[2023-03-18 07:06:19,985] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:19,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:19,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ac32929-9709-43ef-99bd-af09bc6a0a95/dqc_reference
[2023-03-18 07:06:21,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:21,101] [INFO] Task started: Prodigal
[2023-03-18 07:06:21,101] [INFO] Running command: cat /var/lib/cwl/stga4670db1-6dc5-470e-912b-be14c1eeaf94/OceanDNA-a4234.fa | prodigal -d OceanDNA-a4234/cds.fna -a OceanDNA-a4234/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:31,216] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:31,216] [INFO] Task started: HMMsearch
[2023-03-18 07:06:31,216] [INFO] Running command: hmmsearch --tblout OceanDNA-a4234/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ac32929-9709-43ef-99bd-af09bc6a0a95/dqc_reference/reference_markers.hmm OceanDNA-a4234/protein.faa > /dev/null
[2023-03-18 07:06:31,375] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:31,375] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga4670db1-6dc5-470e-912b-be14c1eeaf94/OceanDNA-a4234.fa]
[2023-03-18 07:06:31,385] [INFO] Query marker FASTA was written to OceanDNA-a4234/markers.fasta
[2023-03-18 07:06:31,385] [INFO] Task started: Blastn
[2023-03-18 07:06:31,385] [INFO] Running command: blastn -query OceanDNA-a4234/markers.fasta -db /var/lib/cwl/stg1ac32929-9709-43ef-99bd-af09bc6a0a95/dqc_reference/reference_markers.fasta -out OceanDNA-a4234/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:31,810] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:31,811] [INFO] Selected 3 target genomes.
[2023-03-18 07:06:31,811] [INFO] Target genome list was writen to OceanDNA-a4234/target_genomes.txt
[2023-03-18 07:06:31,813] [INFO] Task started: fastANI
[2023-03-18 07:06:31,813] [INFO] Running command: fastANI --query /var/lib/cwl/stga4670db1-6dc5-470e-912b-be14c1eeaf94/OceanDNA-a4234.fa --refList OceanDNA-a4234/target_genomes.txt --output OceanDNA-a4234/fastani_result.tsv --threads 1
[2023-03-18 07:06:33,309] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:33,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ac32929-9709-43ef-99bd-af09bc6a0a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:33,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ac32929-9709-43ef-99bd-af09bc6a0a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:33,310] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:33,310] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:33,310] [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
--------------------------------------------------------------------------------
[2023-03-18 07:06:33,310] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4234/tc_result.tsv
[2023-03-18 07:06:33,310] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:33,311] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:33,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ac32929-9709-43ef-99bd-af09bc6a0a95/dqc_reference/checkm_data
[2023-03-18 07:06:33,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:33,316] [INFO] Task started: CheckM
[2023-03-18 07:06:33,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4234/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4234/checkm_input OceanDNA-a4234/checkm_result
[2023-03-18 07:07:03,711] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:03,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.32%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:03,714] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:03,714] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:03,714] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4234/markers.fasta)
[2023-03-18 07:07:03,714] [INFO] Task started: Blastn
[2023-03-18 07:07:03,714] [INFO] Running command: blastn -query OceanDNA-a4234/markers.fasta -db /var/lib/cwl/stg1ac32929-9709-43ef-99bd-af09bc6a0a95/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4234/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:04,148] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:04,149] [INFO] Selected 7 target genomes.
[2023-03-18 07:07:04,149] [INFO] Target genome list was writen to OceanDNA-a4234/target_genomes_gtdb.txt
[2023-03-18 07:07:04,239] [INFO] Task started: fastANI
[2023-03-18 07:07:04,239] [INFO] Running command: fastANI --query /var/lib/cwl/stga4670db1-6dc5-470e-912b-be14c1eeaf94/OceanDNA-a4234.fa --refList OceanDNA-a4234/target_genomes_gtdb.txt --output OceanDNA-a4234/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:06,117] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:06,122] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:07:06,122] [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_001628485.1	s__MGIIb-O3 sp001628485	99.2858	350	396	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.15	97.12	0.88	0.79	10	conclusive
GCA_001629235.1	s__MGIIb-O3 sp001629235	93.9323	267	396	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.45	95.03	0.80	0.68	7	-
GCA_902573015.1	s__MGIIb-O3 sp902573015	92.7923	245	396	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625325.1	s__MGIIb-O3 sp902625325	92.6911	317	396	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601345.1	s__MGIIb-O3 sp902601345	92.1929	268	396	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001629255.1	s__MGIIb-O3 sp001629255	91.9824	305	396	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.42	97.36	0.80	0.70	6	-
GCA_902573085.1	s__MGIIb-O3 sp902573085	89.3751	229	396	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:06,122] [INFO] GTDB search result was written to OceanDNA-a4234/result_gtdb.tsv
[2023-03-18 07:07:06,122] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:06,123] [INFO] DFAST_QC result json was written to OceanDNA-a4234/dqc_result.json
[2023-03-18 07:07:06,123] [INFO] DFAST_QC completed!
[2023-03-18 07:07:06,123] [INFO] Total running time: 0h0m46s