[2023-03-15 09:48:18,546] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:18,547] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:18,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg4345faa6-7f6d-4f61-bb32-0a0d688df95d/dqc_reference
[2023-03-15 09:48:19,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:19,656] [INFO] Task started: Prodigal
[2023-03-15 09:48:19,657] [INFO] Running command: cat /var/lib/cwl/stg81092b0b-c559-4ca6-9e99-4a94a46d68c3/OceanDNA-b36303.fa | prodigal -d OceanDNA-b36303/cds.fna -a OceanDNA-b36303/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:24,048] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:24,048] [INFO] Task started: HMMsearch
[2023-03-15 09:48:24,049] [INFO] Running command: hmmsearch --tblout OceanDNA-b36303/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4345faa6-7f6d-4f61-bb32-0a0d688df95d/dqc_reference/reference_markers.hmm OceanDNA-b36303/protein.faa > /dev/null
[2023-03-15 09:48:24,258] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:24,259] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg81092b0b-c559-4ca6-9e99-4a94a46d68c3/OceanDNA-b36303.fa]
[2023-03-15 09:48:24,271] [INFO] Query marker FASTA was written to OceanDNA-b36303/markers.fasta
[2023-03-15 09:48:24,271] [INFO] Task started: Blastn
[2023-03-15 09:48:24,271] [INFO] Running command: blastn -query OceanDNA-b36303/markers.fasta -db /var/lib/cwl/stg4345faa6-7f6d-4f61-bb32-0a0d688df95d/dqc_reference/reference_markers.fasta -out OceanDNA-b36303/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:24,957] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:24,958] [INFO] Selected 19 target genomes.
[2023-03-15 09:48:24,958] [INFO] Target genome list was writen to OceanDNA-b36303/target_genomes.txt
[2023-03-15 09:48:24,970] [INFO] Task started: fastANI
[2023-03-15 09:48:24,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg81092b0b-c559-4ca6-9e99-4a94a46d68c3/OceanDNA-b36303.fa --refList OceanDNA-b36303/target_genomes.txt --output OceanDNA-b36303/fastani_result.tsv --threads 1
[2023-03-15 09:48:37,010] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:37,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4345faa6-7f6d-4f61-bb32-0a0d688df95d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:37,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4345faa6-7f6d-4f61-bb32-0a0d688df95d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:37,011] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:37,011] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:37,011] [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
--------------------------------------------------------------------------------
[2023-03-15 09:48:37,011] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36303/tc_result.tsv
[2023-03-15 09:48:37,011] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:37,012] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:37,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4345faa6-7f6d-4f61-bb32-0a0d688df95d/dqc_reference/checkm_data
[2023-03-15 09:48:37,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:37,017] [INFO] Task started: CheckM
[2023-03-15 09:48:37,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36303/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36303/checkm_input OceanDNA-b36303/checkm_result
[2023-03-15 09:48:55,073] [INFO] Task succeeded: CheckM
[2023-03-15 09:48:55,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:48:55,075] [INFO] ===== Completeness check finished =====
[2023-03-15 09:48:55,075] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:48:55,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36303/markers.fasta)
[2023-03-15 09:48:55,075] [INFO] Task started: Blastn
[2023-03-15 09:48:55,076] [INFO] Running command: blastn -query OceanDNA-b36303/markers.fasta -db /var/lib/cwl/stg4345faa6-7f6d-4f61-bb32-0a0d688df95d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36303/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:55,904] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:55,904] [INFO] Selected 16 target genomes.
[2023-03-15 09:48:55,905] [INFO] Target genome list was writen to OceanDNA-b36303/target_genomes_gtdb.txt
[2023-03-15 09:48:56,386] [INFO] Task started: fastANI
[2023-03-15 09:48:56,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg81092b0b-c559-4ca6-9e99-4a94a46d68c3/OceanDNA-b36303.fa --refList OceanDNA-b36303/target_genomes_gtdb.txt --output OceanDNA-b36303/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:04,537] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:04,540] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:04,540] [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_009711715.1	s__Methylophaga sp009711715	79.937	60	94	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762585.1	s__Methylophaga sp014762585	79.2608	51	94	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:04,540] [INFO] GTDB search result was written to OceanDNA-b36303/result_gtdb.tsv
[2023-03-15 09:49:04,540] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:04,540] [INFO] DFAST_QC result json was written to OceanDNA-b36303/dqc_result.json
[2023-03-15 09:49:04,541] [INFO] DFAST_QC completed!
[2023-03-15 09:49:04,541] [INFO] Total running time: 0h0m46s