[2023-03-18 10:05:40,231] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:05:40,231] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:05:40,231] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b281f3f-43f3-49cf-b5f6-9ab6b8f062ca/dqc_reference
[2023-03-18 10:05:41,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:05:41,356] [INFO] Task started: Prodigal
[2023-03-18 10:05:41,356] [INFO] Running command: cat /var/lib/cwl/stg02e278fa-851c-4cbf-aac4-e65210dbe843/OceanDNA-b37194.fa | prodigal -d OceanDNA-b37194/cds.fna -a OceanDNA-b37194/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:05:58,376] [INFO] Task succeeded: Prodigal
[2023-03-18 10:05:58,376] [INFO] Task started: HMMsearch
[2023-03-18 10:05:58,376] [INFO] Running command: hmmsearch --tblout OceanDNA-b37194/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b281f3f-43f3-49cf-b5f6-9ab6b8f062ca/dqc_reference/reference_markers.hmm OceanDNA-b37194/protein.faa > /dev/null
[2023-03-18 10:05:58,584] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:05:58,584] [INFO] Found 6/6 markers.
[2023-03-18 10:05:58,625] [INFO] Query marker FASTA was written to OceanDNA-b37194/markers.fasta
[2023-03-18 10:05:58,627] [INFO] Task started: Blastn
[2023-03-18 10:05:58,627] [INFO] Running command: blastn -query OceanDNA-b37194/markers.fasta -db /var/lib/cwl/stg6b281f3f-43f3-49cf-b5f6-9ab6b8f062ca/dqc_reference/reference_markers.fasta -out OceanDNA-b37194/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:05:59,178] [INFO] Task succeeded: Blastn
[2023-03-18 10:05:59,184] [INFO] Selected 29 target genomes.
[2023-03-18 10:05:59,184] [INFO] Target genome list was writen to OceanDNA-b37194/target_genomes.txt
[2023-03-18 10:05:59,203] [INFO] Task started: fastANI
[2023-03-18 10:05:59,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg02e278fa-851c-4cbf-aac4-e65210dbe843/OceanDNA-b37194.fa --refList OceanDNA-b37194/target_genomes.txt --output OceanDNA-b37194/fastani_result.tsv --threads 1
[2023-03-18 10:06:18,412] [INFO] Task succeeded: fastANI
[2023-03-18 10:06:18,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b281f3f-43f3-49cf-b5f6-9ab6b8f062ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:06:18,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b281f3f-43f3-49cf-b5f6-9ab6b8f062ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:06:18,413] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:06:18,413] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:06:18,413] [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
--------------------------------------------------------------------------------
[2023-03-18 10:06:18,421] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37194/tc_result.tsv
[2023-03-18 10:06:18,440] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:06:18,441] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:06:18,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b281f3f-43f3-49cf-b5f6-9ab6b8f062ca/dqc_reference/checkm_data
[2023-03-18 10:06:18,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:06:18,450] [INFO] Task started: CheckM
[2023-03-18 10:06:18,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37194/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37194/checkm_input OceanDNA-b37194/checkm_result
[2023-03-18 10:07:03,544] [INFO] Task succeeded: CheckM
[2023-03-18 10:07:03,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:07:03,571] [INFO] ===== Completeness check finished =====
[2023-03-18 10:07:03,571] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:07:03,571] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37194/markers.fasta)
[2023-03-18 10:07:03,572] [INFO] Task started: Blastn
[2023-03-18 10:07:03,572] [INFO] Running command: blastn -query OceanDNA-b37194/markers.fasta -db /var/lib/cwl/stg6b281f3f-43f3-49cf-b5f6-9ab6b8f062ca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37194/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:07:04,419] [INFO] Task succeeded: Blastn
[2023-03-18 10:07:04,454] [INFO] Selected 20 target genomes.
[2023-03-18 10:07:04,454] [INFO] Target genome list was writen to OceanDNA-b37194/target_genomes_gtdb.txt
[2023-03-18 10:07:04,493] [INFO] Task started: fastANI
[2023-03-18 10:07:04,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg02e278fa-851c-4cbf-aac4-e65210dbe843/OceanDNA-b37194.fa --refList OceanDNA-b37194/target_genomes_gtdb.txt --output OceanDNA-b37194/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:07:18,504] [INFO] Task succeeded: fastANI
[2023-03-18 10:07:18,507] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:07:18,507] [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_018607725.1	s__UBA4582 sp002386885	99.2272	821	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	99.32	99.32	0.90	0.90	2	conclusive
GCA_002389265.1	s__UBA4582 sp002389265	91.2966	738	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	99.27	99.04	0.79	0.76	8	-
GCA_013204195.1	s__UBA4582 sp013204195	88.9406	563	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:07:18,509] [INFO] GTDB search result was written to OceanDNA-b37194/result_gtdb.tsv
[2023-03-18 10:07:18,510] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:07:18,513] [INFO] DFAST_QC result json was written to OceanDNA-b37194/dqc_result.json
[2023-03-18 10:07:18,513] [INFO] DFAST_QC completed!
[2023-03-18 10:07:18,513] [INFO] Total running time: 0h1m38s