[2023-03-16 06:55:55,687] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:55:55,688] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:55:55,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a90d6a5-4fc5-42f7-ae72-b92bb2bebf00/dqc_reference
[2023-03-16 06:56:00,612] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:56:00,613] [INFO] Task started: Prodigal
[2023-03-16 06:56:00,613] [INFO] Running command: cat /var/lib/cwl/stg691fb504-5fd4-4f18-871c-e6773880a358/OceanDNA-b20346.fa | prodigal -d OceanDNA-b20346/cds.fna -a OceanDNA-b20346/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:56:10,215] [INFO] Task succeeded: Prodigal
[2023-03-16 06:56:10,216] [INFO] Task started: HMMsearch
[2023-03-16 06:56:10,216] [INFO] Running command: hmmsearch --tblout OceanDNA-b20346/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a90d6a5-4fc5-42f7-ae72-b92bb2bebf00/dqc_reference/reference_markers.hmm OceanDNA-b20346/protein.faa > /dev/null
[2023-03-16 06:56:10,424] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:56:10,425] [INFO] Found 6/6 markers.
[2023-03-16 06:56:10,443] [INFO] Query marker FASTA was written to OceanDNA-b20346/markers.fasta
[2023-03-16 06:56:10,453] [INFO] Task started: Blastn
[2023-03-16 06:56:10,453] [INFO] Running command: blastn -query OceanDNA-b20346/markers.fasta -db /var/lib/cwl/stg5a90d6a5-4fc5-42f7-ae72-b92bb2bebf00/dqc_reference/reference_markers.fasta -out OceanDNA-b20346/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:56:14,094] [INFO] Task succeeded: Blastn
[2023-03-16 06:56:14,096] [INFO] Selected 7 target genomes.
[2023-03-16 06:56:14,097] [INFO] Target genome list was writen to OceanDNA-b20346/target_genomes.txt
[2023-03-16 06:56:14,101] [INFO] Task started: fastANI
[2023-03-16 06:56:14,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg691fb504-5fd4-4f18-871c-e6773880a358/OceanDNA-b20346.fa --refList OceanDNA-b20346/target_genomes.txt --output OceanDNA-b20346/fastani_result.tsv --threads 1
[2023-03-16 06:56:18,198] [INFO] Task succeeded: fastANI
[2023-03-16 06:56:18,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a90d6a5-4fc5-42f7-ae72-b92bb2bebf00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:56:18,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a90d6a5-4fc5-42f7-ae72-b92bb2bebf00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:56:18,199] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:56:18,199] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:56:18,199] [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 06:56:18,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20346/tc_result.tsv
[2023-03-16 06:56:18,201] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:56:18,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:56:18,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a90d6a5-4fc5-42f7-ae72-b92bb2bebf00/dqc_reference/checkm_data
[2023-03-16 06:56:18,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:56:18,210] [INFO] Task started: CheckM
[2023-03-16 06:56:18,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20346/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20346/checkm_input OceanDNA-b20346/checkm_result
[2023-03-16 06:56:49,452] [INFO] Task succeeded: CheckM
[2023-03-16 06:56:49,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:56:49,508] [INFO] ===== Completeness check finished =====
[2023-03-16 06:56:49,508] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:56:49,508] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20346/markers.fasta)
[2023-03-16 06:56:49,509] [INFO] Task started: Blastn
[2023-03-16 06:56:49,509] [INFO] Running command: blastn -query OceanDNA-b20346/markers.fasta -db /var/lib/cwl/stg5a90d6a5-4fc5-42f7-ae72-b92bb2bebf00/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20346/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:56:50,382] [INFO] Task succeeded: Blastn
[2023-03-16 06:56:50,384] [INFO] Selected 26 target genomes.
[2023-03-16 06:56:50,385] [INFO] Target genome list was writen to OceanDNA-b20346/target_genomes_gtdb.txt
[2023-03-16 06:56:50,436] [INFO] Task started: fastANI
[2023-03-16 06:56:50,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg691fb504-5fd4-4f18-871c-e6773880a358/OceanDNA-b20346.fa --refList OceanDNA-b20346/target_genomes_gtdb.txt --output OceanDNA-b20346/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:57:01,600] [INFO] Task succeeded: fastANI
[2023-03-16 06:57:01,602] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:57:01,602] [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_002346675.1	s__AB-629-J13 sp002346675	76.72	111	572	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__AB-629-J13	95.0	99.90	99.90	0.66	0.66	2	-
--------------------------------------------------------------------------------
[2023-03-16 06:57:01,603] [INFO] GTDB search result was written to OceanDNA-b20346/result_gtdb.tsv
[2023-03-16 06:57:01,604] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:57:01,606] [INFO] DFAST_QC result json was written to OceanDNA-b20346/dqc_result.json
[2023-03-16 06:57:01,607] [INFO] DFAST_QC completed!
[2023-03-16 06:57:01,607] [INFO] Total running time: 0h1m6s