[2023-03-16 00:42:12,742] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:42:12,742] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:42:12,742] [INFO] DQC Reference Directory: /var/lib/cwl/stgad812034-e512-4bc1-b3cf-377f57ef8cd2/dqc_reference
[2023-03-16 00:42:14,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:42:14,523] [INFO] Task started: Prodigal
[2023-03-16 00:42:14,523] [INFO] Running command: cat /var/lib/cwl/stgeb81d2ed-8d51-4da5-a2a8-2eb1373c5d01/OceanDNA-b14001.fa | prodigal -d OceanDNA-b14001/cds.fna -a OceanDNA-b14001/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:42:19,565] [INFO] Task succeeded: Prodigal
[2023-03-16 00:42:19,565] [INFO] Task started: HMMsearch
[2023-03-16 00:42:19,565] [INFO] Running command: hmmsearch --tblout OceanDNA-b14001/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad812034-e512-4bc1-b3cf-377f57ef8cd2/dqc_reference/reference_markers.hmm OceanDNA-b14001/protein.faa > /dev/null
[2023-03-16 00:42:19,768] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:42:19,769] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb81d2ed-8d51-4da5-a2a8-2eb1373c5d01/OceanDNA-b14001.fa]
[2023-03-16 00:42:19,778] [INFO] Query marker FASTA was written to OceanDNA-b14001/markers.fasta
[2023-03-16 00:42:19,780] [INFO] Task started: Blastn
[2023-03-16 00:42:19,780] [INFO] Running command: blastn -query OceanDNA-b14001/markers.fasta -db /var/lib/cwl/stgad812034-e512-4bc1-b3cf-377f57ef8cd2/dqc_reference/reference_markers.fasta -out OceanDNA-b14001/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:42:21,813] [INFO] Task succeeded: Blastn
[2023-03-16 00:42:21,814] [INFO] Selected 12 target genomes.
[2023-03-16 00:42:21,814] [INFO] Target genome list was writen to OceanDNA-b14001/target_genomes.txt
[2023-03-16 00:42:21,827] [INFO] Task started: fastANI
[2023-03-16 00:42:21,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb81d2ed-8d51-4da5-a2a8-2eb1373c5d01/OceanDNA-b14001.fa --refList OceanDNA-b14001/target_genomes.txt --output OceanDNA-b14001/fastani_result.tsv --threads 1
[2023-03-16 00:42:27,746] [INFO] Task succeeded: fastANI
[2023-03-16 00:42:27,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad812034-e512-4bc1-b3cf-377f57ef8cd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:42:27,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad812034-e512-4bc1-b3cf-377f57ef8cd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:42:27,747] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:42:27,747] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:42:27,747] [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 00:42:27,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14001/tc_result.tsv
[2023-03-16 00:42:27,748] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:42:27,748] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:42:27,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad812034-e512-4bc1-b3cf-377f57ef8cd2/dqc_reference/checkm_data
[2023-03-16 00:42:27,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:42:27,806] [INFO] Task started: CheckM
[2023-03-16 00:42:27,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14001/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14001/checkm_input OceanDNA-b14001/checkm_result
[2023-03-16 00:42:50,584] [INFO] Task succeeded: CheckM
[2023-03-16 00:42:50,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:42:50,586] [INFO] ===== Completeness check finished =====
[2023-03-16 00:42:50,586] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:42:50,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14001/markers.fasta)
[2023-03-16 00:42:50,588] [INFO] Task started: Blastn
[2023-03-16 00:42:50,588] [INFO] Running command: blastn -query OceanDNA-b14001/markers.fasta -db /var/lib/cwl/stgad812034-e512-4bc1-b3cf-377f57ef8cd2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14001/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:42:51,696] [INFO] Task succeeded: Blastn
[2023-03-16 00:42:51,697] [INFO] Selected 19 target genomes.
[2023-03-16 00:42:51,698] [INFO] Target genome list was writen to OceanDNA-b14001/target_genomes_gtdb.txt
[2023-03-16 00:42:51,715] [INFO] Task started: fastANI
[2023-03-16 00:42:51,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb81d2ed-8d51-4da5-a2a8-2eb1373c5d01/OceanDNA-b14001.fa --refList OceanDNA-b14001/target_genomes_gtdb.txt --output OceanDNA-b14001/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:42:56,450] [INFO] Task succeeded: fastANI
[2023-03-16 00:42:56,452] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:42:56,452] [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_003213095.1	s__AG-426-M11 sp003213095	82.6181	235	328	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__AG-426-M11	95.0	97.10	96.18	0.80	0.72	9	-
--------------------------------------------------------------------------------
[2023-03-16 00:42:56,452] [INFO] GTDB search result was written to OceanDNA-b14001/result_gtdb.tsv
[2023-03-16 00:42:56,453] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:42:56,453] [INFO] DFAST_QC result json was written to OceanDNA-b14001/dqc_result.json
[2023-03-16 00:42:56,454] [INFO] DFAST_QC completed!
[2023-03-16 00:42:56,454] [INFO] Total running time: 0h0m44s