[2023-03-15 23:15:05,778] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:15:05,780] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:15:05,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f5434aa-ac7d-4541-aab2-20e1b62fc9f5/dqc_reference
[2023-03-15 23:15:07,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:15:07,541] [INFO] Task started: Prodigal
[2023-03-15 23:15:07,541] [INFO] Running command: cat /var/lib/cwl/stg0006a5d3-964f-4722-992f-d08afd71c318/OceanDNA-a1876.fa | prodigal -d OceanDNA-a1876/cds.fna -a OceanDNA-a1876/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:15:13,650] [INFO] Task succeeded: Prodigal
[2023-03-15 23:15:13,650] [INFO] Task started: HMMsearch
[2023-03-15 23:15:13,650] [INFO] Running command: hmmsearch --tblout OceanDNA-a1876/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f5434aa-ac7d-4541-aab2-20e1b62fc9f5/dqc_reference/reference_markers.hmm OceanDNA-a1876/protein.faa > /dev/null
[2023-03-15 23:15:13,878] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:15:13,879] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0006a5d3-964f-4722-992f-d08afd71c318/OceanDNA-a1876.fa]
[2023-03-15 23:15:13,901] [INFO] Query marker FASTA was written to OceanDNA-a1876/markers.fasta
[2023-03-15 23:15:13,903] [INFO] Task started: Blastn
[2023-03-15 23:15:13,903] [INFO] Running command: blastn -query OceanDNA-a1876/markers.fasta -db /var/lib/cwl/stg0f5434aa-ac7d-4541-aab2-20e1b62fc9f5/dqc_reference/reference_markers.fasta -out OceanDNA-a1876/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:15,732] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:15,734] [INFO] Selected 6 target genomes.
[2023-03-15 23:15:15,734] [INFO] Target genome list was writen to OceanDNA-a1876/target_genomes.txt
[2023-03-15 23:15:15,740] [INFO] Task started: fastANI
[2023-03-15 23:15:15,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg0006a5d3-964f-4722-992f-d08afd71c318/OceanDNA-a1876.fa --refList OceanDNA-a1876/target_genomes.txt --output OceanDNA-a1876/fastani_result.tsv --threads 1
[2023-03-15 23:15:17,527] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:17,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f5434aa-ac7d-4541-aab2-20e1b62fc9f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:15:17,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f5434aa-ac7d-4541-aab2-20e1b62fc9f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:15:17,527] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:15:17,527] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:15:17,527] [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 23:15:17,529] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1876/tc_result.tsv
[2023-03-15 23:15:17,531] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:15:17,531] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:15:17,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f5434aa-ac7d-4541-aab2-20e1b62fc9f5/dqc_reference/checkm_data
[2023-03-15 23:15:17,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:15:17,540] [INFO] Task started: CheckM
[2023-03-15 23:15:17,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1876/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1876/checkm_input OceanDNA-a1876/checkm_result
[2023-03-15 23:15:39,439] [INFO] Task succeeded: CheckM
[2023-03-15 23:15:39,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:15:39,488] [INFO] ===== Completeness check finished =====
[2023-03-15 23:15:39,489] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:15:39,489] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1876/markers.fasta)
[2023-03-15 23:15:39,489] [INFO] Task started: Blastn
[2023-03-15 23:15:39,489] [INFO] Running command: blastn -query OceanDNA-a1876/markers.fasta -db /var/lib/cwl/stg0f5434aa-ac7d-4541-aab2-20e1b62fc9f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1876/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:40,078] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:40,088] [INFO] Selected 6 target genomes.
[2023-03-15 23:15:40,088] [INFO] Target genome list was writen to OceanDNA-a1876/target_genomes_gtdb.txt
[2023-03-15 23:15:40,096] [INFO] Task started: fastANI
[2023-03-15 23:15:40,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg0006a5d3-964f-4722-992f-d08afd71c318/OceanDNA-a1876.fa --refList OceanDNA-a1876/target_genomes_gtdb.txt --output OceanDNA-a1876/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:15:41,993] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:41,998] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:15:41,998] [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	93.5785	279	335	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_002709705.1	s__MGIIa-K1 sp002709705	85.2934	260	335	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	83.0961	278	335	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_002727695.1	s__MGIIa-K1 sp002727695	83.085	250	335	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	81.7954	234	335	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_902563095.1	s__MGIIa-K1 sp902563095	81.7304	198	335	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
--------------------------------------------------------------------------------
[2023-03-15 23:15:42,002] [INFO] GTDB search result was written to OceanDNA-a1876/result_gtdb.tsv
[2023-03-15 23:15:42,009] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:15:42,014] [INFO] DFAST_QC result json was written to OceanDNA-a1876/dqc_result.json
[2023-03-15 23:15:42,014] [INFO] DFAST_QC completed!
[2023-03-15 23:15:42,014] [INFO] Total running time: 0h0m36s