[2023-03-15 13:54:06,138] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:54:06,139] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:54:06,139] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d328e7d-3a8e-42ee-b126-c0041e13527f/dqc_reference
[2023-03-15 13:54:07,245] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:54:07,245] [INFO] Task started: Prodigal
[2023-03-15 13:54:07,245] [INFO] Running command: cat /var/lib/cwl/stg4312a28f-432f-43c0-b94e-b5d3f9ae01f5/OceanDNA-b4491.fa | prodigal -d OceanDNA-b4491/cds.fna -a OceanDNA-b4491/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:54:24,136] [INFO] Task succeeded: Prodigal
[2023-03-15 13:54:24,136] [INFO] Task started: HMMsearch
[2023-03-15 13:54:24,136] [INFO] Running command: hmmsearch --tblout OceanDNA-b4491/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d328e7d-3a8e-42ee-b126-c0041e13527f/dqc_reference/reference_markers.hmm OceanDNA-b4491/protein.faa > /dev/null
[2023-03-15 13:54:24,346] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:54:24,347] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4312a28f-432f-43c0-b94e-b5d3f9ae01f5/OceanDNA-b4491.fa]
[2023-03-15 13:54:24,393] [INFO] Query marker FASTA was written to OceanDNA-b4491/markers.fasta
[2023-03-15 13:54:24,394] [INFO] Task started: Blastn
[2023-03-15 13:54:24,395] [INFO] Running command: blastn -query OceanDNA-b4491/markers.fasta -db /var/lib/cwl/stg7d328e7d-3a8e-42ee-b126-c0041e13527f/dqc_reference/reference_markers.fasta -out OceanDNA-b4491/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:24,939] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:24,943] [INFO] Selected 23 target genomes.
[2023-03-15 13:54:24,943] [INFO] Target genome list was writen to OceanDNA-b4491/target_genomes.txt
[2023-03-15 13:54:24,968] [INFO] Task started: fastANI
[2023-03-15 13:54:24,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg4312a28f-432f-43c0-b94e-b5d3f9ae01f5/OceanDNA-b4491.fa --refList OceanDNA-b4491/target_genomes.txt --output OceanDNA-b4491/fastani_result.tsv --threads 1
[2023-03-15 13:54:39,911] [INFO] Task succeeded: fastANI
[2023-03-15 13:54:39,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d328e7d-3a8e-42ee-b126-c0041e13527f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:54:39,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d328e7d-3a8e-42ee-b126-c0041e13527f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:54:39,915] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:54:39,916] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:54:39,916] [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
Arcticibacterium luteifluviistationis	strain=SM1504	GCA_003258705.1	1784714	1784714	type	True	77.267	133	594	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:54:39,918] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4491/tc_result.tsv
[2023-03-15 13:54:39,922] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:54:39,922] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:54:39,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d328e7d-3a8e-42ee-b126-c0041e13527f/dqc_reference/checkm_data
[2023-03-15 13:54:39,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:54:39,931] [INFO] Task started: CheckM
[2023-03-15 13:54:39,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4491/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4491/checkm_input OceanDNA-b4491/checkm_result
[2023-03-15 13:55:22,912] [INFO] Task succeeded: CheckM
[2023-03-15 13:55:22,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.84%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:55:22,967] [INFO] ===== Completeness check finished =====
[2023-03-15 13:55:22,967] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:55:22,967] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4491/markers.fasta)
[2023-03-15 13:55:22,968] [INFO] Task started: Blastn
[2023-03-15 13:55:22,969] [INFO] Running command: blastn -query OceanDNA-b4491/markers.fasta -db /var/lib/cwl/stg7d328e7d-3a8e-42ee-b126-c0041e13527f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4491/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:55:23,777] [INFO] Task succeeded: Blastn
[2023-03-15 13:55:23,781] [INFO] Selected 26 target genomes.
[2023-03-15 13:55:23,781] [INFO] Target genome list was writen to OceanDNA-b4491/target_genomes_gtdb.txt
[2023-03-15 13:55:23,801] [INFO] Task started: fastANI
[2023-03-15 13:55:23,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg4312a28f-432f-43c0-b94e-b5d3f9ae01f5/OceanDNA-b4491.fa --refList OceanDNA-b4491/target_genomes_gtdb.txt --output OceanDNA-b4491/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:55:39,765] [INFO] Task succeeded: fastANI
[2023-03-15 13:55:39,767] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:55:39,768] [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
GCF_003258705.1	s__Arcticibacterium luteifluviistationis	77.267	133	594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:55:39,768] [INFO] GTDB search result was written to OceanDNA-b4491/result_gtdb.tsv
[2023-03-15 13:55:39,769] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:55:39,770] [INFO] DFAST_QC result json was written to OceanDNA-b4491/dqc_result.json
[2023-03-15 13:55:39,770] [INFO] DFAST_QC completed!
[2023-03-15 13:55:39,770] [INFO] Total running time: 0h1m34s