[2023-03-15 10:52:57,299] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,299] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg9443a3bf-a75c-41e0-aad7-afa595be9027/dqc_reference
[2023-03-15 10:52:58,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,863] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,863] [INFO] Running command: cat /var/lib/cwl/stg098b823c-ae72-470a-9828-371c936357ff/OceanDNA-a4074.fa | prodigal -d OceanDNA-a4074/cds.fna -a OceanDNA-a4074/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:06,314] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:06,314] [INFO] Task started: HMMsearch
[2023-03-15 10:53:06,314] [INFO] Running command: hmmsearch --tblout OceanDNA-a4074/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9443a3bf-a75c-41e0-aad7-afa595be9027/dqc_reference/reference_markers.hmm OceanDNA-a4074/protein.faa > /dev/null
[2023-03-15 10:53:06,473] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:06,474] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg098b823c-ae72-470a-9828-371c936357ff/OceanDNA-a4074.fa]
[2023-03-15 10:53:06,484] [INFO] Query marker FASTA was written to OceanDNA-a4074/markers.fasta
[2023-03-15 10:53:06,484] [INFO] Task started: Blastn
[2023-03-15 10:53:06,485] [INFO] Running command: blastn -query OceanDNA-a4074/markers.fasta -db /var/lib/cwl/stg9443a3bf-a75c-41e0-aad7-afa595be9027/dqc_reference/reference_markers.fasta -out OceanDNA-a4074/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:06,932] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:06,933] [INFO] Selected 5 target genomes.
[2023-03-15 10:53:06,933] [INFO] Target genome list was writen to OceanDNA-a4074/target_genomes.txt
[2023-03-15 10:53:06,938] [INFO] Task started: fastANI
[2023-03-15 10:53:06,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg098b823c-ae72-470a-9828-371c936357ff/OceanDNA-a4074.fa --refList OceanDNA-a4074/target_genomes.txt --output OceanDNA-a4074/fastani_result.tsv --threads 1
[2023-03-15 10:53:08,580] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:08,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9443a3bf-a75c-41e0-aad7-afa595be9027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:08,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9443a3bf-a75c-41e0-aad7-afa595be9027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:08,581] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:08,581] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:53:08,581] [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 10:53:08,581] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4074/tc_result.tsv
[2023-03-15 10:53:08,581] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:08,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:08,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9443a3bf-a75c-41e0-aad7-afa595be9027/dqc_reference/checkm_data
[2023-03-15 10:53:08,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:09,050] [INFO] Task started: CheckM
[2023-03-15 10:53:09,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4074/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4074/checkm_input OceanDNA-a4074/checkm_result
[2023-03-15 10:53:32,876] [INFO] Task succeeded: CheckM
[2023-03-15 10:53:32,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:53:32,878] [INFO] ===== Completeness check finished =====
[2023-03-15 10:53:32,878] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:53:32,878] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4074/markers.fasta)
[2023-03-15 10:53:32,879] [INFO] Task started: Blastn
[2023-03-15 10:53:32,879] [INFO] Running command: blastn -query OceanDNA-a4074/markers.fasta -db /var/lib/cwl/stg9443a3bf-a75c-41e0-aad7-afa595be9027/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4074/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:33,286] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:33,287] [INFO] Selected 10 target genomes.
[2023-03-15 10:53:33,287] [INFO] Target genome list was writen to OceanDNA-a4074/target_genomes_gtdb.txt
[2023-03-15 10:53:33,317] [INFO] Task started: fastANI
[2023-03-15 10:53:33,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg098b823c-ae72-470a-9828-371c936357ff/OceanDNA-a4074.fa --refList OceanDNA-a4074/target_genomes_gtdb.txt --output OceanDNA-a4074/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:53:36,358] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:36,362] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:53:36,363] [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_905182515.1	s__MGIIb-O3 sp905182515	99.9018	371	465	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002503285.1	s__MGIIb-O3 sp002503285	78.9583	263	465	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.00	95.68	0.94	0.92	11	-
GCA_002712575.1	s__MGIIb-O3 sp002712575	77.2139	115	465	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457145.1	s__MGIIb-O3 sp002457145	77.1123	128	465	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.76	99.72	0.89	0.85	3	-
GCA_002172375.1	s__MGIIb-O3 sp002172375	76.8061	106	465	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777225.1	s__MGIIb-O2 sp016777225	76.7596	57	465	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:53:36,363] [INFO] GTDB search result was written to OceanDNA-a4074/result_gtdb.tsv
[2023-03-15 10:53:36,363] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:53:36,364] [INFO] DFAST_QC result json was written to OceanDNA-a4074/dqc_result.json
[2023-03-15 10:53:36,364] [INFO] DFAST_QC completed!
[2023-03-15 10:53:36,364] [INFO] Total running time: 0h0m39s