[2023-03-19 23:03:45,041] [INFO] DFAST_QC pipeline started.
[2023-03-19 23:03:45,041] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 23:03:45,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaa5a446-2693-4ae5-a2cd-2b1a486c65d1/dqc_reference
[2023-03-19 23:03:46,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 23:03:46,888] [INFO] Task started: Prodigal
[2023-03-19 23:03:46,889] [INFO] Running command: cat /var/lib/cwl/stgf4b2dc81-c28a-4079-ae78-9b31ae4fc516/OceanDNA-b15208.fa | prodigal -d OceanDNA-b15208/cds.fna -a OceanDNA-b15208/protein.faa -g 11 -q > /dev/null
[2023-03-19 23:03:56,687] [INFO] Task succeeded: Prodigal
[2023-03-19 23:03:56,687] [INFO] Task started: HMMsearch
[2023-03-19 23:03:56,687] [INFO] Running command: hmmsearch --tblout OceanDNA-b15208/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaa5a446-2693-4ae5-a2cd-2b1a486c65d1/dqc_reference/reference_markers.hmm OceanDNA-b15208/protein.faa > /dev/null
[2023-03-19 23:03:56,829] [INFO] Task succeeded: HMMsearch
[2023-03-19 23:03:56,829] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf4b2dc81-c28a-4079-ae78-9b31ae4fc516/OceanDNA-b15208.fa]
[2023-03-19 23:03:56,840] [INFO] Query marker FASTA was written to OceanDNA-b15208/markers.fasta
[2023-03-19 23:03:56,840] [INFO] Task started: Blastn
[2023-03-19 23:03:56,840] [INFO] Running command: blastn -query OceanDNA-b15208/markers.fasta -db /var/lib/cwl/stgdaa5a446-2693-4ae5-a2cd-2b1a486c65d1/dqc_reference/reference_markers.fasta -out OceanDNA-b15208/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 23:03:57,337] [INFO] Task succeeded: Blastn
[2023-03-19 23:03:57,338] [INFO] Selected 12 target genomes.
[2023-03-19 23:03:57,338] [INFO] Target genome list was writen to OceanDNA-b15208/target_genomes.txt
[2023-03-19 23:03:57,345] [INFO] Task started: fastANI
[2023-03-19 23:03:57,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4b2dc81-c28a-4079-ae78-9b31ae4fc516/OceanDNA-b15208.fa --refList OceanDNA-b15208/target_genomes.txt --output OceanDNA-b15208/fastani_result.tsv --threads 1
[2023-03-19 23:04:03,597] [INFO] Task succeeded: fastANI
[2023-03-19 23:04:03,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaa5a446-2693-4ae5-a2cd-2b1a486c65d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 23:04:03,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaa5a446-2693-4ae5-a2cd-2b1a486c65d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 23:04:03,598] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 23:04:03,598] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 23:04:03,598] [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 23:04:03,598] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15208/tc_result.tsv
[2023-03-19 23:04:03,598] [INFO] ===== Taxonomy check completed =====
[2023-03-19 23:04:03,598] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 23:04:03,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaa5a446-2693-4ae5-a2cd-2b1a486c65d1/dqc_reference/checkm_data
[2023-03-19 23:04:03,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 23:04:03,605] [INFO] Task started: CheckM
[2023-03-19 23:04:03,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15208/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15208/checkm_input OceanDNA-b15208/checkm_result
[2023-03-19 23:04:32,414] [INFO] Task succeeded: CheckM
[2023-03-19 23:04:32,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 23:04:32,416] [INFO] ===== Completeness check finished =====
[2023-03-19 23:04:32,416] [INFO] ===== Start GTDB Search =====
[2023-03-19 23:04:32,416] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15208/markers.fasta)
[2023-03-19 23:04:32,417] [INFO] Task started: Blastn
[2023-03-19 23:04:32,417] [INFO] Running command: blastn -query OceanDNA-b15208/markers.fasta -db /var/lib/cwl/stgdaa5a446-2693-4ae5-a2cd-2b1a486c65d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15208/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 23:04:33,096] [INFO] Task succeeded: Blastn
[2023-03-19 23:04:33,097] [INFO] Selected 15 target genomes.
[2023-03-19 23:04:33,097] [INFO] Target genome list was writen to OceanDNA-b15208/target_genomes_gtdb.txt
[2023-03-19 23:04:33,406] [INFO] Task started: fastANI
[2023-03-19 23:04:33,406] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4b2dc81-c28a-4079-ae78-9b31ae4fc516/OceanDNA-b15208.fa --refList OceanDNA-b15208/target_genomes_gtdb.txt --output OceanDNA-b15208/fastani_result_gtdb.tsv --threads 1
[2023-03-19 23:04:39,029] [INFO] Task succeeded: fastANI
[2023-03-19 23:04:39,032] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 23:04:39,032] [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_002348225.1	s__UBA2979 sp002348225	99.8254	439	566	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__UBA2979	95.0	99.11	99.11	0.88	0.88	2	conclusive
GCA_002725365.1	s__UBA2979 sp002725365	94.1524	397	566	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__UBA2979	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 23:04:39,032] [INFO] GTDB search result was written to OceanDNA-b15208/result_gtdb.tsv
[2023-03-19 23:04:39,032] [INFO] ===== GTDB Search completed =====
[2023-03-19 23:04:39,033] [INFO] DFAST_QC result json was written to OceanDNA-b15208/dqc_result.json
[2023-03-19 23:04:39,033] [INFO] DFAST_QC completed!
[2023-03-19 23:04:39,033] [INFO] Total running time: 0h0m54s