[2023-03-18 01:54:19,360] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:19,360] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:19,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e8c6aff-1e62-417b-981c-7f98c4636531/dqc_reference
[2023-03-18 01:54:20,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:20,448] [INFO] Task started: Prodigal
[2023-03-18 01:54:20,448] [INFO] Running command: cat /var/lib/cwl/stgea8554c9-907d-4576-b3d8-a07ced53c77a/OceanDNA-a133.fa | prodigal -d OceanDNA-a133/cds.fna -a OceanDNA-a133/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:22,341] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:22,341] [INFO] Task started: HMMsearch
[2023-03-18 01:54:22,341] [INFO] Running command: hmmsearch --tblout OceanDNA-a133/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e8c6aff-1e62-417b-981c-7f98c4636531/dqc_reference/reference_markers.hmm OceanDNA-a133/protein.faa > /dev/null
[2023-03-18 01:54:22,457] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:22,457] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgea8554c9-907d-4576-b3d8-a07ced53c77a/OceanDNA-a133.fa]
[2023-03-18 01:54:22,462] [INFO] Query marker FASTA was written to OceanDNA-a133/markers.fasta
[2023-03-18 01:54:22,464] [INFO] Task started: Blastn
[2023-03-18 01:54:22,464] [INFO] Running command: blastn -query OceanDNA-a133/markers.fasta -db /var/lib/cwl/stg4e8c6aff-1e62-417b-981c-7f98c4636531/dqc_reference/reference_markers.fasta -out OceanDNA-a133/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:22,929] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:22,943] [INFO] Selected 2 target genomes.
[2023-03-18 01:54:22,943] [INFO] Target genome list was writen to OceanDNA-a133/target_genomes.txt
[2023-03-18 01:54:22,944] [INFO] Task started: fastANI
[2023-03-18 01:54:22,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgea8554c9-907d-4576-b3d8-a07ced53c77a/OceanDNA-a133.fa --refList OceanDNA-a133/target_genomes.txt --output OceanDNA-a133/fastani_result.tsv --threads 1
[2023-03-18 01:54:23,431] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:23,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e8c6aff-1e62-417b-981c-7f98c4636531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:23,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e8c6aff-1e62-417b-981c-7f98c4636531/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:23,432] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:23,432] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:54:23,432] [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 01:54:23,443] [INFO] DFAST Taxonomy check result was written to OceanDNA-a133/tc_result.tsv
[2023-03-18 01:54:23,444] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:23,444] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:23,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e8c6aff-1e62-417b-981c-7f98c4636531/dqc_reference/checkm_data
[2023-03-18 01:54:23,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:23,471] [INFO] Task started: CheckM
[2023-03-18 01:54:23,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a133/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a133/checkm_input OceanDNA-a133/checkm_result
[2023-03-18 01:54:35,544] [INFO] Task succeeded: CheckM
[2023-03-18 01:54:35,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.09%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:54:35,567] [INFO] ===== Completeness check finished =====
[2023-03-18 01:54:35,567] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:54:35,567] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a133/markers.fasta)
[2023-03-18 01:54:35,568] [INFO] Task started: Blastn
[2023-03-18 01:54:35,569] [INFO] Running command: blastn -query OceanDNA-a133/markers.fasta -db /var/lib/cwl/stg4e8c6aff-1e62-417b-981c-7f98c4636531/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a133/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:36,095] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:36,098] [INFO] Selected 5 target genomes.
[2023-03-18 01:54:36,098] [INFO] Target genome list was writen to OceanDNA-a133/target_genomes_gtdb.txt
[2023-03-18 01:54:36,104] [INFO] Task started: fastANI
[2023-03-18 01:54:36,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgea8554c9-907d-4576-b3d8-a07ced53c77a/OceanDNA-a133.fa --refList OceanDNA-a133/target_genomes_gtdb.txt --output OceanDNA-a133/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:54:36,892] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:36,896] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:54:36,896] [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_018647405.1	s__Nitrosopelagicus sp018647405	86.4644	93	102	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	-
GCA_001510295.1	s__Nitrosopelagicus sp001510295	85.9512	68	102	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812185.1	s__Nitrosopelagicus brevis	84.8377	96	102	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.23	96.14	0.93	0.87	7	-
GCA_902511735.1	s__Nitrosopelagicus sp902511735	84.5523	62	102	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:54:36,919] [INFO] GTDB search result was written to OceanDNA-a133/result_gtdb.tsv
[2023-03-18 01:54:36,962] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:54:36,986] [INFO] DFAST_QC result json was written to OceanDNA-a133/dqc_result.json
[2023-03-18 01:54:36,986] [INFO] DFAST_QC completed!
[2023-03-18 01:54:36,986] [INFO] Total running time: 0h0m18s