[2023-03-15 18:39:12,218] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,218] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,218] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f0dc20f-eab4-4d50-9917-9dfbf40c6b7a/dqc_reference
[2023-03-15 18:39:13,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,658] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stg92fe69d9-018c-460b-87f2-8cb51091e66d/OceanDNA-a1919.fa | prodigal -d OceanDNA-a1919/cds.fna -a OceanDNA-a1919/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:21,072] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:21,073] [INFO] Task started: HMMsearch
[2023-03-15 18:39:21,073] [INFO] Running command: hmmsearch --tblout OceanDNA-a1919/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f0dc20f-eab4-4d50-9917-9dfbf40c6b7a/dqc_reference/reference_markers.hmm OceanDNA-a1919/protein.faa > /dev/null
[2023-03-15 18:39:21,220] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:21,221] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg92fe69d9-018c-460b-87f2-8cb51091e66d/OceanDNA-a1919.fa]
[2023-03-15 18:39:21,232] [INFO] Query marker FASTA was written to OceanDNA-a1919/markers.fasta
[2023-03-15 18:39:21,233] [INFO] Task started: Blastn
[2023-03-15 18:39:21,233] [INFO] Running command: blastn -query OceanDNA-a1919/markers.fasta -db /var/lib/cwl/stg1f0dc20f-eab4-4d50-9917-9dfbf40c6b7a/dqc_reference/reference_markers.fasta -out OceanDNA-a1919/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:21,702] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:21,703] [INFO] Selected 5 target genomes.
[2023-03-15 18:39:21,703] [INFO] Target genome list was writen to OceanDNA-a1919/target_genomes.txt
[2023-03-15 18:39:21,706] [INFO] Task started: fastANI
[2023-03-15 18:39:21,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg92fe69d9-018c-460b-87f2-8cb51091e66d/OceanDNA-a1919.fa --refList OceanDNA-a1919/target_genomes.txt --output OceanDNA-a1919/fastani_result.tsv --threads 1
[2023-03-15 18:39:24,918] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:24,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f0dc20f-eab4-4d50-9917-9dfbf40c6b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:24,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f0dc20f-eab4-4d50-9917-9dfbf40c6b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:24,919] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:24,919] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:24,919] [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 18:39:24,919] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1919/tc_result.tsv
[2023-03-15 18:39:24,919] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:24,919] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:24,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f0dc20f-eab4-4d50-9917-9dfbf40c6b7a/dqc_reference/checkm_data
[2023-03-15 18:39:24,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:24,924] [INFO] Task started: CheckM
[2023-03-15 18:39:24,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1919/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1919/checkm_input OceanDNA-a1919/checkm_result
[2023-03-15 18:39:48,760] [INFO] Task succeeded: CheckM
[2023-03-15 18:39:48,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.64%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 18:39:48,762] [INFO] ===== Completeness check finished =====
[2023-03-15 18:39:48,762] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:39:48,762] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1919/markers.fasta)
[2023-03-15 18:39:48,762] [INFO] Task started: Blastn
[2023-03-15 18:39:48,762] [INFO] Running command: blastn -query OceanDNA-a1919/markers.fasta -db /var/lib/cwl/stg1f0dc20f-eab4-4d50-9917-9dfbf40c6b7a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1919/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:49,470] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:49,470] [INFO] Selected 11 target genomes.
[2023-03-15 18:39:49,470] [INFO] Target genome list was writen to OceanDNA-a1919/target_genomes_gtdb.txt
[2023-03-15 18:39:49,896] [INFO] Task started: fastANI
[2023-03-15 18:39:49,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg92fe69d9-018c-460b-87f2-8cb51091e66d/OceanDNA-a1919.fa --refList OceanDNA-a1919/target_genomes_gtdb.txt --output OceanDNA-a1919/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:39:53,075] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:53,080] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:39:53,080] [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_018650165.1	s__MGIIa-K1 sp018650165	78.5631	191	417	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	-
GCA_902605365.1	s__MGIIa-K1 sp902605365	78.2934	147	417	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701145.1	s__MGIIa-K1 sp002701145	78.0991	191	417	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689345.1	s__MGIIa-K1 sp002689345	77.5723	164	417	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	77.0014	96	417	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	76.5888	82	417	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525095.1	s__MGIIa-K1 sp011525095	76.4725	65	417	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:39:53,080] [INFO] GTDB search result was written to OceanDNA-a1919/result_gtdb.tsv
[2023-03-15 18:39:53,080] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:39:53,081] [INFO] DFAST_QC result json was written to OceanDNA-a1919/dqc_result.json
[2023-03-15 18:39:53,081] [INFO] DFAST_QC completed!
[2023-03-15 18:39:53,081] [INFO] Total running time: 0h0m41s