[2023-03-16 04:35:06,172] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:35:06,172] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:35:06,172] [INFO] DQC Reference Directory: /var/lib/cwl/stg564b547b-1192-46bb-af03-f95efee0796e/dqc_reference
[2023-03-16 04:35:07,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:35:07,275] [INFO] Task started: Prodigal
[2023-03-16 04:35:07,275] [INFO] Running command: cat /var/lib/cwl/stg2ed18162-d5e4-47f2-a167-5264b8877a86/OceanDNA-b45763.fa | prodigal -d OceanDNA-b45763/cds.fna -a OceanDNA-b45763/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:35:24,603] [INFO] Task succeeded: Prodigal
[2023-03-16 04:35:24,603] [INFO] Task started: HMMsearch
[2023-03-16 04:35:24,603] [INFO] Running command: hmmsearch --tblout OceanDNA-b45763/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg564b547b-1192-46bb-af03-f95efee0796e/dqc_reference/reference_markers.hmm OceanDNA-b45763/protein.faa > /dev/null
[2023-03-16 04:35:24,770] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:35:24,771] [INFO] Found 6/6 markers.
[2023-03-16 04:35:24,786] [INFO] Query marker FASTA was written to OceanDNA-b45763/markers.fasta
[2023-03-16 04:35:24,787] [INFO] Task started: Blastn
[2023-03-16 04:35:24,787] [INFO] Running command: blastn -query OceanDNA-b45763/markers.fasta -db /var/lib/cwl/stg564b547b-1192-46bb-af03-f95efee0796e/dqc_reference/reference_markers.fasta -out OceanDNA-b45763/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:35:25,294] [INFO] Task succeeded: Blastn
[2023-03-16 04:35:25,294] [INFO] Selected 12 target genomes.
[2023-03-16 04:35:25,294] [INFO] Target genome list was writen to OceanDNA-b45763/target_genomes.txt
[2023-03-16 04:35:25,300] [INFO] Task started: fastANI
[2023-03-16 04:35:25,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ed18162-d5e4-47f2-a167-5264b8877a86/OceanDNA-b45763.fa --refList OceanDNA-b45763/target_genomes.txt --output OceanDNA-b45763/fastani_result.tsv --threads 1
[2023-03-16 04:35:31,943] [INFO] Task succeeded: fastANI
[2023-03-16 04:35:31,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg564b547b-1192-46bb-af03-f95efee0796e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:35:31,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg564b547b-1192-46bb-af03-f95efee0796e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:35:31,944] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:35:31,944] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:35:31,944] [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
--------------------------------------------------------------------------------
[2023-03-16 04:35:31,947] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45763/tc_result.tsv
[2023-03-16 04:35:31,947] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:35:31,948] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:35:31,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg564b547b-1192-46bb-af03-f95efee0796e/dqc_reference/checkm_data
[2023-03-16 04:35:31,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:35:31,956] [INFO] Task started: CheckM
[2023-03-16 04:35:31,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45763/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45763/checkm_input OceanDNA-b45763/checkm_result
[2023-03-16 04:36:18,747] [INFO] Task succeeded: CheckM
[2023-03-16 04:36:18,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:36:18,753] [INFO] ===== Completeness check finished =====
[2023-03-16 04:36:18,753] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:36:18,753] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45763/markers.fasta)
[2023-03-16 04:36:18,753] [INFO] Task started: Blastn
[2023-03-16 04:36:18,754] [INFO] Running command: blastn -query OceanDNA-b45763/markers.fasta -db /var/lib/cwl/stg564b547b-1192-46bb-af03-f95efee0796e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45763/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:36:19,457] [INFO] Task succeeded: Blastn
[2023-03-16 04:36:19,458] [INFO] Selected 22 target genomes.
[2023-03-16 04:36:19,458] [INFO] Target genome list was writen to OceanDNA-b45763/target_genomes_gtdb.txt
[2023-03-16 04:36:19,480] [INFO] Task started: fastANI
[2023-03-16 04:36:19,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ed18162-d5e4-47f2-a167-5264b8877a86/OceanDNA-b45763.fa --refList OceanDNA-b45763/target_genomes_gtdb.txt --output OceanDNA-b45763/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:36:29,350] [INFO] Task succeeded: fastANI
[2023-03-16 04:36:29,353] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:36:29,353] [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_002686835.1	s__MB11C04 sp002686835	99.5905	574	676	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.34	99.34	0.82	0.82	2	conclusive
GCA_900299365.1	s__MB11C04 sp900299365	81.1969	271	676	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:36:29,353] [INFO] GTDB search result was written to OceanDNA-b45763/result_gtdb.tsv
[2023-03-16 04:36:29,353] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:36:29,353] [INFO] DFAST_QC result json was written to OceanDNA-b45763/dqc_result.json
[2023-03-16 04:36:29,354] [INFO] DFAST_QC completed!
[2023-03-16 04:36:29,354] [INFO] Total running time: 0h1m23s