[2023-03-17 08:20:27,847] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:20:27,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:20:27,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg731939c1-c0d8-4d71-a4f6-c4956e23bee6/dqc_reference
[2023-03-17 08:20:29,922] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:20:29,923] [INFO] Task started: Prodigal
[2023-03-17 08:20:29,923] [INFO] Running command: cat /var/lib/cwl/stgf12300d0-9e30-4b40-b5f3-c8834aeab7ad/OceanDNA-b44168.fa | prodigal -d OceanDNA-b44168/cds.fna -a OceanDNA-b44168/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:20:43,207] [INFO] Task succeeded: Prodigal
[2023-03-17 08:20:43,207] [INFO] Task started: HMMsearch
[2023-03-17 08:20:43,207] [INFO] Running command: hmmsearch --tblout OceanDNA-b44168/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg731939c1-c0d8-4d71-a4f6-c4956e23bee6/dqc_reference/reference_markers.hmm OceanDNA-b44168/protein.faa > /dev/null
[2023-03-17 08:20:43,403] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:20:43,404] [INFO] Found 6/6 markers.
[2023-03-17 08:20:43,419] [INFO] Query marker FASTA was written to OceanDNA-b44168/markers.fasta
[2023-03-17 08:20:43,419] [INFO] Task started: Blastn
[2023-03-17 08:20:43,419] [INFO] Running command: blastn -query OceanDNA-b44168/markers.fasta -db /var/lib/cwl/stg731939c1-c0d8-4d71-a4f6-c4956e23bee6/dqc_reference/reference_markers.fasta -out OceanDNA-b44168/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:20:43,984] [INFO] Task succeeded: Blastn
[2023-03-17 08:20:43,985] [INFO] Selected 27 target genomes.
[2023-03-17 08:20:43,985] [INFO] Target genome list was writen to OceanDNA-b44168/target_genomes.txt
[2023-03-17 08:20:44,026] [INFO] Task started: fastANI
[2023-03-17 08:20:44,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12300d0-9e30-4b40-b5f3-c8834aeab7ad/OceanDNA-b44168.fa --refList OceanDNA-b44168/target_genomes.txt --output OceanDNA-b44168/fastani_result.tsv --threads 1
[2023-03-17 08:20:59,630] [INFO] Task succeeded: fastANI
[2023-03-17 08:20:59,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg731939c1-c0d8-4d71-a4f6-c4956e23bee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:20:59,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg731939c1-c0d8-4d71-a4f6-c4956e23bee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:20:59,631] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:20:59,631] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:20:59,631] [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
--------------------------------------------------------------------------------
[2023-03-17 08:20:59,631] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44168/tc_result.tsv
[2023-03-17 08:20:59,631] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:20:59,632] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:20:59,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg731939c1-c0d8-4d71-a4f6-c4956e23bee6/dqc_reference/checkm_data
[2023-03-17 08:20:59,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:20:59,638] [INFO] Task started: CheckM
[2023-03-17 08:20:59,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44168/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44168/checkm_input OceanDNA-b44168/checkm_result
[2023-03-17 08:21:36,129] [INFO] Task succeeded: CheckM
[2023-03-17 08:21:36,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:21:36,360] [INFO] ===== Completeness check finished =====
[2023-03-17 08:21:36,360] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:21:36,360] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44168/markers.fasta)
[2023-03-17 08:21:36,361] [INFO] Task started: Blastn
[2023-03-17 08:21:36,362] [INFO] Running command: blastn -query OceanDNA-b44168/markers.fasta -db /var/lib/cwl/stg731939c1-c0d8-4d71-a4f6-c4956e23bee6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44168/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:21:37,264] [INFO] Task succeeded: Blastn
[2023-03-17 08:21:37,268] [INFO] Selected 12 target genomes.
[2023-03-17 08:21:37,268] [INFO] Target genome list was writen to OceanDNA-b44168/target_genomes_gtdb.txt
[2023-03-17 08:21:37,716] [INFO] Task started: fastANI
[2023-03-17 08:21:37,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12300d0-9e30-4b40-b5f3-c8834aeab7ad/OceanDNA-b44168.fa --refList OceanDNA-b44168/target_genomes_gtdb.txt --output OceanDNA-b44168/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:21:43,005] [INFO] Task succeeded: fastANI
[2023-03-17 08:21:43,009] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:21:43,010] [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_002292815.1	s__UBA7359 sp002292815	99.9699	772	803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.97	99.97	0.97	0.97	2	conclusive
GCA_905182825.1	s__UBA7359 sp905182825	80.8999	315	803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470825.1	s__UBA7359 sp002470825	80.3701	362	803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.91	99.91	0.91	0.91	2	-
GCA_012960105.1	s__UBA7359 sp012960105	77.3906	171	803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.96	99.96	0.93	0.93	2	-
GCA_013112535.1	s__UBA7359 sp013112535	77.1917	185	803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:21:43,011] [INFO] GTDB search result was written to OceanDNA-b44168/result_gtdb.tsv
[2023-03-17 08:21:43,013] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:21:43,015] [INFO] DFAST_QC result json was written to OceanDNA-b44168/dqc_result.json
[2023-03-17 08:21:43,015] [INFO] DFAST_QC completed!
[2023-03-17 08:21:43,015] [INFO] Total running time: 0h1m15s