[2023-03-17 04:48:53,990] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:53,991] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:53,991] [INFO] DQC Reference Directory: /var/lib/cwl/stgf59cb5db-4376-441d-a696-820a874c80a1/dqc_reference
[2023-03-17 04:48:55,177] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,177] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,177] [INFO] Running command: cat /var/lib/cwl/stg19c9fef7-d9e0-43f3-b76d-80463b8c2b41/OceanDNA-a1972.fa | prodigal -d OceanDNA-a1972/cds.fna -a OceanDNA-a1972/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:04,546] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:04,547] [INFO] Task started: HMMsearch
[2023-03-17 04:49:04,547] [INFO] Running command: hmmsearch --tblout OceanDNA-a1972/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf59cb5db-4376-441d-a696-820a874c80a1/dqc_reference/reference_markers.hmm OceanDNA-a1972/protein.faa > /dev/null
[2023-03-17 04:49:04,704] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:04,704] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg19c9fef7-d9e0-43f3-b76d-80463b8c2b41/OceanDNA-a1972.fa]
[2023-03-17 04:49:04,717] [INFO] Query marker FASTA was written to OceanDNA-a1972/markers.fasta
[2023-03-17 04:49:04,717] [INFO] Task started: Blastn
[2023-03-17 04:49:04,717] [INFO] Running command: blastn -query OceanDNA-a1972/markers.fasta -db /var/lib/cwl/stgf59cb5db-4376-441d-a696-820a874c80a1/dqc_reference/reference_markers.fasta -out OceanDNA-a1972/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:05,177] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:05,177] [INFO] Selected 3 target genomes.
[2023-03-17 04:49:05,177] [INFO] Target genome list was writen to OceanDNA-a1972/target_genomes.txt
[2023-03-17 04:49:05,179] [INFO] Task started: fastANI
[2023-03-17 04:49:05,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c9fef7-d9e0-43f3-b76d-80463b8c2b41/OceanDNA-a1972.fa --refList OceanDNA-a1972/target_genomes.txt --output OceanDNA-a1972/fastani_result.tsv --threads 1
[2023-03-17 04:49:06,933] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:06,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf59cb5db-4376-441d-a696-820a874c80a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:06,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf59cb5db-4376-441d-a696-820a874c80a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:06,934] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:06,934] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:06,934] [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 04:49:06,934] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1972/tc_result.tsv
[2023-03-17 04:49:06,934] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:06,934] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:06,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf59cb5db-4376-441d-a696-820a874c80a1/dqc_reference/checkm_data
[2023-03-17 04:49:06,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:06,940] [INFO] Task started: CheckM
[2023-03-17 04:49:06,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1972/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1972/checkm_input OceanDNA-a1972/checkm_result
[2023-03-17 04:49:34,909] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:34,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:49:34,911] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:34,911] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:34,911] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1972/markers.fasta)
[2023-03-17 04:49:34,912] [INFO] Task started: Blastn
[2023-03-17 04:49:34,912] [INFO] Running command: blastn -query OceanDNA-a1972/markers.fasta -db /var/lib/cwl/stgf59cb5db-4376-441d-a696-820a874c80a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1972/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:35,496] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:35,497] [INFO] Selected 9 target genomes.
[2023-03-17 04:49:35,497] [INFO] Target genome list was writen to OceanDNA-a1972/target_genomes_gtdb.txt
[2023-03-17 04:49:35,705] [INFO] Task started: fastANI
[2023-03-17 04:49:35,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg19c9fef7-d9e0-43f3-b76d-80463b8c2b41/OceanDNA-a1972.fa --refList OceanDNA-a1972/target_genomes_gtdb.txt --output OceanDNA-a1972/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:49:38,374] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:38,379] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:49:38,379] [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_002701145.1	s__MGIIa-K1 sp002701145	97.1044	413	538	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_902605365.1	s__MGIIa-K1 sp902605365	93.2056	344	538	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_018650165.1	s__MGIIa-K1 sp018650165	79.0673	220	538	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	-
GCA_902563095.1	s__MGIIa-K1 sp902563095	78.4563	136	538	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_003602535.1	s__MGIIa-K1 sp003602535	78.3033	191	538	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_002715725.1	s__MGIIa-K1 sp002715725	78.1662	166	538	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	77.4427	106	538	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_002506705.1	s__MGIIa-K1 sp002506705	77.2181	85	538	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:49:38,379] [INFO] GTDB search result was written to OceanDNA-a1972/result_gtdb.tsv
[2023-03-17 04:49:38,380] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:49:38,380] [INFO] DFAST_QC result json was written to OceanDNA-a1972/dqc_result.json
[2023-03-17 04:49:38,380] [INFO] DFAST_QC completed!
[2023-03-17 04:49:38,380] [INFO] Total running time: 0h0m44s