23 target genomes.
[2023-03-15 19:04:29,195] [INFO] Target genome list was writen to OceanDNA-b23122/target_genomes_gtdb.txt
[2023-03-15 19:04:30,383] [INFO] Task started: fastANI
[2023-03-15 19:04:30,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgb723c013-51eb-48a5-a72d-f2ae23793772/OceanDNA-b23122.fa --refList OceanDNA-b23122/target_genomes_gtdb.txt --output OceanDNA-b23122/fastani_result_gtdb.tsv --threads 1
[2023-03-15 19:04:45,241] [INFO] Task succeeded: fastANI
[2023-03-15 19:04:45,245] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 19:04:45,245] [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_017859655.1	s__JAFMMO01 sp017859655	77.3839	284	1518	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__JAFMMO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235155.1	s__JACRLW01 sp016235155	74.905	60	1518	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JACRLW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795345.1	s__JAEUHO01 sp016795345	74.8656	50	1518	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__JAEUHO01;g__JAEUHO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 19:04:45,246] [INFO] GTDB search result was written to OceanDNA-b23122/result_gtdb.tsv
[2023-03-15 19:04:45,246] [INFO] ===== GTDB Search completed =====
[2023-03-15 19:04:45,247] [INFO] DFAST_QC result json was written to OceanDNA-b23122/dqc_result.json
[2023-03-15 19:04:45,247] [INFO] DFAST_QC completed!
[2023-03-15 19:04:45,247] [INFO] Total running time: 0h2m15s