[2023-03-15 21:24:36,534] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,534] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,534] [INFO] DQC Reference Directory: /var/lib/cwl/stge82f7d6a-ef0c-443a-9d6f-446843d687df/dqc_reference
[2023-03-15 21:24:37,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,658] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,658] [INFO] Running command: cat /var/lib/cwl/stg34f8f304-31c3-4cc0-9c75-17c3ff6b6cbd/OceanDNA-a2204.fa | prodigal -d OceanDNA-a2204/cds.fna -a OceanDNA-a2204/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:44,364] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:44,364] [INFO] Task started: HMMsearch
[2023-03-15 21:24:44,364] [INFO] Running command: hmmsearch --tblout OceanDNA-a2204/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge82f7d6a-ef0c-443a-9d6f-446843d687df/dqc_reference/reference_markers.hmm OceanDNA-a2204/protein.faa > /dev/null
[2023-03-15 21:24:44,523] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:44,523] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg34f8f304-31c3-4cc0-9c75-17c3ff6b6cbd/OceanDNA-a2204.fa]
[2023-03-15 21:24:44,535] [INFO] Query marker FASTA was written to OceanDNA-a2204/markers.fasta
[2023-03-15 21:24:44,536] [INFO] Task started: Blastn
[2023-03-15 21:24:44,536] [INFO] Running command: blastn -query OceanDNA-a2204/markers.fasta -db /var/lib/cwl/stge82f7d6a-ef0c-443a-9d6f-446843d687df/dqc_reference/reference_markers.fasta -out OceanDNA-a2204/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:44,953] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:44,954] [INFO] Selected 5 target genomes.
[2023-03-15 21:24:44,954] [INFO] Target genome list was writen to OceanDNA-a2204/target_genomes.txt
[2023-03-15 21:24:44,960] [INFO] Task started: fastANI
[2023-03-15 21:24:44,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg34f8f304-31c3-4cc0-9c75-17c3ff6b6cbd/OceanDNA-a2204.fa --refList OceanDNA-a2204/target_genomes.txt --output OceanDNA-a2204/fastani_result.tsv --threads 1
[2023-03-15 21:24:46,833] [INFO] Task succeeded: fastANI
[2023-03-15 21:24:46,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge82f7d6a-ef0c-443a-9d6f-446843d687df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:24:46,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge82f7d6a-ef0c-443a-9d6f-446843d687df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:24:46,834] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:24:46,834] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:24:46,834] [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 21:24:46,834] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2204/tc_result.tsv
[2023-03-15 21:24:46,834] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:24:46,834] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:24:46,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge82f7d6a-ef0c-443a-9d6f-446843d687df/dqc_reference/checkm_data
[2023-03-15 21:24:46,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:24:46,840] [INFO] Task started: CheckM
[2023-03-15 21:24:46,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2204/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2204/checkm_input OceanDNA-a2204/checkm_result
[2023-03-15 21:25:09,216] [INFO] Task succeeded: CheckM
[2023-03-15 21:25:09,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:25:09,218] [INFO] ===== Completeness check finished =====
[2023-03-15 21:25:09,218] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:25:09,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2204/markers.fasta)
[2023-03-15 21:25:09,220] [INFO] Task started: Blastn
[2023-03-15 21:25:09,220] [INFO] Running command: blastn -query OceanDNA-a2204/markers.fasta -db /var/lib/cwl/stge82f7d6a-ef0c-443a-9d6f-446843d687df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2204/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:09,627] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:09,628] [INFO] Selected 9 target genomes.
[2023-03-15 21:25:09,628] [INFO] Target genome list was writen to OceanDNA-a2204/target_genomes_gtdb.txt
[2023-03-15 21:25:09,670] [INFO] Task started: fastANI
[2023-03-15 21:25:09,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg34f8f304-31c3-4cc0-9c75-17c3ff6b6cbd/OceanDNA-a2204.fa --refList OceanDNA-a2204/target_genomes_gtdb.txt --output OceanDNA-a2204/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:25:12,074] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:12,078] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:25:12,078] [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	96.9287	358	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013329295.1	s__MGIIa-L1 sp9596u	78.4417	151	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
GCA_013329925.1	s__MGIIa-L1 sp8734u	77.5217	88	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_003602575.1	s__MGIIa-L1 sp003602575	76.427	66	384	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_018667575.1	s__MGIIa-L1 sp018667575	76.3616	56	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.28	99.11	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-15 21:25:12,078] [INFO] GTDB search result was written to OceanDNA-a2204/result_gtdb.tsv
[2023-03-15 21:25:12,079] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:25:12,079] [INFO] DFAST_QC result json was written to OceanDNA-a2204/dqc_result.json
[2023-03-15 21:25:12,079] [INFO] DFAST_QC completed!
[2023-03-15 21:25:12,079] [INFO] Total running time: 0h0m36s