[2023-03-16 17:54:39,736] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:54:39,737] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:54:39,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg72571927-76bd-41f6-8158-b27cc42c51dc/dqc_reference
[2023-03-16 17:54:42,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:54:42,074] [INFO] Task started: Prodigal
[2023-03-16 17:54:42,075] [INFO] Running command: cat /var/lib/cwl/stg181575df-4b63-444b-8956-00bcaa5047e3/OceanDNA-b46110.fa | prodigal -d OceanDNA-b46110/cds.fna -a OceanDNA-b46110/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:54:50,025] [INFO] Task succeeded: Prodigal
[2023-03-16 17:54:50,025] [INFO] Task started: HMMsearch
[2023-03-16 17:54:50,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b46110/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72571927-76bd-41f6-8158-b27cc42c51dc/dqc_reference/reference_markers.hmm OceanDNA-b46110/protein.faa > /dev/null
[2023-03-16 17:54:50,165] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:54:50,166] [INFO] Found 6/6 markers.
[2023-03-16 17:54:50,175] [INFO] Query marker FASTA was written to OceanDNA-b46110/markers.fasta
[2023-03-16 17:54:50,176] [INFO] Task started: Blastn
[2023-03-16 17:54:50,176] [INFO] Running command: blastn -query OceanDNA-b46110/markers.fasta -db /var/lib/cwl/stg72571927-76bd-41f6-8158-b27cc42c51dc/dqc_reference/reference_markers.fasta -out OceanDNA-b46110/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:54:50,689] [INFO] Task succeeded: Blastn
[2023-03-16 17:54:50,690] [INFO] Selected 9 target genomes.
[2023-03-16 17:54:50,691] [INFO] Target genome list was writen to OceanDNA-b46110/target_genomes.txt
[2023-03-16 17:54:50,698] [INFO] Task started: fastANI
[2023-03-16 17:54:50,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg181575df-4b63-444b-8956-00bcaa5047e3/OceanDNA-b46110.fa --refList OceanDNA-b46110/target_genomes.txt --output OceanDNA-b46110/fastani_result.tsv --threads 1
[2023-03-16 17:54:57,251] [INFO] Task succeeded: fastANI
[2023-03-16 17:54:57,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72571927-76bd-41f6-8158-b27cc42c51dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:54:57,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72571927-76bd-41f6-8158-b27cc42c51dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:54:57,252] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:54:57,252] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:54:57,252] [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 17:54:57,252] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46110/tc_result.tsv
[2023-03-16 17:54:57,252] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:54:57,253] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:54:57,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72571927-76bd-41f6-8158-b27cc42c51dc/dqc_reference/checkm_data
[2023-03-16 17:54:57,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:54:57,259] [INFO] Task started: CheckM
[2023-03-16 17:54:57,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46110/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46110/checkm_input OceanDNA-b46110/checkm_result
[2023-03-16 17:55:29,445] [INFO] Task succeeded: CheckM
[2023-03-16 17:55:29,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:55:29,448] [INFO] ===== Completeness check finished =====
[2023-03-16 17:55:29,448] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:55:29,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46110/markers.fasta)
[2023-03-16 17:55:29,449] [INFO] Task started: Blastn
[2023-03-16 17:55:29,449] [INFO] Running command: blastn -query OceanDNA-b46110/markers.fasta -db /var/lib/cwl/stg72571927-76bd-41f6-8158-b27cc42c51dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46110/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:55:30,192] [INFO] Task succeeded: Blastn
[2023-03-16 17:55:30,193] [INFO] Selected 21 target genomes.
[2023-03-16 17:55:30,193] [INFO] Target genome list was writen to OceanDNA-b46110/target_genomes_gtdb.txt
[2023-03-16 17:55:30,216] [INFO] Task started: fastANI
[2023-03-16 17:55:30,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg181575df-4b63-444b-8956-00bcaa5047e3/OceanDNA-b46110.fa --refList OceanDNA-b46110/target_genomes_gtdb.txt --output OceanDNA-b46110/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:55:40,775] [INFO] Task succeeded: fastANI
[2023-03-16 17:55:40,778] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:55:40,778] [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_011522825.1	s__GCA-2690565 sp011522825	95.7176	146	267	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__GCA-2690565	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002457235.1	s__GCA-2690565 sp002457235	82.086	126	267	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__GCA-2690565	95.0	99.55	99.48	0.94	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 17:55:40,779] [INFO] GTDB search result was written to OceanDNA-b46110/result_gtdb.tsv
[2023-03-16 17:55:40,779] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:55:40,780] [INFO] DFAST_QC result json was written to OceanDNA-b46110/dqc_result.json
[2023-03-16 17:55:40,780] [INFO] DFAST_QC completed!
[2023-03-16 17:55:40,780] [INFO] Total running time: 0h1m1s