[2023-03-16 20:47:10,620] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:47:10,620] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:47:10,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg712e2de5-f52d-40ee-a602-b4008ce1d0b8/dqc_reference
[2023-03-16 20:47:11,712] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:47:11,712] [INFO] Task started: Prodigal
[2023-03-16 20:47:11,712] [INFO] Running command: cat /var/lib/cwl/stg7e9e0e9c-3f44-44b7-b363-1c56e4e99aed/OceanDNA-a1909.fa | prodigal -d OceanDNA-a1909/cds.fna -a OceanDNA-a1909/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:47:18,912] [INFO] Task succeeded: Prodigal
[2023-03-16 20:47:18,913] [INFO] Task started: HMMsearch
[2023-03-16 20:47:18,913] [INFO] Running command: hmmsearch --tblout OceanDNA-a1909/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg712e2de5-f52d-40ee-a602-b4008ce1d0b8/dqc_reference/reference_markers.hmm OceanDNA-a1909/protein.faa > /dev/null
[2023-03-16 20:47:19,072] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:47:19,073] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7e9e0e9c-3f44-44b7-b363-1c56e4e99aed/OceanDNA-a1909.fa]
[2023-03-16 20:47:19,085] [INFO] Query marker FASTA was written to OceanDNA-a1909/markers.fasta
[2023-03-16 20:47:19,086] [INFO] Task started: Blastn
[2023-03-16 20:47:19,086] [INFO] Running command: blastn -query OceanDNA-a1909/markers.fasta -db /var/lib/cwl/stg712e2de5-f52d-40ee-a602-b4008ce1d0b8/dqc_reference/reference_markers.fasta -out OceanDNA-a1909/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:19,513] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:19,514] [INFO] Selected 6 target genomes.
[2023-03-16 20:47:19,514] [INFO] Target genome list was writen to OceanDNA-a1909/target_genomes.txt
[2023-03-16 20:47:19,518] [INFO] Task started: fastANI
[2023-03-16 20:47:19,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e9e0e9c-3f44-44b7-b363-1c56e4e99aed/OceanDNA-a1909.fa --refList OceanDNA-a1909/target_genomes.txt --output OceanDNA-a1909/fastani_result.tsv --threads 1
[2023-03-16 20:47:23,210] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:23,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg712e2de5-f52d-40ee-a602-b4008ce1d0b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:47:23,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg712e2de5-f52d-40ee-a602-b4008ce1d0b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:47:23,211] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:47:23,211] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:47:23,211] [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
--------------------------------------------------------------------------------
[2023-03-16 20:47:23,211] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1909/tc_result.tsv
[2023-03-16 20:47:23,211] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:47:23,211] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:47:23,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg712e2de5-f52d-40ee-a602-b4008ce1d0b8/dqc_reference/checkm_data
[2023-03-16 20:47:23,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:47:23,217] [INFO] Task started: CheckM
[2023-03-16 20:47:23,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1909/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1909/checkm_input OceanDNA-a1909/checkm_result
[2023-03-16 20:47:46,605] [INFO] Task succeeded: CheckM
[2023-03-16 20:47:46,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:47:46,607] [INFO] ===== Completeness check finished =====
[2023-03-16 20:47:46,607] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:47:46,607] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1909/markers.fasta)
[2023-03-16 20:47:46,608] [INFO] Task started: Blastn
[2023-03-16 20:47:46,608] [INFO] Running command: blastn -query OceanDNA-a1909/markers.fasta -db /var/lib/cwl/stg712e2de5-f52d-40ee-a602-b4008ce1d0b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1909/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:47:47,000] [INFO] Task succeeded: Blastn
[2023-03-16 20:47:47,001] [INFO] Selected 8 target genomes.
[2023-03-16 20:47:47,001] [INFO] Target genome list was writen to OceanDNA-a1909/target_genomes_gtdb.txt
[2023-03-16 20:47:47,020] [INFO] Task started: fastANI
[2023-03-16 20:47:47,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e9e0e9c-3f44-44b7-b363-1c56e4e99aed/OceanDNA-a1909.fa --refList OceanDNA-a1909/target_genomes_gtdb.txt --output OceanDNA-a1909/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:47:49,337] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:49,342] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:47:49,342] [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_009936765.1	s__MGIIa-K1 sp009936765	85.1783	314	405	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.29	98.25	0.77	0.75	3	-
GCA_003602535.1	s__MGIIa-K1 sp003602535	79.1824	207	405	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_902605365.1	s__MGIIa-K1 sp902605365	78.2901	134	405	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	77.2447	115	405	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	76.8138	117	405	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_002694245.1	s__MGIIa-K1 sp002694245	76.6523	86	405	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:47:49,342] [INFO] GTDB search result was written to OceanDNA-a1909/result_gtdb.tsv
[2023-03-16 20:47:49,342] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:47:49,343] [INFO] DFAST_QC result json was written to OceanDNA-a1909/dqc_result.json
[2023-03-16 20:47:49,343] [INFO] DFAST_QC completed!
[2023-03-16 20:47:49,343] [INFO] Total running time: 0h0m39s