[2023-03-18 00:38:49,915] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:38:49,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:38:49,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg68706f1b-a3c1-4ad4-a8c0-bb026525da13/dqc_reference
[2023-03-18 00:38:51,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:38:51,109] [INFO] Task started: Prodigal
[2023-03-18 00:38:51,109] [INFO] Running command: cat /var/lib/cwl/stgc6b06bb8-8334-49ba-a846-70b6d4cd506b/OceanDNA-b20259.fa | prodigal -d OceanDNA-b20259/cds.fna -a OceanDNA-b20259/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:38:58,809] [INFO] Task succeeded: Prodigal
[2023-03-18 00:38:58,810] [INFO] Task started: HMMsearch
[2023-03-18 00:38:58,810] [INFO] Running command: hmmsearch --tblout OceanDNA-b20259/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68706f1b-a3c1-4ad4-a8c0-bb026525da13/dqc_reference/reference_markers.hmm OceanDNA-b20259/protein.faa > /dev/null
[2023-03-18 00:38:58,946] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:38:58,946] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc6b06bb8-8334-49ba-a846-70b6d4cd506b/OceanDNA-b20259.fa]
[2023-03-18 00:38:58,958] [INFO] Query marker FASTA was written to OceanDNA-b20259/markers.fasta
[2023-03-18 00:38:58,959] [INFO] Task started: Blastn
[2023-03-18 00:38:58,959] [INFO] Running command: blastn -query OceanDNA-b20259/markers.fasta -db /var/lib/cwl/stg68706f1b-a3c1-4ad4-a8c0-bb026525da13/dqc_reference/reference_markers.fasta -out OceanDNA-b20259/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:38:59,398] [INFO] Task succeeded: Blastn
[2023-03-18 00:38:59,398] [INFO] Selected 16 target genomes.
[2023-03-18 00:38:59,399] [INFO] Target genome list was writen to OceanDNA-b20259/target_genomes.txt
[2023-03-18 00:38:59,411] [INFO] Task started: fastANI
[2023-03-18 00:38:59,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b06bb8-8334-49ba-a846-70b6d4cd506b/OceanDNA-b20259.fa --refList OceanDNA-b20259/target_genomes.txt --output OceanDNA-b20259/fastani_result.tsv --threads 1
[2023-03-18 00:39:08,222] [INFO] Task succeeded: fastANI
[2023-03-18 00:39:08,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68706f1b-a3c1-4ad4-a8c0-bb026525da13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:39:08,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68706f1b-a3c1-4ad4-a8c0-bb026525da13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:39:08,223] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:39:08,223] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:39:08,223] [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 00:39:08,225] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20259/tc_result.tsv
[2023-03-18 00:39:08,225] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:39:08,225] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:39:08,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68706f1b-a3c1-4ad4-a8c0-bb026525da13/dqc_reference/checkm_data
[2023-03-18 00:39:08,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:39:08,259] [INFO] Task started: CheckM
[2023-03-18 00:39:08,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20259/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20259/checkm_input OceanDNA-b20259/checkm_result
[2023-03-18 00:39:32,382] [INFO] Task succeeded: CheckM
[2023-03-18 00:39:32,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:39:32,447] [INFO] ===== Completeness check finished =====
[2023-03-18 00:39:32,448] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:39:32,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20259/markers.fasta)
[2023-03-18 00:39:32,449] [INFO] Task started: Blastn
[2023-03-18 00:39:32,449] [INFO] Running command: blastn -query OceanDNA-b20259/markers.fasta -db /var/lib/cwl/stg68706f1b-a3c1-4ad4-a8c0-bb026525da13/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20259/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:39:32,881] [INFO] Task succeeded: Blastn
[2023-03-18 00:39:32,882] [INFO] Selected 19 target genomes.
[2023-03-18 00:39:32,882] [INFO] Target genome list was writen to OceanDNA-b20259/target_genomes_gtdb.txt
[2023-03-18 00:39:32,895] [INFO] Task started: fastANI
[2023-03-18 00:39:32,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b06bb8-8334-49ba-a846-70b6d4cd506b/OceanDNA-b20259.fa --refList OceanDNA-b20259/target_genomes_gtdb.txt --output OceanDNA-b20259/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:39:39,018] [INFO] Task succeeded: fastANI
[2023-03-18 00:39:39,020] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:39:39,020] [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_002718285.1	s__UBA2134 sp002718285	78.8013	175	497	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA2134	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:39:39,022] [INFO] GTDB search result was written to OceanDNA-b20259/result_gtdb.tsv
[2023-03-18 00:39:39,022] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:39:39,023] [INFO] DFAST_QC result json was written to OceanDNA-b20259/dqc_result.json
[2023-03-18 00:39:39,023] [INFO] DFAST_QC completed!
[2023-03-18 00:39:39,023] [INFO] Total running time: 0h0m49s