[2023-03-15 21:16:33,624] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:16:33,625] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:16:33,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg17d8a84c-b690-4d70-9130-2752008fcad6/dqc_reference
[2023-03-15 21:16:35,470] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:16:35,471] [INFO] Task started: Prodigal
[2023-03-15 21:16:35,471] [INFO] Running command: cat /var/lib/cwl/stg6df775e8-276d-4896-97ac-5b9edf31355e/OceanDNA-a4829.fa | prodigal -d OceanDNA-a4829/cds.fna -a OceanDNA-a4829/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:16:43,658] [INFO] Task succeeded: Prodigal
[2023-03-15 21:16:43,658] [INFO] Task started: HMMsearch
[2023-03-15 21:16:43,658] [INFO] Running command: hmmsearch --tblout OceanDNA-a4829/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17d8a84c-b690-4d70-9130-2752008fcad6/dqc_reference/reference_markers.hmm OceanDNA-a4829/protein.faa > /dev/null
[2023-03-15 21:16:43,822] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:16:43,822] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6df775e8-276d-4896-97ac-5b9edf31355e/OceanDNA-a4829.fa]
[2023-03-15 21:16:43,834] [INFO] Query marker FASTA was written to OceanDNA-a4829/markers.fasta
[2023-03-15 21:16:43,834] [INFO] Task started: Blastn
[2023-03-15 21:16:43,834] [INFO] Running command: blastn -query OceanDNA-a4829/markers.fasta -db /var/lib/cwl/stg17d8a84c-b690-4d70-9130-2752008fcad6/dqc_reference/reference_markers.fasta -out OceanDNA-a4829/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:16:44,256] [INFO] Task succeeded: Blastn
[2023-03-15 21:16:44,257] [INFO] Selected 5 target genomes.
[2023-03-15 21:16:44,257] [INFO] Target genome list was writen to OceanDNA-a4829/target_genomes.txt
[2023-03-15 21:16:44,260] [INFO] Task started: fastANI
[2023-03-15 21:16:44,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df775e8-276d-4896-97ac-5b9edf31355e/OceanDNA-a4829.fa --refList OceanDNA-a4829/target_genomes.txt --output OceanDNA-a4829/fastani_result.tsv --threads 1
[2023-03-15 21:16:46,970] [INFO] Task succeeded: fastANI
[2023-03-15 21:16:46,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17d8a84c-b690-4d70-9130-2752008fcad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:16:46,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17d8a84c-b690-4d70-9130-2752008fcad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:16:46,970] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:16:46,970] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:16:46,970] [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 21:16:46,971] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4829/tc_result.tsv
[2023-03-15 21:16:46,971] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:16:46,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:16:46,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17d8a84c-b690-4d70-9130-2752008fcad6/dqc_reference/checkm_data
[2023-03-15 21:16:46,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:16:46,985] [INFO] Task started: CheckM
[2023-03-15 21:16:46,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4829/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4829/checkm_input OceanDNA-a4829/checkm_result
[2023-03-15 21:17:14,466] [INFO] Task succeeded: CheckM
[2023-03-15 21:17:14,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:17:14,468] [INFO] ===== Completeness check finished =====
[2023-03-15 21:17:14,468] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:17:14,469] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4829/markers.fasta)
[2023-03-15 21:17:14,469] [INFO] Task started: Blastn
[2023-03-15 21:17:14,469] [INFO] Running command: blastn -query OceanDNA-a4829/markers.fasta -db /var/lib/cwl/stg17d8a84c-b690-4d70-9130-2752008fcad6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4829/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:17:14,939] [INFO] Task succeeded: Blastn
[2023-03-15 21:17:14,940] [INFO] Selected 10 target genomes.
[2023-03-15 21:17:14,940] [INFO] Target genome list was writen to OceanDNA-a4829/target_genomes_gtdb.txt
[2023-03-15 21:17:15,031] [INFO] Task started: fastANI
[2023-03-15 21:17:15,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df775e8-276d-4896-97ac-5b9edf31355e/OceanDNA-a4829.fa --refList OceanDNA-a4829/target_genomes_gtdb.txt --output OceanDNA-a4829/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:17:17,805] [INFO] Task succeeded: fastANI
[2023-03-15 21:17:17,808] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:17:17,808] [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_002685895.1	s__MGIIb-Q1 sp002685895	81.6188	304	488	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.01	99.01	0.75	0.75	3	-
GCA_002727675.1	s__MGIIb-Q1 sp002727675	78.0535	142	488	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.36	99.36	0.80	0.80	2	-
GCA_016845345.1	s__MGIIb-Q1 sp016845345	77.0333	95	488	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:17:17,808] [INFO] GTDB search result was written to OceanDNA-a4829/result_gtdb.tsv
[2023-03-15 21:17:17,809] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:17:17,809] [INFO] DFAST_QC result json was written to OceanDNA-a4829/dqc_result.json
[2023-03-15 21:17:17,809] [INFO] DFAST_QC completed!
[2023-03-15 21:17:17,809] [INFO] Total running time: 0h0m44s