[2023-03-16 18:33:25,951] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:33:25,951] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:33:25,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ef8685a-ac32-4a20-a654-e11b45d5e5d6/dqc_reference
[2023-03-16 18:33:27,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:33:27,535] [INFO] Task started: Prodigal
[2023-03-16 18:33:27,535] [INFO] Running command: cat /var/lib/cwl/stgc287a017-4eb0-48cc-b875-1357a59461ef/OceanDNA-b21628.fa | prodigal -d OceanDNA-b21628/cds.fna -a OceanDNA-b21628/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:33:39,714] [INFO] Task succeeded: Prodigal
[2023-03-16 18:33:39,714] [INFO] Task started: HMMsearch
[2023-03-16 18:33:39,715] [INFO] Running command: hmmsearch --tblout OceanDNA-b21628/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ef8685a-ac32-4a20-a654-e11b45d5e5d6/dqc_reference/reference_markers.hmm OceanDNA-b21628/protein.faa > /dev/null
[2023-03-16 18:33:40,104] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:33:40,104] [INFO] Found 6/6 markers.
[2023-03-16 18:33:40,119] [INFO] Query marker FASTA was written to OceanDNA-b21628/markers.fasta
[2023-03-16 18:33:40,121] [INFO] Task started: Blastn
[2023-03-16 18:33:40,121] [INFO] Running command: blastn -query OceanDNA-b21628/markers.fasta -db /var/lib/cwl/stg8ef8685a-ac32-4a20-a654-e11b45d5e5d6/dqc_reference/reference_markers.fasta -out OceanDNA-b21628/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:33:41,291] [INFO] Task succeeded: Blastn
[2023-03-16 18:33:41,293] [INFO] Selected 17 target genomes.
[2023-03-16 18:33:41,293] [INFO] Target genome list was writen to OceanDNA-b21628/target_genomes.txt
[2023-03-16 18:33:41,303] [INFO] Task started: fastANI
[2023-03-16 18:33:41,303] [INFO] Running command: fastANI --query /var/lib/cwl/stgc287a017-4eb0-48cc-b875-1357a59461ef/OceanDNA-b21628.fa --refList OceanDNA-b21628/target_genomes.txt --output OceanDNA-b21628/fastani_result.tsv --threads 1
[2023-03-16 18:33:52,967] [INFO] Task succeeded: fastANI
[2023-03-16 18:33:52,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ef8685a-ac32-4a20-a654-e11b45d5e5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:33:52,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ef8685a-ac32-4a20-a654-e11b45d5e5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:33:52,968] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:33:52,968] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:33:52,968] [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
--------------------------------------------------------------------------------
[2023-03-16 18:33:52,969] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21628/tc_result.tsv
[2023-03-16 18:33:52,970] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:33:52,970] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:33:52,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ef8685a-ac32-4a20-a654-e11b45d5e5d6/dqc_reference/checkm_data
[2023-03-16 18:33:52,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:33:52,997] [INFO] Task started: CheckM
[2023-03-16 18:33:52,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21628/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21628/checkm_input OceanDNA-b21628/checkm_result
[2023-03-16 18:34:27,594] [INFO] Task succeeded: CheckM
[2023-03-16 18:34:27,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:34:27,598] [INFO] ===== Completeness check finished =====
[2023-03-16 18:34:27,599] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:34:27,599] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21628/markers.fasta)
[2023-03-16 18:34:27,601] [INFO] Task started: Blastn
[2023-03-16 18:34:27,601] [INFO] Running command: blastn -query OceanDNA-b21628/markers.fasta -db /var/lib/cwl/stg8ef8685a-ac32-4a20-a654-e11b45d5e5d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21628/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:34:28,535] [INFO] Task succeeded: Blastn
[2023-03-16 18:34:28,540] [INFO] Selected 19 target genomes.
[2023-03-16 18:34:28,540] [INFO] Target genome list was writen to OceanDNA-b21628/target_genomes_gtdb.txt
[2023-03-16 18:34:28,656] [INFO] Task started: fastANI
[2023-03-16 18:34:28,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgc287a017-4eb0-48cc-b875-1357a59461ef/OceanDNA-b21628.fa --refList OceanDNA-b21628/target_genomes_gtdb.txt --output OceanDNA-b21628/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:34:35,302] [INFO] Task succeeded: fastANI
[2023-03-16 18:34:35,304] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:34:35,304] [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_018659585.1	s__JABJMC01 sp018659585	79.2038	122	324	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__UBA1369;f__UBA12473;g__JABJMC01	95.0	99.93	99.93	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:34:35,306] [INFO] GTDB search result was written to OceanDNA-b21628/result_gtdb.tsv
[2023-03-16 18:34:35,306] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:34:35,307] [INFO] DFAST_QC result json was written to OceanDNA-b21628/dqc_result.json
[2023-03-16 18:34:35,307] [INFO] DFAST_QC completed!
[2023-03-16 18:34:35,308] [INFO] Total running time: 0h1m9s