[2023-03-16 11:50:51,201] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:50:51,201] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:50:51,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg71c4ca98-985c-4682-ae4c-5e20f18e81d4/dqc_reference
[2023-03-16 11:50:54,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:50:54,101] [INFO] Task started: Prodigal
[2023-03-16 11:50:54,101] [INFO] Running command: cat /var/lib/cwl/stgc9466a59-e646-4452-bfc0-396af580c1f1/OceanDNA-b32830.fa | prodigal -d OceanDNA-b32830/cds.fna -a OceanDNA-b32830/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:50:58,558] [INFO] Task succeeded: Prodigal
[2023-03-16 11:50:58,558] [INFO] Task started: HMMsearch
[2023-03-16 11:50:58,558] [INFO] Running command: hmmsearch --tblout OceanDNA-b32830/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71c4ca98-985c-4682-ae4c-5e20f18e81d4/dqc_reference/reference_markers.hmm OceanDNA-b32830/protein.faa > /dev/null
[2023-03-16 11:50:58,741] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:50:58,742] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc9466a59-e646-4452-bfc0-396af580c1f1/OceanDNA-b32830.fa]
[2023-03-16 11:50:58,750] [INFO] Query marker FASTA was written to OceanDNA-b32830/markers.fasta
[2023-03-16 11:50:58,750] [INFO] Task started: Blastn
[2023-03-16 11:50:58,750] [INFO] Running command: blastn -query OceanDNA-b32830/markers.fasta -db /var/lib/cwl/stg71c4ca98-985c-4682-ae4c-5e20f18e81d4/dqc_reference/reference_markers.fasta -out OceanDNA-b32830/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:50:59,494] [INFO] Task succeeded: Blastn
[2023-03-16 11:50:59,494] [INFO] Selected 9 target genomes.
[2023-03-16 11:50:59,495] [INFO] Target genome list was writen to OceanDNA-b32830/target_genomes.txt
[2023-03-16 11:50:59,500] [INFO] Task started: fastANI
[2023-03-16 11:50:59,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9466a59-e646-4452-bfc0-396af580c1f1/OceanDNA-b32830.fa --refList OceanDNA-b32830/target_genomes.txt --output OceanDNA-b32830/fastani_result.tsv --threads 1
[2023-03-16 11:51:04,910] [INFO] Task succeeded: fastANI
[2023-03-16 11:51:04,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71c4ca98-985c-4682-ae4c-5e20f18e81d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:51:04,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71c4ca98-985c-4682-ae4c-5e20f18e81d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:51:04,911] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:51:04,911] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:51:04,911] [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 11:51:04,911] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32830/tc_result.tsv
[2023-03-16 11:51:04,911] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:51:04,911] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:51:04,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71c4ca98-985c-4682-ae4c-5e20f18e81d4/dqc_reference/checkm_data
[2023-03-16 11:51:04,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:51:04,916] [INFO] Task started: CheckM
[2023-03-16 11:51:04,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32830/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32830/checkm_input OceanDNA-b32830/checkm_result
[2023-03-16 11:51:21,446] [INFO] Task succeeded: CheckM
[2023-03-16 11:51:21,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.16%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 11:51:21,448] [INFO] ===== Completeness check finished =====
[2023-03-16 11:51:21,448] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:51:21,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32830/markers.fasta)
[2023-03-16 11:51:21,448] [INFO] Task started: Blastn
[2023-03-16 11:51:21,448] [INFO] Running command: blastn -query OceanDNA-b32830/markers.fasta -db /var/lib/cwl/stg71c4ca98-985c-4682-ae4c-5e20f18e81d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32830/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:51:22,096] [INFO] Task succeeded: Blastn
[2023-03-16 11:51:22,097] [INFO] Selected 12 target genomes.
[2023-03-16 11:51:22,097] [INFO] Target genome list was writen to OceanDNA-b32830/target_genomes_gtdb.txt
[2023-03-16 11:51:22,493] [INFO] Task started: fastANI
[2023-03-16 11:51:22,493] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9466a59-e646-4452-bfc0-396af580c1f1/OceanDNA-b32830.fa --refList OceanDNA-b32830/target_genomes_gtdb.txt --output OceanDNA-b32830/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:51:26,939] [INFO] Task succeeded: fastANI
[2023-03-16 11:51:26,941] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:51:26,941] [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_902562525.1	s__GCA-2728255 sp902562525	82.2332	128	257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7887;f__UBA7887;g__GCA-2728255	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728255.1	s__GCA-2728255 sp002728255	80.386	172	257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7887;f__UBA7887;g__GCA-2728255	95.0	99.54	99.54	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-16 11:51:26,942] [INFO] GTDB search result was written to OceanDNA-b32830/result_gtdb.tsv
[2023-03-16 11:51:26,942] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:51:26,942] [INFO] DFAST_QC result json was written to OceanDNA-b32830/dqc_result.json
[2023-03-16 11:51:26,942] [INFO] DFAST_QC completed!
[2023-03-16 11:51:26,943] [INFO] Total running time: 0h0m36s