[2023-03-19 04:29:37,757] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg48abd042-f3d4-4e9c-9cbc-b227c8d332ff/dqc_reference
[2023-03-19 04:29:38,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stge14664b5-e5f4-4759-abba-0b35d54a3c9e/OceanDNA-b17382.fa | prodigal -d OceanDNA-b17382/cds.fna -a OceanDNA-b17382/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:46,080] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:46,080] [INFO] Task started: HMMsearch
[2023-03-19 04:29:46,080] [INFO] Running command: hmmsearch --tblout OceanDNA-b17382/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48abd042-f3d4-4e9c-9cbc-b227c8d332ff/dqc_reference/reference_markers.hmm OceanDNA-b17382/protein.faa > /dev/null
[2023-03-19 04:29:46,249] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:46,249] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge14664b5-e5f4-4759-abba-0b35d54a3c9e/OceanDNA-b17382.fa]
[2023-03-19 04:29:46,260] [INFO] Query marker FASTA was written to OceanDNA-b17382/markers.fasta
[2023-03-19 04:29:46,260] [INFO] Task started: Blastn
[2023-03-19 04:29:46,260] [INFO] Running command: blastn -query OceanDNA-b17382/markers.fasta -db /var/lib/cwl/stg48abd042-f3d4-4e9c-9cbc-b227c8d332ff/dqc_reference/reference_markers.fasta -out OceanDNA-b17382/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:46,776] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:46,777] [INFO] Selected 21 target genomes.
[2023-03-19 04:29:46,777] [INFO] Target genome list was writen to OceanDNA-b17382/target_genomes.txt
[2023-03-19 04:29:46,788] [INFO] Task started: fastANI
[2023-03-19 04:29:46,788] [INFO] Running command: fastANI --query /var/lib/cwl/stge14664b5-e5f4-4759-abba-0b35d54a3c9e/OceanDNA-b17382.fa --refList OceanDNA-b17382/target_genomes.txt --output OceanDNA-b17382/fastani_result.tsv --threads 1
[2023-03-19 04:30:01,117] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:01,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48abd042-f3d4-4e9c-9cbc-b227c8d332ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:01,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48abd042-f3d4-4e9c-9cbc-b227c8d332ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:01,117] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:01,118] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:30:01,118] [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
--------------------------------------------------------------------------------
[2023-03-19 04:30:01,118] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17382/tc_result.tsv
[2023-03-19 04:30:01,118] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:01,118] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:01,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48abd042-f3d4-4e9c-9cbc-b227c8d332ff/dqc_reference/checkm_data
[2023-03-19 04:30:01,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:01,123] [INFO] Task started: CheckM
[2023-03-19 04:30:01,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17382/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17382/checkm_input OceanDNA-b17382/checkm_result
[2023-03-19 04:30:24,071] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:24,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:24,074] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:24,074] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:24,074] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17382/markers.fasta)
[2023-03-19 04:30:24,074] [INFO] Task started: Blastn
[2023-03-19 04:30:24,074] [INFO] Running command: blastn -query OceanDNA-b17382/markers.fasta -db /var/lib/cwl/stg48abd042-f3d4-4e9c-9cbc-b227c8d332ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17382/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:24,813] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:24,813] [INFO] Selected 21 target genomes.
[2023-03-19 04:30:24,814] [INFO] Target genome list was writen to OceanDNA-b17382/target_genomes_gtdb.txt
[2023-03-19 04:30:24,913] [INFO] Task started: fastANI
[2023-03-19 04:30:24,913] [INFO] Running command: fastANI --query /var/lib/cwl/stge14664b5-e5f4-4759-abba-0b35d54a3c9e/OceanDNA-b17382.fa --refList OceanDNA-b17382/target_genomes_gtdb.txt --output OceanDNA-b17382/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:35,405] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:35,407] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:35,407] [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_002346665.1	s__UBA2988 sp002346665	81.6294	279	388	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2988	95.0	99.85	99.85	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:35,408] [INFO] GTDB search result was written to OceanDNA-b17382/result_gtdb.tsv
[2023-03-19 04:30:35,408] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:35,408] [INFO] DFAST_QC result json was written to OceanDNA-b17382/dqc_result.json
[2023-03-19 04:30:35,408] [INFO] DFAST_QC completed!
[2023-03-19 04:30:35,408] [INFO] Total running time: 0h0m58s