[2023-03-15 05:36:19,902] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:36:19,902] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:36:19,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg68f2996e-c1f4-4feb-8264-35d02e70f3e9/dqc_reference
[2023-03-15 05:36:21,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:36:21,005] [INFO] Task started: Prodigal
[2023-03-15 05:36:21,005] [INFO] Running command: cat /var/lib/cwl/stg3935977e-cb35-435d-9478-d5c4a255780b/OceanDNA-b15077.fa | prodigal -d OceanDNA-b15077/cds.fna -a OceanDNA-b15077/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:36:31,492] [INFO] Task succeeded: Prodigal
[2023-03-15 05:36:31,492] [INFO] Task started: HMMsearch
[2023-03-15 05:36:31,492] [INFO] Running command: hmmsearch --tblout OceanDNA-b15077/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68f2996e-c1f4-4feb-8264-35d02e70f3e9/dqc_reference/reference_markers.hmm OceanDNA-b15077/protein.faa > /dev/null
[2023-03-15 05:36:31,652] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:36:31,652] [INFO] Found 6/6 markers.
[2023-03-15 05:36:31,665] [INFO] Query marker FASTA was written to OceanDNA-b15077/markers.fasta
[2023-03-15 05:36:31,666] [INFO] Task started: Blastn
[2023-03-15 05:36:31,666] [INFO] Running command: blastn -query OceanDNA-b15077/markers.fasta -db /var/lib/cwl/stg68f2996e-c1f4-4feb-8264-35d02e70f3e9/dqc_reference/reference_markers.fasta -out OceanDNA-b15077/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:36:32,173] [INFO] Task succeeded: Blastn
[2023-03-15 05:36:32,173] [INFO] Selected 6 target genomes.
[2023-03-15 05:36:32,174] [INFO] Target genome list was writen to OceanDNA-b15077/target_genomes.txt
[2023-03-15 05:36:32,178] [INFO] Task started: fastANI
[2023-03-15 05:36:32,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg3935977e-cb35-435d-9478-d5c4a255780b/OceanDNA-b15077.fa --refList OceanDNA-b15077/target_genomes.txt --output OceanDNA-b15077/fastani_result.tsv --threads 1
[2023-03-15 05:36:35,077] [INFO] Task succeeded: fastANI
[2023-03-15 05:36:35,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68f2996e-c1f4-4feb-8264-35d02e70f3e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:36:35,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68f2996e-c1f4-4feb-8264-35d02e70f3e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:36:35,078] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:36:35,078] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:36:35,078] [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 05:36:35,078] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15077/tc_result.tsv
[2023-03-15 05:36:35,078] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:36:35,078] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:36:35,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68f2996e-c1f4-4feb-8264-35d02e70f3e9/dqc_reference/checkm_data
[2023-03-15 05:36:35,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:36:35,084] [INFO] Task started: CheckM
[2023-03-15 05:36:35,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15077/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15077/checkm_input OceanDNA-b15077/checkm_result
[2023-03-15 05:37:05,586] [INFO] Task succeeded: CheckM
[2023-03-15 05:37:05,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 05:37:05,588] [INFO] ===== Completeness check finished =====
[2023-03-15 05:37:05,588] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:37:05,588] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15077/markers.fasta)
[2023-03-15 05:37:05,589] [INFO] Task started: Blastn
[2023-03-15 05:37:05,589] [INFO] Running command: blastn -query OceanDNA-b15077/markers.fasta -db /var/lib/cwl/stg68f2996e-c1f4-4feb-8264-35d02e70f3e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15077/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:37:06,981] [INFO] Task succeeded: Blastn
[2023-03-15 05:37:06,981] [INFO] Selected 14 target genomes.
[2023-03-15 05:37:06,981] [INFO] Target genome list was writen to OceanDNA-b15077/target_genomes_gtdb.txt
[2023-03-15 05:37:06,989] [INFO] Task started: fastANI
[2023-03-15 05:37:06,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg3935977e-cb35-435d-9478-d5c4a255780b/OceanDNA-b15077.fa --refList OceanDNA-b15077/target_genomes_gtdb.txt --output OceanDNA-b15077/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:37:13,238] [INFO] Task succeeded: fastANI
[2023-03-15 05:37:13,241] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:37:13,241] [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_014239685.1	s__GCA-2730555 sp014239685	98.9416	466	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002730555.1	s__GCA-2730555 sp002730555	78.7131	290	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.68	99.68	0.93	0.93	2	-
GCA_018650185.1	s__GCA-2730555 sp018650185	77.6259	222	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.67	99.66	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-15 05:37:13,241] [INFO] GTDB search result was written to OceanDNA-b15077/result_gtdb.tsv
[2023-03-15 05:37:13,241] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:37:13,242] [INFO] DFAST_QC result json was written to OceanDNA-b15077/dqc_result.json
[2023-03-15 05:37:13,242] [INFO] DFAST_QC completed!
[2023-03-15 05:37:13,242] [INFO] Total running time: 0h0m53s