[2023-03-15 07:52:40,241] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,241] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg52a4fc15-5fc9-4f53-8c9f-4b7d3383acd2/dqc_reference
[2023-03-15 07:52:41,493] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,494] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,494] [INFO] Running command: cat /var/lib/cwl/stg4556fc46-6a71-44bf-af5d-a117a9642db2/OceanDNA-a2181.fa | prodigal -d OceanDNA-a2181/cds.fna -a OceanDNA-a2181/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:47,123] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:47,123] [INFO] Task started: HMMsearch
[2023-03-15 07:52:47,123] [INFO] Running command: hmmsearch --tblout OceanDNA-a2181/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52a4fc15-5fc9-4f53-8c9f-4b7d3383acd2/dqc_reference/reference_markers.hmm OceanDNA-a2181/protein.faa > /dev/null
[2023-03-15 07:52:47,371] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:47,372] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4556fc46-6a71-44bf-af5d-a117a9642db2/OceanDNA-a2181.fa]
[2023-03-15 07:52:47,386] [INFO] Query marker FASTA was written to OceanDNA-a2181/markers.fasta
[2023-03-15 07:52:47,386] [INFO] Task started: Blastn
[2023-03-15 07:52:47,386] [INFO] Running command: blastn -query OceanDNA-a2181/markers.fasta -db /var/lib/cwl/stg52a4fc15-5fc9-4f53-8c9f-4b7d3383acd2/dqc_reference/reference_markers.fasta -out OceanDNA-a2181/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:47,824] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:47,824] [INFO] Selected 5 target genomes.
[2023-03-15 07:52:47,825] [INFO] Target genome list was writen to OceanDNA-a2181/target_genomes.txt
[2023-03-15 07:52:47,828] [INFO] Task started: fastANI
[2023-03-15 07:52:47,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg4556fc46-6a71-44bf-af5d-a117a9642db2/OceanDNA-a2181.fa --refList OceanDNA-a2181/target_genomes.txt --output OceanDNA-a2181/fastani_result.tsv --threads 1
[2023-03-15 07:52:50,784] [INFO] Task succeeded: fastANI
[2023-03-15 07:52:50,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52a4fc15-5fc9-4f53-8c9f-4b7d3383acd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:52:50,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52a4fc15-5fc9-4f53-8c9f-4b7d3383acd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:52:50,784] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:52:50,785] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:52:50,785] [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 07:52:50,785] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2181/tc_result.tsv
[2023-03-15 07:52:50,785] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:52:50,785] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:52:50,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52a4fc15-5fc9-4f53-8c9f-4b7d3383acd2/dqc_reference/checkm_data
[2023-03-15 07:52:50,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:52:50,791] [INFO] Task started: CheckM
[2023-03-15 07:52:50,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2181/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2181/checkm_input OceanDNA-a2181/checkm_result
[2023-03-15 07:53:11,232] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:11,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.63%
Contamintation: 5.09%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:11,235] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:11,235] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:11,235] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2181/markers.fasta)
[2023-03-15 07:53:11,235] [INFO] Task started: Blastn
[2023-03-15 07:53:11,235] [INFO] Running command: blastn -query OceanDNA-a2181/markers.fasta -db /var/lib/cwl/stg52a4fc15-5fc9-4f53-8c9f-4b7d3383acd2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2181/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:11,672] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:11,673] [INFO] Selected 10 target genomes.
[2023-03-15 07:53:11,673] [INFO] Target genome list was writen to OceanDNA-a2181/target_genomes_gtdb.txt
[2023-03-15 07:53:11,686] [INFO] Task started: fastANI
[2023-03-15 07:53:11,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg4556fc46-6a71-44bf-af5d-a117a9642db2/OceanDNA-a2181.fa --refList OceanDNA-a2181/target_genomes_gtdb.txt --output OceanDNA-a2181/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:14,520] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:14,523] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:53:14,524] [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_011526375.1	s__MGIIa-L1 sp011526375	81.2904	237	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009887195.1	s__MGIIa-L1 sp009887195	77.2276	66	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.91	98.88	0.90	0.86	3	-
GCA_013329355.1	s__MGIIa-L1 sp9354u	77.1735	58	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.57	99.13	0.80	0.62	3	-
GCA_002702945.1	s__MGIIa-L1 sp002702945	76.442	66	319	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.55	98.53	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:14,524] [INFO] GTDB search result was written to OceanDNA-a2181/result_gtdb.tsv
[2023-03-15 07:53:14,524] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:14,525] [INFO] DFAST_QC result json was written to OceanDNA-a2181/dqc_result.json
[2023-03-15 07:53:14,525] [INFO] DFAST_QC completed!
[2023-03-15 07:53:14,525] [INFO] Total running time: 0h0m34s