[2023-03-17 11:08:00,482] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,482] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgd49629fc-0f9e-44e9-8e7b-4f62a6a07ee2/dqc_reference
[2023-03-17 11:08:01,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,568] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,568] [INFO] Running command: cat /var/lib/cwl/stge221a20e-04f9-42a7-b90c-3d26c2c2ecb1/OceanDNA-a2024.fa | prodigal -d OceanDNA-a2024/cds.fna -a OceanDNA-a2024/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:09,483] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:09,484] [INFO] Task started: HMMsearch
[2023-03-17 11:08:09,484] [INFO] Running command: hmmsearch --tblout OceanDNA-a2024/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd49629fc-0f9e-44e9-8e7b-4f62a6a07ee2/dqc_reference/reference_markers.hmm OceanDNA-a2024/protein.faa > /dev/null
[2023-03-17 11:08:09,644] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:09,645] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge221a20e-04f9-42a7-b90c-3d26c2c2ecb1/OceanDNA-a2024.fa]
[2023-03-17 11:08:09,656] [INFO] Query marker FASTA was written to OceanDNA-a2024/markers.fasta
[2023-03-17 11:08:09,657] [INFO] Task started: Blastn
[2023-03-17 11:08:09,657] [INFO] Running command: blastn -query OceanDNA-a2024/markers.fasta -db /var/lib/cwl/stgd49629fc-0f9e-44e9-8e7b-4f62a6a07ee2/dqc_reference/reference_markers.fasta -out OceanDNA-a2024/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:10,081] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:10,082] [INFO] Selected 5 target genomes.
[2023-03-17 11:08:10,082] [INFO] Target genome list was writen to OceanDNA-a2024/target_genomes.txt
[2023-03-17 11:08:10,085] [INFO] Task started: fastANI
[2023-03-17 11:08:10,086] [INFO] Running command: fastANI --query /var/lib/cwl/stge221a20e-04f9-42a7-b90c-3d26c2c2ecb1/OceanDNA-a2024.fa --refList OceanDNA-a2024/target_genomes.txt --output OceanDNA-a2024/fastani_result.tsv --threads 1
[2023-03-17 11:08:12,216] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:12,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd49629fc-0f9e-44e9-8e7b-4f62a6a07ee2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:12,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd49629fc-0f9e-44e9-8e7b-4f62a6a07ee2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:12,216] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:12,216] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:12,216] [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
--------------------------------------------------------------------------------
[2023-03-17 11:08:12,217] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2024/tc_result.tsv
[2023-03-17 11:08:12,217] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:12,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:12,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd49629fc-0f9e-44e9-8e7b-4f62a6a07ee2/dqc_reference/checkm_data
[2023-03-17 11:08:12,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:12,268] [INFO] Task started: CheckM
[2023-03-17 11:08:12,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2024/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2024/checkm_input OceanDNA-a2024/checkm_result
[2023-03-17 11:08:37,657] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:37,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.88%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:37,660] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:37,660] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:37,660] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2024/markers.fasta)
[2023-03-17 11:08:37,661] [INFO] Task started: Blastn
[2023-03-17 11:08:37,662] [INFO] Running command: blastn -query OceanDNA-a2024/markers.fasta -db /var/lib/cwl/stgd49629fc-0f9e-44e9-8e7b-4f62a6a07ee2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2024/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:38,106] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:38,107] [INFO] Selected 10 target genomes.
[2023-03-17 11:08:38,107] [INFO] Target genome list was writen to OceanDNA-a2024/target_genomes_gtdb.txt
[2023-03-17 11:08:38,163] [INFO] Task started: fastANI
[2023-03-17 11:08:38,163] [INFO] Running command: fastANI --query /var/lib/cwl/stge221a20e-04f9-42a7-b90c-3d26c2c2ecb1/OceanDNA-a2024.fa --refList OceanDNA-a2024/target_genomes_gtdb.txt --output OceanDNA-a2024/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:08:41,442] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:41,447] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:08:41,448] [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_002710205.1	s__MGIIa-K1 sp002710205	99.4783	377	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002709705.1	s__MGIIa-K1 sp002709705	84.0657	336	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	83.0825	329	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	82.956	349	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_002715725.1	s__MGIIa-K1 sp002715725	81.4368	317	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.59	99.59	0.80	0.80	2	-
GCA_002689565.1	s__MGIIa-K1 sp002689565	78.4939	123	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602535.1	s__MGIIa-K1 sp003602535	77.8996	143	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689345.1	s__MGIIa-K1 sp002689345	77.5381	162	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710015.1	s__MGIIa-K1 sp002710015	76.9401	68	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.68	99.68	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:08:41,448] [INFO] GTDB search result was written to OceanDNA-a2024/result_gtdb.tsv
[2023-03-17 11:08:41,448] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:08:41,449] [INFO] DFAST_QC result json was written to OceanDNA-a2024/dqc_result.json
[2023-03-17 11:08:41,449] [INFO] DFAST_QC completed!
[2023-03-17 11:08:41,449] [INFO] Total running time: 0h0m41s