[2023-03-18 20:13:32,220] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,220] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fa41195-1bc4-44bb-8b07-2658d3e89d71/dqc_reference
[2023-03-18 20:13:33,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,430] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,430] [INFO] Running command: cat /var/lib/cwl/stg1a48817f-5af0-4eb9-9bc0-09f337b73e6d/OceanDNA-a2857.fa | prodigal -d OceanDNA-a2857/cds.fna -a OceanDNA-a2857/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:44,682] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:44,683] [INFO] Task started: HMMsearch
[2023-03-18 20:13:44,683] [INFO] Running command: hmmsearch --tblout OceanDNA-a2857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fa41195-1bc4-44bb-8b07-2658d3e89d71/dqc_reference/reference_markers.hmm OceanDNA-a2857/protein.faa > /dev/null
[2023-03-18 20:13:44,850] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:44,851] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1a48817f-5af0-4eb9-9bc0-09f337b73e6d/OceanDNA-a2857.fa]
[2023-03-18 20:13:44,863] [INFO] Query marker FASTA was written to OceanDNA-a2857/markers.fasta
[2023-03-18 20:13:44,863] [INFO] Task started: Blastn
[2023-03-18 20:13:44,864] [INFO] Running command: blastn -query OceanDNA-a2857/markers.fasta -db /var/lib/cwl/stg5fa41195-1bc4-44bb-8b07-2658d3e89d71/dqc_reference/reference_markers.fasta -out OceanDNA-a2857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:45,300] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:45,300] [INFO] Selected 5 target genomes.
[2023-03-18 20:13:45,301] [INFO] Target genome list was writen to OceanDNA-a2857/target_genomes.txt
[2023-03-18 20:13:45,304] [INFO] Task started: fastANI
[2023-03-18 20:13:45,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a48817f-5af0-4eb9-9bc0-09f337b73e6d/OceanDNA-a2857.fa --refList OceanDNA-a2857/target_genomes.txt --output OceanDNA-a2857/fastani_result.tsv --threads 1
[2023-03-18 20:13:49,117] [INFO] Task succeeded: fastANI
[2023-03-18 20:13:49,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fa41195-1bc4-44bb-8b07-2658d3e89d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:13:49,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fa41195-1bc4-44bb-8b07-2658d3e89d71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:13:49,118] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:13:49,118] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:13:49,118] [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
--------------------------------------------------------------------------------
[2023-03-18 20:13:49,118] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2857/tc_result.tsv
[2023-03-18 20:13:49,118] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:13:49,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:13:49,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fa41195-1bc4-44bb-8b07-2658d3e89d71/dqc_reference/checkm_data
[2023-03-18 20:13:49,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:13:49,124] [INFO] Task started: CheckM
[2023-03-18 20:13:49,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2857/checkm_input OceanDNA-a2857/checkm_result
[2023-03-18 20:14:22,650] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:22,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:22,652] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:22,652] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:22,653] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2857/markers.fasta)
[2023-03-18 20:14:22,653] [INFO] Task started: Blastn
[2023-03-18 20:14:22,653] [INFO] Running command: blastn -query OceanDNA-a2857/markers.fasta -db /var/lib/cwl/stg5fa41195-1bc4-44bb-8b07-2658d3e89d71/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:23,171] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:23,172] [INFO] Selected 8 target genomes.
[2023-03-18 20:14:23,172] [INFO] Target genome list was writen to OceanDNA-a2857/target_genomes_gtdb.txt
[2023-03-18 20:14:23,440] [INFO] Task started: fastANI
[2023-03-18 20:14:23,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a48817f-5af0-4eb9-9bc0-09f337b73e6d/OceanDNA-a2857.fa --refList OceanDNA-a2857/target_genomes_gtdb.txt --output OceanDNA-a2857/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:14:26,159] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:26,165] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:14:26,165] [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_002722615.1	s__MGIIa-L2 sp002722615	96.1005	490	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	conclusive
GCA_013911465.1	s__MGIIa-L2 sp013911465	91.834	362	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270265.1	s__MGIIa-L2 sp012270265	79.4291	207	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013330015.1	s__MGIIa-L2 sp8574u	79.2918	170	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_018623995.1	s__MGIIa-L2 sp018623995	79.1659	212	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719815.1	s__MGIIa-L2 sp002719815	78.8222	235	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698145.1	s__MGIIa-L2 sp002698145	78.7469	262	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.10	97.13	0.94	0.83	7	-
GCA_016777125.1	s__MGIIa-L2 sp016777125	77.7378	157	581	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.94	99.94	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:14:26,165] [INFO] GTDB search result was written to OceanDNA-a2857/result_gtdb.tsv
[2023-03-18 20:14:26,166] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:14:26,166] [INFO] DFAST_QC result json was written to OceanDNA-a2857/dqc_result.json
[2023-03-18 20:14:26,166] [INFO] DFAST_QC completed!
[2023-03-18 20:14:26,167] [INFO] Total running time: 0h0m54s