[2023-03-19 01:19:34,272] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:19:34,272] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:19:34,272] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a46c6dd-ace7-47d4-9530-899f46593cc3/dqc_reference
[2023-03-19 01:19:35,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:19:35,411] [INFO] Task started: Prodigal
[2023-03-19 01:19:35,411] [INFO] Running command: cat /var/lib/cwl/stgf486f81d-c7d0-4d0c-92c1-4dcdb5593a60/OceanDNA-b24654.fa | prodigal -d OceanDNA-b24654/cds.fna -a OceanDNA-b24654/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:19:49,054] [INFO] Task succeeded: Prodigal
[2023-03-19 01:19:49,054] [INFO] Task started: HMMsearch
[2023-03-19 01:19:49,054] [INFO] Running command: hmmsearch --tblout OceanDNA-b24654/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a46c6dd-ace7-47d4-9530-899f46593cc3/dqc_reference/reference_markers.hmm OceanDNA-b24654/protein.faa > /dev/null
[2023-03-19 01:19:49,235] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:19:49,235] [INFO] Found 6/6 markers.
[2023-03-19 01:19:49,249] [INFO] Query marker FASTA was written to OceanDNA-b24654/markers.fasta
[2023-03-19 01:19:49,251] [INFO] Task started: Blastn
[2023-03-19 01:19:49,251] [INFO] Running command: blastn -query OceanDNA-b24654/markers.fasta -db /var/lib/cwl/stg3a46c6dd-ace7-47d4-9530-899f46593cc3/dqc_reference/reference_markers.fasta -out OceanDNA-b24654/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:19:50,000] [INFO] Task succeeded: Blastn
[2023-03-19 01:19:50,001] [INFO] Selected 30 target genomes.
[2023-03-19 01:19:50,002] [INFO] Target genome list was writen to OceanDNA-b24654/target_genomes.txt
[2023-03-19 01:19:50,025] [INFO] Task started: fastANI
[2023-03-19 01:19:50,025] [INFO] Running command: fastANI --query /var/lib/cwl/stgf486f81d-c7d0-4d0c-92c1-4dcdb5593a60/OceanDNA-b24654.fa --refList OceanDNA-b24654/target_genomes.txt --output OceanDNA-b24654/fastani_result.tsv --threads 1
[2023-03-19 01:20:04,871] [INFO] Task succeeded: fastANI
[2023-03-19 01:20:04,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a46c6dd-ace7-47d4-9530-899f46593cc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:20:04,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a46c6dd-ace7-47d4-9530-899f46593cc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:20:04,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:20:04,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:20:04,872] [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
--------------------------------------------------------------------------------
[2023-03-19 01:20:04,872] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24654/tc_result.tsv
[2023-03-19 01:20:04,872] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:20:04,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:20:04,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a46c6dd-ace7-47d4-9530-899f46593cc3/dqc_reference/checkm_data
[2023-03-19 01:20:04,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:20:04,888] [INFO] Task started: CheckM
[2023-03-19 01:20:04,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24654/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24654/checkm_input OceanDNA-b24654/checkm_result
[2023-03-19 01:20:42,071] [INFO] Task succeeded: CheckM
[2023-03-19 01:20:42,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:20:42,074] [INFO] ===== Completeness check finished =====
[2023-03-19 01:20:42,074] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:20:42,074] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24654/markers.fasta)
[2023-03-19 01:20:42,076] [INFO] Task started: Blastn
[2023-03-19 01:20:42,076] [INFO] Running command: blastn -query OceanDNA-b24654/markers.fasta -db /var/lib/cwl/stg3a46c6dd-ace7-47d4-9530-899f46593cc3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24654/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:20:43,213] [INFO] Task succeeded: Blastn
[2023-03-19 01:20:43,214] [INFO] Selected 23 target genomes.
[2023-03-19 01:20:43,215] [INFO] Target genome list was writen to OceanDNA-b24654/target_genomes_gtdb.txt
[2023-03-19 01:20:43,232] [INFO] Task started: fastANI
[2023-03-19 01:20:43,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgf486f81d-c7d0-4d0c-92c1-4dcdb5593a60/OceanDNA-b24654.fa --refList OceanDNA-b24654/target_genomes_gtdb.txt --output OceanDNA-b24654/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:20:52,850] [INFO] Task succeeded: fastANI
[2023-03-19 01:20:52,852] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:20:52,852] [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_002359735.1	s__UBA2638 sp002359735	99.1334	680	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__UBA2638	95.0	99.67	99.12	0.89	0.85	4	conclusive
--------------------------------------------------------------------------------
[2023-03-19 01:20:52,852] [INFO] GTDB search result was written to OceanDNA-b24654/result_gtdb.tsv
[2023-03-19 01:20:52,852] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:20:52,853] [INFO] DFAST_QC result json was written to OceanDNA-b24654/dqc_result.json
[2023-03-19 01:20:52,853] [INFO] DFAST_QC completed!
[2023-03-19 01:20:52,853] [INFO] Total running time: 0h1m19s