[2023-03-18 07:29:30,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3552758-1faa-47de-8080-203dd7ce23c1/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,934] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg95f6c6be-5d2c-453e-8088-3d7ff10046f6/OceanDNA-b19403.fa | prodigal -d OceanDNA-b19403/cds.fna -a OceanDNA-b19403/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:38,599] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:38,599] [INFO] Task started: HMMsearch
[2023-03-18 07:29:38,599] [INFO] Running command: hmmsearch --tblout OceanDNA-b19403/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3552758-1faa-47de-8080-203dd7ce23c1/dqc_reference/reference_markers.hmm OceanDNA-b19403/protein.faa > /dev/null
[2023-03-18 07:29:38,761] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:38,762] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg95f6c6be-5d2c-453e-8088-3d7ff10046f6/OceanDNA-b19403.fa]
[2023-03-18 07:29:38,774] [INFO] Query marker FASTA was written to OceanDNA-b19403/markers.fasta
[2023-03-18 07:29:38,774] [INFO] Task started: Blastn
[2023-03-18 07:29:38,774] [INFO] Running command: blastn -query OceanDNA-b19403/markers.fasta -db /var/lib/cwl/stgd3552758-1faa-47de-8080-203dd7ce23c1/dqc_reference/reference_markers.fasta -out OceanDNA-b19403/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:39,261] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:39,262] [INFO] Selected 5 target genomes.
[2023-03-18 07:29:39,262] [INFO] Target genome list was writen to OceanDNA-b19403/target_genomes.txt
[2023-03-18 07:29:39,265] [INFO] Task started: fastANI
[2023-03-18 07:29:39,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg95f6c6be-5d2c-453e-8088-3d7ff10046f6/OceanDNA-b19403.fa --refList OceanDNA-b19403/target_genomes.txt --output OceanDNA-b19403/fastani_result.tsv --threads 1
[2023-03-18 07:29:41,354] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:41,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3552758-1faa-47de-8080-203dd7ce23c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:41,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3552758-1faa-47de-8080-203dd7ce23c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:41,355] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:41,355] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:41,355] [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 07:29:41,355] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19403/tc_result.tsv
[2023-03-18 07:29:41,355] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:41,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:41,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3552758-1faa-47de-8080-203dd7ce23c1/dqc_reference/checkm_data
[2023-03-18 07:29:41,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:41,361] [INFO] Task started: CheckM
[2023-03-18 07:29:41,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19403/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19403/checkm_input OceanDNA-b19403/checkm_result
[2023-03-18 07:30:03,837] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:03,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:03,839] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:03,840] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:03,840] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19403/markers.fasta)
[2023-03-18 07:30:03,840] [INFO] Task started: Blastn
[2023-03-18 07:30:03,840] [INFO] Running command: blastn -query OceanDNA-b19403/markers.fasta -db /var/lib/cwl/stgd3552758-1faa-47de-8080-203dd7ce23c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19403/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:04,513] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:04,514] [INFO] Selected 18 target genomes.
[2023-03-18 07:30:04,514] [INFO] Target genome list was writen to OceanDNA-b19403/target_genomes_gtdb.txt
[2023-03-18 07:30:04,915] [INFO] Task started: fastANI
[2023-03-18 07:30:04,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg95f6c6be-5d2c-453e-8088-3d7ff10046f6/OceanDNA-b19403.fa --refList OceanDNA-b19403/target_genomes_gtdb.txt --output OceanDNA-b19403/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:11,532] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:11,536] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:30:11,536] [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_002724735.1	s__TMED108 sp002724735	99.1938	343	401	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002724475.1	s__TMED108 sp002724475	79.7647	205	401	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	97.60	97.08	0.73	0.61	4	-
GCA_002717765.1	s__TMED108 sp002717765	77.0523	65	401	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172545.1	s__TMED108 sp002172545	76.4938	72	401	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	99.45	99.45	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:11,536] [INFO] GTDB search result was written to OceanDNA-b19403/result_gtdb.tsv
[2023-03-18 07:30:11,536] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:11,537] [INFO] DFAST_QC result json was written to OceanDNA-b19403/dqc_result.json
[2023-03-18 07:30:11,537] [INFO] DFAST_QC completed!
[2023-03-18 07:30:11,537] [INFO] Total running time: 0h0m41s