[2023-03-15 10:49:28,600] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,600] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f1bdf95-737b-401b-a98e-eab44b179c90/dqc_reference
[2023-03-15 10:49:29,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,729] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,729] [INFO] Running command: cat /var/lib/cwl/stg9c87b8b5-1587-4cec-b229-d7d870c9478b/OceanDNA-b45442.fa | prodigal -d OceanDNA-b45442/cds.fna -a OceanDNA-b45442/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:51,811] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:51,812] [INFO] Task started: HMMsearch
[2023-03-15 10:49:51,812] [INFO] Running command: hmmsearch --tblout OceanDNA-b45442/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f1bdf95-737b-401b-a98e-eab44b179c90/dqc_reference/reference_markers.hmm OceanDNA-b45442/protein.faa > /dev/null
[2023-03-15 10:49:52,144] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:52,145] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9c87b8b5-1587-4cec-b229-d7d870c9478b/OceanDNA-b45442.fa]
[2023-03-15 10:49:52,167] [INFO] Query marker FASTA was written to OceanDNA-b45442/markers.fasta
[2023-03-15 10:49:52,167] [INFO] Task started: Blastn
[2023-03-15 10:49:52,167] [INFO] Running command: blastn -query OceanDNA-b45442/markers.fasta -db /var/lib/cwl/stg7f1bdf95-737b-401b-a98e-eab44b179c90/dqc_reference/reference_markers.fasta -out OceanDNA-b45442/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:52,736] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:52,737] [INFO] Selected 12 target genomes.
[2023-03-15 10:49:52,737] [INFO] Target genome list was writen to OceanDNA-b45442/target_genomes.txt
[2023-03-15 10:49:52,750] [INFO] Task started: fastANI
[2023-03-15 10:49:52,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c87b8b5-1587-4cec-b229-d7d870c9478b/OceanDNA-b45442.fa --refList OceanDNA-b45442/target_genomes.txt --output OceanDNA-b45442/fastani_result.tsv --threads 1
[2023-03-15 10:49:59,968] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:59,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f1bdf95-737b-401b-a98e-eab44b179c90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:59,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f1bdf95-737b-401b-a98e-eab44b179c90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:59,970] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:59,970] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:59,970] [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
--------------------------------------------------------------------------------
[2023-03-15 10:49:59,970] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45442/tc_result.tsv
[2023-03-15 10:49:59,970] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:59,970] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:59,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f1bdf95-737b-401b-a98e-eab44b179c90/dqc_reference/checkm_data
[2023-03-15 10:49:59,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:59,978] [INFO] Task started: CheckM
[2023-03-15 10:49:59,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45442/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45442/checkm_input OceanDNA-b45442/checkm_result
[2023-03-15 10:50:58,441] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:58,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:58,444] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:58,444] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:58,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45442/markers.fasta)
[2023-03-15 10:50:58,446] [INFO] Task started: Blastn
[2023-03-15 10:50:58,446] [INFO] Running command: blastn -query OceanDNA-b45442/markers.fasta -db /var/lib/cwl/stg7f1bdf95-737b-401b-a98e-eab44b179c90/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45442/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:59,368] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:59,369] [INFO] Selected 29 target genomes.
[2023-03-15 10:50:59,369] [INFO] Target genome list was writen to OceanDNA-b45442/target_genomes_gtdb.txt
[2023-03-15 10:50:59,402] [INFO] Task started: fastANI
[2023-03-15 10:50:59,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c87b8b5-1587-4cec-b229-d7d870c9478b/OceanDNA-b45442.fa --refList OceanDNA-b45442/target_genomes_gtdb.txt --output OceanDNA-b45442/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:51:13,478] [INFO] Task succeeded: fastANI
[2023-03-15 10:51:13,480] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:51:13,480] [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_018668635.1	s__JABJCN01 sp018668635	86.1932	575	690	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__JABJCN01;g__JABJCN01	95.0	99.52	99.29	0.87	0.84	6	-
--------------------------------------------------------------------------------
[2023-03-15 10:51:13,480] [INFO] GTDB search result was written to OceanDNA-b45442/result_gtdb.tsv
[2023-03-15 10:51:13,480] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:51:13,480] [INFO] DFAST_QC result json was written to OceanDNA-b45442/dqc_result.json
[2023-03-15 10:51:13,481] [INFO] DFAST_QC completed!
[2023-03-15 10:51:13,481] [INFO] Total running time: 0h1m45s