[2023-03-18 09:41:07,850] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,850] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,850] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbeffd9d-2ec0-4ac7-9f84-02a26a1a8f3b/dqc_reference
[2023-03-18 09:41:11,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:11,617] [INFO] Task started: Prodigal
[2023-03-18 09:41:11,617] [INFO] Running command: cat /var/lib/cwl/stg3d8d6436-4dfd-4d50-98dc-da8881c019f9/OceanDNA-b20972.fa | prodigal -d OceanDNA-b20972/cds.fna -a OceanDNA-b20972/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:32,931] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:32,932] [INFO] Task started: HMMsearch
[2023-03-18 09:41:32,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b20972/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbeffd9d-2ec0-4ac7-9f84-02a26a1a8f3b/dqc_reference/reference_markers.hmm OceanDNA-b20972/protein.faa > /dev/null
[2023-03-18 09:41:33,153] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:33,154] [INFO] Found 6/6 markers.
[2023-03-18 09:41:33,180] [INFO] Query marker FASTA was written to OceanDNA-b20972/markers.fasta
[2023-03-18 09:41:33,180] [INFO] Task started: Blastn
[2023-03-18 09:41:33,180] [INFO] Running command: blastn -query OceanDNA-b20972/markers.fasta -db /var/lib/cwl/stgbbeffd9d-2ec0-4ac7-9f84-02a26a1a8f3b/dqc_reference/reference_markers.fasta -out OceanDNA-b20972/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:36,107] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:36,108] [INFO] Selected 22 target genomes.
[2023-03-18 09:41:36,108] [INFO] Target genome list was writen to OceanDNA-b20972/target_genomes.txt
[2023-03-18 09:41:36,118] [INFO] Task started: fastANI
[2023-03-18 09:41:36,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8d6436-4dfd-4d50-98dc-da8881c019f9/OceanDNA-b20972.fa --refList OceanDNA-b20972/target_genomes.txt --output OceanDNA-b20972/fastani_result.tsv --threads 1
[2023-03-18 09:41:49,261] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:49,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbeffd9d-2ec0-4ac7-9f84-02a26a1a8f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:49,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbeffd9d-2ec0-4ac7-9f84-02a26a1a8f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:49,262] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:49,262] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:49,262] [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 09:41:49,263] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20972/tc_result.tsv
[2023-03-18 09:41:49,263] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:49,263] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:49,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbeffd9d-2ec0-4ac7-9f84-02a26a1a8f3b/dqc_reference/checkm_data
[2023-03-18 09:41:49,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:49,272] [INFO] Task started: CheckM
[2023-03-18 09:41:49,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20972/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20972/checkm_input OceanDNA-b20972/checkm_result
[2023-03-18 09:42:44,573] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:44,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:44,576] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:44,576] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:44,577] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20972/markers.fasta)
[2023-03-18 09:42:44,578] [INFO] Task started: Blastn
[2023-03-18 09:42:44,578] [INFO] Running command: blastn -query OceanDNA-b20972/markers.fasta -db /var/lib/cwl/stgbbeffd9d-2ec0-4ac7-9f84-02a26a1a8f3b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20972/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:45,352] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:45,354] [INFO] Selected 31 target genomes.
[2023-03-18 09:42:45,354] [INFO] Target genome list was writen to OceanDNA-b20972/target_genomes_gtdb.txt
[2023-03-18 09:42:45,402] [INFO] Task started: fastANI
[2023-03-18 09:42:45,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8d6436-4dfd-4d50-98dc-da8881c019f9/OceanDNA-b20972.fa --refList OceanDNA-b20972/target_genomes_gtdb.txt --output OceanDNA-b20972/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:43:03,498] [INFO] Task succeeded: fastANI
[2023-03-18 09:43:03,501] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:43:03,501] [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_002296975.1	s__UBA796 sp002296975	76.2216	81	1019	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA796;g__UBA796	95.0	99.43	99.40	0.83	0.82	3	-
GCA_002348535.1	s__UBA796 sp002348535	76.2136	96	1019	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA796;g__UBA796	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:43:03,501] [INFO] GTDB search result was written to OceanDNA-b20972/result_gtdb.tsv
[2023-03-18 09:43:03,501] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:43:03,502] [INFO] DFAST_QC result json was written to OceanDNA-b20972/dqc_result.json
[2023-03-18 09:43:03,502] [INFO] DFAST_QC completed!
[2023-03-18 09:43:03,502] [INFO] Total running time: 0h1m56s