[2023-03-17 08:20:27,847] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:20:27,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:20:27,847] [INFO] DQC Reference Directory: /var/lib/cwl/stge6526019-8c9b-4eb3-b6e1-c8cbb0704196/dqc_reference
[2023-03-17 08:20:29,922] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:20:29,923] [INFO] Task started: Prodigal
[2023-03-17 08:20:29,924] [INFO] Running command: cat /var/lib/cwl/stg6456056c-0a0f-4a70-af93-cb032688b9bb/OceanDNA-b17584.fa | prodigal -d OceanDNA-b17584/cds.fna -a OceanDNA-b17584/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:21:02,103] [INFO] Task succeeded: Prodigal
[2023-03-17 08:21:02,104] [INFO] Task started: HMMsearch
[2023-03-17 08:21:02,104] [INFO] Running command: hmmsearch --tblout OceanDNA-b17584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6526019-8c9b-4eb3-b6e1-c8cbb0704196/dqc_reference/reference_markers.hmm OceanDNA-b17584/protein.faa > /dev/null
[2023-03-17 08:21:02,342] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:21:02,343] [INFO] Found 6/6 markers.
[2023-03-17 08:21:02,374] [INFO] Query marker FASTA was written to OceanDNA-b17584/markers.fasta
[2023-03-17 08:21:02,375] [INFO] Task started: Blastn
[2023-03-17 08:21:02,375] [INFO] Running command: blastn -query OceanDNA-b17584/markers.fasta -db /var/lib/cwl/stge6526019-8c9b-4eb3-b6e1-c8cbb0704196/dqc_reference/reference_markers.fasta -out OceanDNA-b17584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:21:02,880] [INFO] Task succeeded: Blastn
[2023-03-17 08:21:02,881] [INFO] Selected 7 target genomes.
[2023-03-17 08:21:02,881] [INFO] Target genome list was writen to OceanDNA-b17584/target_genomes.txt
[2023-03-17 08:21:02,886] [INFO] Task started: fastANI
[2023-03-17 08:21:02,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg6456056c-0a0f-4a70-af93-cb032688b9bb/OceanDNA-b17584.fa --refList OceanDNA-b17584/target_genomes.txt --output OceanDNA-b17584/fastani_result.tsv --threads 1
[2023-03-17 08:21:08,605] [INFO] Task succeeded: fastANI
[2023-03-17 08:21:08,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6526019-8c9b-4eb3-b6e1-c8cbb0704196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:21:08,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6526019-8c9b-4eb3-b6e1-c8cbb0704196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:21:08,606] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:21:08,606] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:21:08,606] [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 08:21:08,606] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17584/tc_result.tsv
[2023-03-17 08:21:08,606] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:21:08,606] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:21:08,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6526019-8c9b-4eb3-b6e1-c8cbb0704196/dqc_reference/checkm_data
[2023-03-17 08:21:08,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:21:08,616] [INFO] Task started: CheckM
[2023-03-17 08:21:08,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17584/checkm_input OceanDNA-b17584/checkm_result
[2023-03-17 08:22:25,844] [INFO] Task succeeded: CheckM
[2023-03-17 08:22:25,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:22:25,966] [INFO] ===== Completeness check finished =====
[2023-03-17 08:22:25,967] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:22:25,967] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17584/markers.fasta)
[2023-03-17 08:22:25,968] [INFO] Task started: Blastn
[2023-03-17 08:22:25,968] [INFO] Running command: blastn -query OceanDNA-b17584/markers.fasta -db /var/lib/cwl/stge6526019-8c9b-4eb3-b6e1-c8cbb0704196/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:22:26,685] [INFO] Task succeeded: Blastn
[2023-03-17 08:22:26,708] [INFO] Selected 23 target genomes.
[2023-03-17 08:22:26,708] [INFO] Target genome list was writen to OceanDNA-b17584/target_genomes_gtdb.txt
[2023-03-17 08:22:27,853] [INFO] Task started: fastANI
[2023-03-17 08:22:27,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg6456056c-0a0f-4a70-af93-cb032688b9bb/OceanDNA-b17584.fa --refList OceanDNA-b17584/target_genomes_gtdb.txt --output OceanDNA-b17584/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:22:41,492] [INFO] Task succeeded: fastANI
[2023-03-17 08:22:41,494] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:22:41,494] [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_002709665.1	s__GCA-2709665 sp002709665	99.7508	1614	1744	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__GCA-2709665;g__GCA-2709665	95.0	99.67	99.61	0.93	0.93	3	conclusive
--------------------------------------------------------------------------------
[2023-03-17 08:22:41,495] [INFO] GTDB search result was written to OceanDNA-b17584/result_gtdb.tsv
[2023-03-17 08:22:41,495] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:22:41,495] [INFO] DFAST_QC result json was written to OceanDNA-b17584/dqc_result.json
[2023-03-17 08:22:41,495] [INFO] DFAST_QC completed!
[2023-03-17 08:22:41,495] [INFO] Total running time: 0h2m14s