[2023-03-15 21:16:33,599] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:16:33,600] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:16:33,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg68bb765d-06a2-400e-9fe8-4bc49fd3e147/dqc_reference
[2023-03-15 21:16:36,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:16:36,708] [INFO] Task started: Prodigal
[2023-03-15 21:16:36,709] [INFO] Running command: cat /var/lib/cwl/stg1c4537f6-3227-4336-b39b-13054a1ac9c1/OceanDNA-a1923.fa | prodigal -d OceanDNA-a1923/cds.fna -a OceanDNA-a1923/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:16:42,637] [INFO] Task succeeded: Prodigal
[2023-03-15 21:16:42,638] [INFO] Task started: HMMsearch
[2023-03-15 21:16:42,638] [INFO] Running command: hmmsearch --tblout OceanDNA-a1923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68bb765d-06a2-400e-9fe8-4bc49fd3e147/dqc_reference/reference_markers.hmm OceanDNA-a1923/protein.faa > /dev/null
[2023-03-15 21:16:42,816] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:16:42,816] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1c4537f6-3227-4336-b39b-13054a1ac9c1/OceanDNA-a1923.fa]
[2023-03-15 21:16:42,825] [INFO] Query marker FASTA was written to OceanDNA-a1923/markers.fasta
[2023-03-15 21:16:42,825] [INFO] Task started: Blastn
[2023-03-15 21:16:42,825] [INFO] Running command: blastn -query OceanDNA-a1923/markers.fasta -db /var/lib/cwl/stg68bb765d-06a2-400e-9fe8-4bc49fd3e147/dqc_reference/reference_markers.fasta -out OceanDNA-a1923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:16:45,915] [INFO] Task succeeded: Blastn
[2023-03-15 21:16:45,915] [INFO] Selected 3 target genomes.
[2023-03-15 21:16:45,916] [INFO] Target genome list was writen to OceanDNA-a1923/target_genomes.txt
[2023-03-15 21:16:45,918] [INFO] Task started: fastANI
[2023-03-15 21:16:45,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c4537f6-3227-4336-b39b-13054a1ac9c1/OceanDNA-a1923.fa --refList OceanDNA-a1923/target_genomes.txt --output OceanDNA-a1923/fastani_result.tsv --threads 1
[2023-03-15 21:16:46,793] [INFO] Task succeeded: fastANI
[2023-03-15 21:16:46,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68bb765d-06a2-400e-9fe8-4bc49fd3e147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:16:46,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68bb765d-06a2-400e-9fe8-4bc49fd3e147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:16:46,794] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:16:46,794] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:16:46,794] [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 21:16:46,794] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1923/tc_result.tsv
[2023-03-15 21:16:46,794] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:16:46,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:16:46,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68bb765d-06a2-400e-9fe8-4bc49fd3e147/dqc_reference/checkm_data
[2023-03-15 21:16:46,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:16:46,851] [INFO] Task started: CheckM
[2023-03-15 21:16:46,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1923/checkm_input OceanDNA-a1923/checkm_result
[2023-03-15 21:17:10,246] [INFO] Task succeeded: CheckM
[2023-03-15 21:17:10,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:17:10,248] [INFO] ===== Completeness check finished =====
[2023-03-15 21:17:10,248] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:17:10,248] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1923/markers.fasta)
[2023-03-15 21:17:10,249] [INFO] Task started: Blastn
[2023-03-15 21:17:10,249] [INFO] Running command: blastn -query OceanDNA-a1923/markers.fasta -db /var/lib/cwl/stg68bb765d-06a2-400e-9fe8-4bc49fd3e147/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:17:10,916] [INFO] Task succeeded: Blastn
[2023-03-15 21:17:10,917] [INFO] Selected 11 target genomes.
[2023-03-15 21:17:10,917] [INFO] Target genome list was writen to OceanDNA-a1923/target_genomes_gtdb.txt
[2023-03-15 21:17:11,212] [INFO] Task started: fastANI
[2023-03-15 21:17:11,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c4537f6-3227-4336-b39b-13054a1ac9c1/OceanDNA-a1923.fa --refList OceanDNA-a1923/target_genomes_gtdb.txt --output OceanDNA-a1923/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:17:14,285] [INFO] Task succeeded: fastANI
[2023-03-15 21:17:14,291] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:17:14,291] [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_902605365.1	s__MGIIa-K1 sp902605365	78.7602	138	348	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	78.7415	169	348	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_018650165.1	s__MGIIa-K1 sp018650165	77.9971	133	348	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_002689345.1	s__MGIIa-K1 sp002689345	77.7297	131	348	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_003602415.1	s__MGIIa-K1 sp003602415	77.2085	125	348	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	77.1074	75	348	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_002710205.1	s__MGIIa-K1 sp002710205	77.0695	88	348	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_902563095.1	s__MGIIa-K1 sp902563095	77.0234	66	348	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_002715725.1	s__MGIIa-K1 sp002715725	77.0214	85	348	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.59	99.59	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:17:14,291] [INFO] GTDB search result was written to OceanDNA-a1923/result_gtdb.tsv
[2023-03-15 21:17:14,291] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:17:14,292] [INFO] DFAST_QC result json was written to OceanDNA-a1923/dqc_result.json
[2023-03-15 21:17:14,292] [INFO] DFAST_QC completed!
[2023-03-15 21:17:14,292] [INFO] Total running time: 0h0m41s