[2023-03-14 12:13:42,699] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:13:42,699] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:13:42,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7e0da94-a789-4305-bb86-bd7f9ebd02af/dqc_reference
[2023-03-14 12:13:44,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:13:44,636] [INFO] Task started: Prodigal
[2023-03-14 12:13:44,637] [INFO] Running command: cat /var/lib/cwl/stg4c8ac42a-05db-4e6e-b263-17946c54774b/OceanDNA-a5021.fa | prodigal -d OceanDNA-a5021/cds.fna -a OceanDNA-a5021/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:13:52,161] [INFO] Task succeeded: Prodigal
[2023-03-14 12:13:52,161] [INFO] Task started: HMMsearch
[2023-03-14 12:13:52,161] [INFO] Running command: hmmsearch --tblout OceanDNA-a5021/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7e0da94-a789-4305-bb86-bd7f9ebd02af/dqc_reference/reference_markers.hmm OceanDNA-a5021/protein.faa > /dev/null
[2023-03-14 12:13:52,319] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:13:52,319] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4c8ac42a-05db-4e6e-b263-17946c54774b/OceanDNA-a5021.fa]
[2023-03-14 12:13:52,329] [INFO] Query marker FASTA was written to OceanDNA-a5021/markers.fasta
[2023-03-14 12:13:52,329] [INFO] Task started: Blastn
[2023-03-14 12:13:52,329] [INFO] Running command: blastn -query OceanDNA-a5021/markers.fasta -db /var/lib/cwl/stgb7e0da94-a789-4305-bb86-bd7f9ebd02af/dqc_reference/reference_markers.fasta -out OceanDNA-a5021/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:13:52,750] [INFO] Task succeeded: Blastn
[2023-03-14 12:13:52,751] [INFO] Selected 2 target genomes.
[2023-03-14 12:13:52,751] [INFO] Target genome list was writen to OceanDNA-a5021/target_genomes.txt
[2023-03-14 12:13:52,753] [INFO] Task started: fastANI
[2023-03-14 12:13:52,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8ac42a-05db-4e6e-b263-17946c54774b/OceanDNA-a5021.fa --refList OceanDNA-a5021/target_genomes.txt --output OceanDNA-a5021/fastani_result.tsv --threads 1
[2023-03-14 12:13:53,409] [INFO] Task succeeded: fastANI
[2023-03-14 12:13:53,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7e0da94-a789-4305-bb86-bd7f9ebd02af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:13:53,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7e0da94-a789-4305-bb86-bd7f9ebd02af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:13:53,410] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:13:53,410] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:13:53,410] [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
--------------------------------------------------------------------------------
[2023-03-14 12:13:53,411] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5021/tc_result.tsv
[2023-03-14 12:13:53,411] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:13:53,411] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:13:53,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7e0da94-a789-4305-bb86-bd7f9ebd02af/dqc_reference/checkm_data
[2023-03-14 12:13:53,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:13:53,424] [INFO] Task started: CheckM
[2023-03-14 12:13:53,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5021/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5021/checkm_input OceanDNA-a5021/checkm_result
[2023-03-14 12:14:18,969] [INFO] Task succeeded: CheckM
[2023-03-14 12:14:18,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.98%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:14:18,979] [INFO] ===== Completeness check finished =====
[2023-03-14 12:14:18,979] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:14:18,979] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5021/markers.fasta)
[2023-03-14 12:14:18,979] [INFO] Task started: Blastn
[2023-03-14 12:14:18,980] [INFO] Running command: blastn -query OceanDNA-a5021/markers.fasta -db /var/lib/cwl/stgb7e0da94-a789-4305-bb86-bd7f9ebd02af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5021/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:14:19,392] [INFO] Task succeeded: Blastn
[2023-03-14 12:14:19,395] [INFO] Selected 7 target genomes.
[2023-03-14 12:14:19,395] [INFO] Target genome list was writen to OceanDNA-a5021/target_genomes_gtdb.txt
[2023-03-14 12:14:19,399] [INFO] Task started: fastANI
[2023-03-14 12:14:19,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8ac42a-05db-4e6e-b263-17946c54774b/OceanDNA-a5021.fa --refList OceanDNA-a5021/target_genomes_gtdb.txt --output OceanDNA-a5021/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:14:21,108] [INFO] Task succeeded: fastANI
[2023-03-14 12:14:21,112] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:14:21,112] [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_002501885.1	s__Thalassarchaeum sp002501885	99.2538	353	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.85	97.05	0.83	0.68	9	conclusive
GCA_002503055.1	s__Thalassarchaeum sp002503055	89.5688	350	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.71	99.22	0.93	0.84	5	-
GCA_002727275.1	s__Thalassarchaeum sp002727275	80.259	263	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714745.1	s__Thalassarchaeum sp002714745	79.7433	224	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	97.82	95.69	0.77	0.69	7	-
GCA_002698225.1	s__Thalassarchaeum sp002698225	78.4742	184	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.66	99.66	0.83	0.83	2	-
GCA_002457605.1	s__Thalassarchaeum sp002457605	76.8412	71	426	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:14:21,113] [INFO] GTDB search result was written to OceanDNA-a5021/result_gtdb.tsv
[2023-03-14 12:14:21,113] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:14:21,113] [INFO] DFAST_QC result json was written to OceanDNA-a5021/dqc_result.json
[2023-03-14 12:14:21,113] [INFO] DFAST_QC completed!
[2023-03-14 12:14:21,113] [INFO] Total running time: 0h0m38s