[2023-03-15 16:15:00,882] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:15:00,883] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:15:00,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e8de3ca-1ccb-4e30-b481-4326de7cd062/dqc_reference
[2023-03-15 16:15:01,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:15:01,976] [INFO] Task started: Prodigal
[2023-03-15 16:15:01,976] [INFO] Running command: cat /var/lib/cwl/stgbafd5205-b693-4a38-a454-a0081809789b/OceanDNA-a2740.fa | prodigal -d OceanDNA-a2740/cds.fna -a OceanDNA-a2740/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:09,530] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:09,530] [INFO] Task started: HMMsearch
[2023-03-15 16:15:09,530] [INFO] Running command: hmmsearch --tblout OceanDNA-a2740/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e8de3ca-1ccb-4e30-b481-4326de7cd062/dqc_reference/reference_markers.hmm OceanDNA-a2740/protein.faa > /dev/null
[2023-03-15 16:15:09,666] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:09,666] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbafd5205-b693-4a38-a454-a0081809789b/OceanDNA-a2740.fa]
[2023-03-15 16:15:09,679] [INFO] Query marker FASTA was written to OceanDNA-a2740/markers.fasta
[2023-03-15 16:15:09,679] [INFO] Task started: Blastn
[2023-03-15 16:15:09,679] [INFO] Running command: blastn -query OceanDNA-a2740/markers.fasta -db /var/lib/cwl/stg8e8de3ca-1ccb-4e30-b481-4326de7cd062/dqc_reference/reference_markers.fasta -out OceanDNA-a2740/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:10,147] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:10,147] [INFO] Selected 5 target genomes.
[2023-03-15 16:15:10,147] [INFO] Target genome list was writen to OceanDNA-a2740/target_genomes.txt
[2023-03-15 16:15:10,151] [INFO] Task started: fastANI
[2023-03-15 16:15:10,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafd5205-b693-4a38-a454-a0081809789b/OceanDNA-a2740.fa --refList OceanDNA-a2740/target_genomes.txt --output OceanDNA-a2740/fastani_result.tsv --threads 1
[2023-03-15 16:15:13,977] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:13,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e8de3ca-1ccb-4e30-b481-4326de7cd062/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:13,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e8de3ca-1ccb-4e30-b481-4326de7cd062/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:13,977] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:15:13,977] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:15:13,977] [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 16:15:13,978] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2740/tc_result.tsv
[2023-03-15 16:15:13,978] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:13,978] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:13,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e8de3ca-1ccb-4e30-b481-4326de7cd062/dqc_reference/checkm_data
[2023-03-15 16:15:13,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:13,991] [INFO] Task started: CheckM
[2023-03-15 16:15:13,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2740/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2740/checkm_input OceanDNA-a2740/checkm_result
[2023-03-15 16:15:39,326] [INFO] Task succeeded: CheckM
[2023-03-15 16:15:39,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.47%
Contamintation: 3.16%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 16:15:39,328] [INFO] ===== Completeness check finished =====
[2023-03-15 16:15:39,328] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:15:39,328] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2740/markers.fasta)
[2023-03-15 16:15:39,329] [INFO] Task started: Blastn
[2023-03-15 16:15:39,330] [INFO] Running command: blastn -query OceanDNA-a2740/markers.fasta -db /var/lib/cwl/stg8e8de3ca-1ccb-4e30-b481-4326de7cd062/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2740/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:39,940] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:39,941] [INFO] Selected 11 target genomes.
[2023-03-15 16:15:39,941] [INFO] Target genome list was writen to OceanDNA-a2740/target_genomes_gtdb.txt
[2023-03-15 16:15:40,025] [INFO] Task started: fastANI
[2023-03-15 16:15:40,025] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafd5205-b693-4a38-a454-a0081809789b/OceanDNA-a2740.fa --refList OceanDNA-a2740/target_genomes_gtdb.txt --output OceanDNA-a2740/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:15:43,081] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:43,088] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:15:43,088] [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_012270265.1	s__MGIIa-L2 sp012270265	81.2222	171	331	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_018623995.1	s__MGIIa-L2 sp018623995	80.6838	184	331	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	80.1412	147	331	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_002692685.1	s__MGIIa-L2 sp002692685	79.7989	116	331	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	79.3911	153	331	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_002499195.1	s__MGIIa-L2 sp002499195	79.1945	211	331	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.80	99.66	0.93	0.91	5	-
GCA_013911465.1	s__MGIIa-L2 sp013911465	78.9441	148	331	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_002722615.1	s__MGIIa-L2 sp002722615	78.7896	162	331	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_018666575.1	s__MGIIa-L2 sp018666575	77.7051	67	331	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	76.9277	74	331	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_002171315.2	s__MGIIa-L2 sp002171315	76.9046	66	331	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:15:43,090] [INFO] GTDB search result was written to OceanDNA-a2740/result_gtdb.tsv
[2023-03-15 16:15:43,091] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:15:43,093] [INFO] DFAST_QC result json was written to OceanDNA-a2740/dqc_result.json
[2023-03-15 16:15:43,094] [INFO] DFAST_QC completed!
[2023-03-15 16:15:43,094] [INFO] Total running time: 0h0m42s