[2023-03-18 01:26:26,349] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,349] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg20245e34-97f7-4bd1-bed1-9b47414129c1/dqc_reference
[2023-03-18 01:26:27,507] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,508] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,508] [INFO] Running command: cat /var/lib/cwl/stgc6913661-de96-4da5-864a-aa5b88b90afd/OceanDNA-a2817.fa | prodigal -d OceanDNA-a2817/cds.fna -a OceanDNA-a2817/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:37,440] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:37,440] [INFO] Task started: HMMsearch
[2023-03-18 01:26:37,440] [INFO] Running command: hmmsearch --tblout OceanDNA-a2817/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20245e34-97f7-4bd1-bed1-9b47414129c1/dqc_reference/reference_markers.hmm OceanDNA-a2817/protein.faa > /dev/null
[2023-03-18 01:26:37,631] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:37,631] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc6913661-de96-4da5-864a-aa5b88b90afd/OceanDNA-a2817.fa]
[2023-03-18 01:26:37,645] [INFO] Query marker FASTA was written to OceanDNA-a2817/markers.fasta
[2023-03-18 01:26:37,645] [INFO] Task started: Blastn
[2023-03-18 01:26:37,645] [INFO] Running command: blastn -query OceanDNA-a2817/markers.fasta -db /var/lib/cwl/stg20245e34-97f7-4bd1-bed1-9b47414129c1/dqc_reference/reference_markers.fasta -out OceanDNA-a2817/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:38,128] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:38,129] [INFO] Selected 5 target genomes.
[2023-03-18 01:26:38,129] [INFO] Target genome list was writen to OceanDNA-a2817/target_genomes.txt
[2023-03-18 01:26:38,133] [INFO] Task started: fastANI
[2023-03-18 01:26:38,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6913661-de96-4da5-864a-aa5b88b90afd/OceanDNA-a2817.fa --refList OceanDNA-a2817/target_genomes.txt --output OceanDNA-a2817/fastani_result.tsv --threads 1
[2023-03-18 01:26:39,988] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:39,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20245e34-97f7-4bd1-bed1-9b47414129c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:39,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20245e34-97f7-4bd1-bed1-9b47414129c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:39,989] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:39,989] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:39,989] [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 01:26:39,989] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2817/tc_result.tsv
[2023-03-18 01:26:39,989] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:39,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:39,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20245e34-97f7-4bd1-bed1-9b47414129c1/dqc_reference/checkm_data
[2023-03-18 01:26:39,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:39,996] [INFO] Task started: CheckM
[2023-03-18 01:26:39,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2817/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2817/checkm_input OceanDNA-a2817/checkm_result
[2023-03-18 01:27:12,377] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:12,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:12,380] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:12,380] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:12,380] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2817/markers.fasta)
[2023-03-18 01:27:12,381] [INFO] Task started: Blastn
[2023-03-18 01:27:12,381] [INFO] Running command: blastn -query OceanDNA-a2817/markers.fasta -db /var/lib/cwl/stg20245e34-97f7-4bd1-bed1-9b47414129c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2817/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:12,976] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:12,977] [INFO] Selected 6 target genomes.
[2023-03-18 01:27:12,978] [INFO] Target genome list was writen to OceanDNA-a2817/target_genomes_gtdb.txt
[2023-03-18 01:27:12,987] [INFO] Task started: fastANI
[2023-03-18 01:27:12,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6913661-de96-4da5-864a-aa5b88b90afd/OceanDNA-a2817.fa --refList OceanDNA-a2817/target_genomes_gtdb.txt --output OceanDNA-a2817/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:15,436] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:15,440] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:27:15,440] [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_009887135.1	s__MGIIa-L2 sp009887135	98.0935	429	538	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.87	98.45	0.83	0.81	3	conclusive
GCA_016777125.1	s__MGIIa-L2 sp016777125	94.428	495	538	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_018645535.1	s__MGIIa-L2 sp018645535	86.7754	328	538	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_003602665.1	s__MGIIa-L2 sp003602665	85.5719	404	538	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	83.5286	337	538	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_018666575.1	s__MGIIa-L2 sp018666575	83.0259	379	538	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:15,441] [INFO] GTDB search result was written to OceanDNA-a2817/result_gtdb.tsv
[2023-03-18 01:27:15,441] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:15,442] [INFO] DFAST_QC result json was written to OceanDNA-a2817/dqc_result.json
[2023-03-18 01:27:15,442] [INFO] DFAST_QC completed!
[2023-03-18 01:27:15,442] [INFO] Total running time: 0h0m49s