[2023-03-15 07:29:11,758] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,758] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg74a2eaf8-f8f3-4dfd-a0da-5b8f7260688c/dqc_reference
[2023-03-15 07:29:13,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,589] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,589] [INFO] Running command: cat /var/lib/cwl/stg283beaa1-57aa-4e28-97d6-20c9625e0682/OceanDNA-b23505.fa | prodigal -d OceanDNA-b23505/cds.fna -a OceanDNA-b23505/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:23,492] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:23,493] [INFO] Task started: HMMsearch
[2023-03-15 07:29:23,493] [INFO] Running command: hmmsearch --tblout OceanDNA-b23505/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74a2eaf8-f8f3-4dfd-a0da-5b8f7260688c/dqc_reference/reference_markers.hmm OceanDNA-b23505/protein.faa > /dev/null
[2023-03-15 07:29:23,645] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:23,646] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg283beaa1-57aa-4e28-97d6-20c9625e0682/OceanDNA-b23505.fa]
[2023-03-15 07:29:23,662] [INFO] Query marker FASTA was written to OceanDNA-b23505/markers.fasta
[2023-03-15 07:29:23,662] [INFO] Task started: Blastn
[2023-03-15 07:29:23,662] [INFO] Running command: blastn -query OceanDNA-b23505/markers.fasta -db /var/lib/cwl/stg74a2eaf8-f8f3-4dfd-a0da-5b8f7260688c/dqc_reference/reference_markers.fasta -out OceanDNA-b23505/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:24,145] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:24,145] [INFO] Selected 5 target genomes.
[2023-03-15 07:29:24,146] [INFO] Target genome list was writen to OceanDNA-b23505/target_genomes.txt
[2023-03-15 07:29:24,149] [INFO] Task started: fastANI
[2023-03-15 07:29:24,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg283beaa1-57aa-4e28-97d6-20c9625e0682/OceanDNA-b23505.fa --refList OceanDNA-b23505/target_genomes.txt --output OceanDNA-b23505/fastani_result.tsv --threads 1
[2023-03-15 07:29:26,940] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:26,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74a2eaf8-f8f3-4dfd-a0da-5b8f7260688c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:26,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74a2eaf8-f8f3-4dfd-a0da-5b8f7260688c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:26,944] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:26,944] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:29:26,944] [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
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	75.9368	54	522	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	75.608	60	522	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:29:26,944] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23505/tc_result.tsv
[2023-03-15 07:29:26,944] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:26,944] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:26,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74a2eaf8-f8f3-4dfd-a0da-5b8f7260688c/dqc_reference/checkm_data
[2023-03-15 07:29:26,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:26,948] [INFO] Task started: CheckM
[2023-03-15 07:29:26,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23505/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23505/checkm_input OceanDNA-b23505/checkm_result
[2023-03-15 07:29:56,596] [INFO] Task succeeded: CheckM
[2023-03-15 07:29:56,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 5.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:29:56,599] [INFO] ===== Completeness check finished =====
[2023-03-15 07:29:56,599] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:29:56,599] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23505/markers.fasta)
[2023-03-15 07:29:56,600] [INFO] Task started: Blastn
[2023-03-15 07:29:56,600] [INFO] Running command: blastn -query OceanDNA-b23505/markers.fasta -db /var/lib/cwl/stg74a2eaf8-f8f3-4dfd-a0da-5b8f7260688c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23505/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:57,069] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:57,070] [INFO] Selected 5 target genomes.
[2023-03-15 07:29:57,070] [INFO] Target genome list was writen to OceanDNA-b23505/target_genomes_gtdb.txt
[2023-03-15 07:29:57,075] [INFO] Task started: fastANI
[2023-03-15 07:29:57,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg283beaa1-57aa-4e28-97d6-20c9625e0682/OceanDNA-b23505.fa --refList OceanDNA-b23505/target_genomes_gtdb.txt --output OceanDNA-b23505/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:00,171] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:00,175] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:30:00,175] [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_001854405.1	s__Henriciella sp001854405	78.1359	200	522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213785.1	s__Henriciella sp013213785	78.1149	199	522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	77.8931	205	522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:00,175] [INFO] GTDB search result was written to OceanDNA-b23505/result_gtdb.tsv
[2023-03-15 07:30:00,176] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:00,176] [INFO] DFAST_QC result json was written to OceanDNA-b23505/dqc_result.json
[2023-03-15 07:30:00,176] [INFO] DFAST_QC completed!
[2023-03-15 07:30:00,177] [INFO] Total running time: 0h0m48s