[2023-03-15 13:54:06,232] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:54:06,232] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:54:06,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgec9bda0d-34b7-4794-b6c3-e57763ac7b37/dqc_reference
[2023-03-15 13:54:07,341] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:54:07,342] [INFO] Task started: Prodigal
[2023-03-15 13:54:07,342] [INFO] Running command: cat /var/lib/cwl/stge920bae2-7518-4c23-9e98-45b79a5ef5e5/OceanDNA-a2747.fa | prodigal -d OceanDNA-a2747/cds.fna -a OceanDNA-a2747/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:54:16,692] [INFO] Task succeeded: Prodigal
[2023-03-15 13:54:16,693] [INFO] Task started: HMMsearch
[2023-03-15 13:54:16,693] [INFO] Running command: hmmsearch --tblout OceanDNA-a2747/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec9bda0d-34b7-4794-b6c3-e57763ac7b37/dqc_reference/reference_markers.hmm OceanDNA-a2747/protein.faa > /dev/null
[2023-03-15 13:54:16,858] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:54:16,859] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge920bae2-7518-4c23-9e98-45b79a5ef5e5/OceanDNA-a2747.fa]
[2023-03-15 13:54:16,891] [INFO] Query marker FASTA was written to OceanDNA-a2747/markers.fasta
[2023-03-15 13:54:16,892] [INFO] Task started: Blastn
[2023-03-15 13:54:16,892] [INFO] Running command: blastn -query OceanDNA-a2747/markers.fasta -db /var/lib/cwl/stgec9bda0d-34b7-4794-b6c3-e57763ac7b37/dqc_reference/reference_markers.fasta -out OceanDNA-a2747/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:17,330] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:17,335] [INFO] Selected 5 target genomes.
[2023-03-15 13:54:17,335] [INFO] Target genome list was writen to OceanDNA-a2747/target_genomes.txt
[2023-03-15 13:54:17,338] [INFO] Task started: fastANI
[2023-03-15 13:54:17,338] [INFO] Running command: fastANI --query /var/lib/cwl/stge920bae2-7518-4c23-9e98-45b79a5ef5e5/OceanDNA-a2747.fa --refList OceanDNA-a2747/target_genomes.txt --output OceanDNA-a2747/fastani_result.tsv --threads 1
[2023-03-15 13:54:18,430] [INFO] Task succeeded: fastANI
[2023-03-15 13:54:18,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec9bda0d-34b7-4794-b6c3-e57763ac7b37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:54:18,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec9bda0d-34b7-4794-b6c3-e57763ac7b37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:54:18,431] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:54:18,431] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:54:18,431] [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 13:54:18,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2747/tc_result.tsv
[2023-03-15 13:54:18,435] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:54:18,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:54:18,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec9bda0d-34b7-4794-b6c3-e57763ac7b37/dqc_reference/checkm_data
[2023-03-15 13:54:18,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:54:18,444] [INFO] Task started: CheckM
[2023-03-15 13:54:18,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2747/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2747/checkm_input OceanDNA-a2747/checkm_result
[2023-03-15 13:54:47,613] [INFO] Task succeeded: CheckM
[2023-03-15 13:54:47,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:54:47,653] [INFO] ===== Completeness check finished =====
[2023-03-15 13:54:47,654] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:54:47,654] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2747/markers.fasta)
[2023-03-15 13:54:47,655] [INFO] Task started: Blastn
[2023-03-15 13:54:47,655] [INFO] Running command: blastn -query OceanDNA-a2747/markers.fasta -db /var/lib/cwl/stgec9bda0d-34b7-4794-b6c3-e57763ac7b37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2747/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:48,081] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:48,085] [INFO] Selected 6 target genomes.
[2023-03-15 13:54:48,085] [INFO] Target genome list was writen to OceanDNA-a2747/target_genomes_gtdb.txt
[2023-03-15 13:54:48,089] [INFO] Task started: fastANI
[2023-03-15 13:54:48,089] [INFO] Running command: fastANI --query /var/lib/cwl/stge920bae2-7518-4c23-9e98-45b79a5ef5e5/OceanDNA-a2747.fa --refList OceanDNA-a2747/target_genomes_gtdb.txt --output OceanDNA-a2747/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:54:50,370] [INFO] Task succeeded: fastANI
[2023-03-15 13:54:50,374] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:54:50,375] [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_018666575.1	s__MGIIa-L2 sp018666575	97.8324	411	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	conclusive
GCA_018645535.1	s__MGIIa-L2 sp018645535	84.1552	293	504	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_016777125.1	s__MGIIa-L2 sp016777125	83.2585	426	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.94	99.94	0.96	0.96	2	-
GCA_009887135.1	s__MGIIa-L2 sp009887135	83.0145	370	504	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.87	98.45	0.83	0.81	3	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	82.4162	364	504	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	81.8951	308	504	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 13:54:50,378] [INFO] GTDB search result was written to OceanDNA-a2747/result_gtdb.tsv
[2023-03-15 13:54:50,379] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:54:50,380] [INFO] DFAST_QC result json was written to OceanDNA-a2747/dqc_result.json
[2023-03-15 13:54:50,380] [INFO] DFAST_QC completed!
[2023-03-15 13:54:50,380] [INFO] Total running time: 0h0m44s