[2023-03-18 04:39:10,642] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:39:10,643] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:39:10,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fc4fce9-403e-404f-8c75-09d15ae37fb6/dqc_reference
[2023-03-18 04:39:11,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:39:11,747] [INFO] Task started: Prodigal
[2023-03-18 04:39:11,747] [INFO] Running command: cat /var/lib/cwl/stgaefafaa7-5e31-4540-97da-af7066451f11/OceanDNA-b22344.fa | prodigal -d OceanDNA-b22344/cds.fna -a OceanDNA-b22344/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:39:39,371] [INFO] Task succeeded: Prodigal
[2023-03-18 04:39:39,372] [INFO] Task started: HMMsearch
[2023-03-18 04:39:39,372] [INFO] Running command: hmmsearch --tblout OceanDNA-b22344/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fc4fce9-403e-404f-8c75-09d15ae37fb6/dqc_reference/reference_markers.hmm OceanDNA-b22344/protein.faa > /dev/null
[2023-03-18 04:39:39,584] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:39:39,585] [INFO] Found 6/6 markers.
[2023-03-18 04:39:39,611] [INFO] Query marker FASTA was written to OceanDNA-b22344/markers.fasta
[2023-03-18 04:39:39,613] [INFO] Task started: Blastn
[2023-03-18 04:39:39,613] [INFO] Running command: blastn -query OceanDNA-b22344/markers.fasta -db /var/lib/cwl/stg6fc4fce9-403e-404f-8c75-09d15ae37fb6/dqc_reference/reference_markers.fasta -out OceanDNA-b22344/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:40,135] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:40,136] [INFO] Selected 18 target genomes.
[2023-03-18 04:39:40,136] [INFO] Target genome list was writen to OceanDNA-b22344/target_genomes.txt
[2023-03-18 04:39:40,145] [INFO] Task started: fastANI
[2023-03-18 04:39:40,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgaefafaa7-5e31-4540-97da-af7066451f11/OceanDNA-b22344.fa --refList OceanDNA-b22344/target_genomes.txt --output OceanDNA-b22344/fastani_result.tsv --threads 1
[2023-03-18 04:39:55,885] [INFO] Task succeeded: fastANI
[2023-03-18 04:39:55,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fc4fce9-403e-404f-8c75-09d15ae37fb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:39:55,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fc4fce9-403e-404f-8c75-09d15ae37fb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:39:55,889] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:39:55,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:39:55,889] [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
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.0003	73	1481	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:39:55,889] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22344/tc_result.tsv
[2023-03-18 04:39:55,889] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:39:55,889] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:39:55,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fc4fce9-403e-404f-8c75-09d15ae37fb6/dqc_reference/checkm_data
[2023-03-18 04:39:55,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:39:55,896] [INFO] Task started: CheckM
[2023-03-18 04:39:55,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22344/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22344/checkm_input OceanDNA-b22344/checkm_result
[2023-03-18 04:41:03,253] [INFO] Task succeeded: CheckM
[2023-03-18 04:41:03,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:41:03,256] [INFO] ===== Completeness check finished =====
[2023-03-18 04:41:03,256] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:41:03,256] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22344/markers.fasta)
[2023-03-18 04:41:03,257] [INFO] Task started: Blastn
[2023-03-18 04:41:03,257] [INFO] Running command: blastn -query OceanDNA-b22344/markers.fasta -db /var/lib/cwl/stg6fc4fce9-403e-404f-8c75-09d15ae37fb6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22344/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:41:03,979] [INFO] Task succeeded: Blastn
[2023-03-18 04:41:03,979] [INFO] Selected 21 target genomes.
[2023-03-18 04:41:03,979] [INFO] Target genome list was writen to OceanDNA-b22344/target_genomes_gtdb.txt
[2023-03-18 04:41:04,102] [INFO] Task started: fastANI
[2023-03-18 04:41:04,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgaefafaa7-5e31-4540-97da-af7066451f11/OceanDNA-b22344.fa --refList OceanDNA-b22344/target_genomes_gtdb.txt --output OceanDNA-b22344/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:41:20,286] [INFO] Task succeeded: fastANI
[2023-03-18 04:41:20,289] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:41:20,289] [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_903863885.1	s__CAIPEB01 sp903863885	75.4769	55	1481	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__CAIPEB01	95.0	99.80	99.80	0.91	0.91	2	-
GCA_016935315.1	s__JAFGRD01 sp016935315	75.3341	52	1481	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515235.1	s__Anammoximicrobium sp012515235	75.204	52	1481	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anammoximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:41:20,289] [INFO] GTDB search result was written to OceanDNA-b22344/result_gtdb.tsv
[2023-03-18 04:41:20,289] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:41:20,290] [INFO] DFAST_QC result json was written to OceanDNA-b22344/dqc_result.json
[2023-03-18 04:41:20,290] [INFO] DFAST_QC completed!
[2023-03-18 04:41:20,290] [INFO] Total running time: 0h2m10s