[2023-03-15 16:25:56,998] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,005] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e66236f-c084-4183-ab25-c5c23d86f4f6/dqc_reference
[2023-03-15 16:25:58,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,596] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,596] [INFO] Running command: cat /var/lib/cwl/stg9b7f8fab-594f-4811-b5d2-d07860537da3/OceanDNA-b47097.fa | prodigal -d OceanDNA-b47097/cds.fna -a OceanDNA-b47097/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:06,505] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:06,505] [INFO] Task started: HMMsearch
[2023-03-15 16:26:06,506] [INFO] Running command: hmmsearch --tblout OceanDNA-b47097/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e66236f-c084-4183-ab25-c5c23d86f4f6/dqc_reference/reference_markers.hmm OceanDNA-b47097/protein.faa > /dev/null
[2023-03-15 16:26:06,680] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:06,680] [INFO] Found 6/6 markers.
[2023-03-15 16:26:06,749] [INFO] Query marker FASTA was written to OceanDNA-b47097/markers.fasta
[2023-03-15 16:26:06,749] [INFO] Task started: Blastn
[2023-03-15 16:26:06,749] [INFO] Running command: blastn -query OceanDNA-b47097/markers.fasta -db /var/lib/cwl/stg1e66236f-c084-4183-ab25-c5c23d86f4f6/dqc_reference/reference_markers.fasta -out OceanDNA-b47097/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:07,314] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:07,321] [INFO] Selected 15 target genomes.
[2023-03-15 16:26:07,321] [INFO] Target genome list was writen to OceanDNA-b47097/target_genomes.txt
[2023-03-15 16:26:07,332] [INFO] Task started: fastANI
[2023-03-15 16:26:07,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b7f8fab-594f-4811-b5d2-d07860537da3/OceanDNA-b47097.fa --refList OceanDNA-b47097/target_genomes.txt --output OceanDNA-b47097/fastani_result.tsv --threads 1
[2023-03-15 16:26:18,998] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:18,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e66236f-c084-4183-ab25-c5c23d86f4f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:18,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e66236f-c084-4183-ab25-c5c23d86f4f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:18,999] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:18,999] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:18,999] [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 16:26:19,005] [INFO] DFAST Taxonomy check result was written to OceanDNA-b47097/tc_result.tsv
[2023-03-15 16:26:19,018] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:19,019] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:19,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e66236f-c084-4183-ab25-c5c23d86f4f6/dqc_reference/checkm_data
[2023-03-15 16:26:19,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:19,029] [INFO] Task started: CheckM
[2023-03-15 16:26:19,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b47097/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b47097/checkm_input OceanDNA-b47097/checkm_result
[2023-03-15 16:26:44,101] [INFO] Task succeeded: CheckM
[2023-03-15 16:26:44,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:26:44,195] [INFO] ===== Completeness check finished =====
[2023-03-15 16:26:44,195] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:26:44,195] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b47097/markers.fasta)
[2023-03-15 16:26:44,196] [INFO] Task started: Blastn
[2023-03-15 16:26:44,196] [INFO] Running command: blastn -query OceanDNA-b47097/markers.fasta -db /var/lib/cwl/stg1e66236f-c084-4183-ab25-c5c23d86f4f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b47097/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:45,131] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:45,140] [INFO] Selected 23 target genomes.
[2023-03-15 16:26:45,140] [INFO] Target genome list was writen to OceanDNA-b47097/target_genomes_gtdb.txt
[2023-03-15 16:26:45,230] [INFO] Task started: fastANI
[2023-03-15 16:26:45,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b7f8fab-594f-4811-b5d2-d07860537da3/OceanDNA-b47097.fa --refList OceanDNA-b47097/target_genomes_gtdb.txt --output OceanDNA-b47097/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:26:55,459] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:55,461] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:26:55,461] [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_018694295.1	s__JABHNK01 sp018694295	99.92	438	466	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__JABHNK01;g__JABHNK01	95.0	99.86	99.76	0.94	0.93	6	conclusive
--------------------------------------------------------------------------------
[2023-03-15 16:26:55,468] [INFO] GTDB search result was written to OceanDNA-b47097/result_gtdb.tsv
[2023-03-15 16:26:55,476] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:26:55,481] [INFO] DFAST_QC result json was written to OceanDNA-b47097/dqc_result.json
[2023-03-15 16:26:55,481] [INFO] DFAST_QC completed!
[2023-03-15 16:26:55,482] [INFO] Total running time: 0h0m58s