[2023-03-18 04:30:02,790] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:30:02,790] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:30:02,790] [INFO] DQC Reference Directory: /var/lib/cwl/stgc532444b-b057-4a10-9167-ce69d94ff51f/dqc_reference
[2023-03-18 04:30:03,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:30:03,997] [INFO] Task started: Prodigal
[2023-03-18 04:30:03,997] [INFO] Running command: cat /var/lib/cwl/stgbe4fc396-9fc3-402a-8abd-f95006f756e3/OceanDNA-b46541.fa | prodigal -d OceanDNA-b46541/cds.fna -a OceanDNA-b46541/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:30:16,983] [INFO] Task succeeded: Prodigal
[2023-03-18 04:30:16,983] [INFO] Task started: HMMsearch
[2023-03-18 04:30:16,983] [INFO] Running command: hmmsearch --tblout OceanDNA-b46541/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc532444b-b057-4a10-9167-ce69d94ff51f/dqc_reference/reference_markers.hmm OceanDNA-b46541/protein.faa > /dev/null
[2023-03-18 04:30:17,126] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:30:17,127] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbe4fc396-9fc3-402a-8abd-f95006f756e3/OceanDNA-b46541.fa]
[2023-03-18 04:30:17,142] [INFO] Query marker FASTA was written to OceanDNA-b46541/markers.fasta
[2023-03-18 04:30:17,143] [INFO] Task started: Blastn
[2023-03-18 04:30:17,143] [INFO] Running command: blastn -query OceanDNA-b46541/markers.fasta -db /var/lib/cwl/stgc532444b-b057-4a10-9167-ce69d94ff51f/dqc_reference/reference_markers.fasta -out OceanDNA-b46541/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:30:17,575] [INFO] Task succeeded: Blastn
[2023-03-18 04:30:17,576] [INFO] Selected 9 target genomes.
[2023-03-18 04:30:17,576] [INFO] Target genome list was writen to OceanDNA-b46541/target_genomes.txt
[2023-03-18 04:30:17,581] [INFO] Task started: fastANI
[2023-03-18 04:30:17,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe4fc396-9fc3-402a-8abd-f95006f756e3/OceanDNA-b46541.fa --refList OceanDNA-b46541/target_genomes.txt --output OceanDNA-b46541/fastani_result.tsv --threads 1
[2023-03-18 04:30:21,444] [INFO] Task succeeded: fastANI
[2023-03-18 04:30:21,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc532444b-b057-4a10-9167-ce69d94ff51f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:30:21,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc532444b-b057-4a10-9167-ce69d94ff51f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:30:21,444] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:30:21,444] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:30:21,444] [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 04:30:21,445] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46541/tc_result.tsv
[2023-03-18 04:30:21,445] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:30:21,445] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:30:21,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc532444b-b057-4a10-9167-ce69d94ff51f/dqc_reference/checkm_data
[2023-03-18 04:30:21,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:30:21,451] [INFO] Task started: CheckM
[2023-03-18 04:30:21,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46541/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46541/checkm_input OceanDNA-b46541/checkm_result
[2023-03-18 04:30:58,674] [INFO] Task succeeded: CheckM
[2023-03-18 04:30:58,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:30:58,676] [INFO] ===== Completeness check finished =====
[2023-03-18 04:30:58,677] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:30:58,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46541/markers.fasta)
[2023-03-18 04:30:58,677] [INFO] Task started: Blastn
[2023-03-18 04:30:58,677] [INFO] Running command: blastn -query OceanDNA-b46541/markers.fasta -db /var/lib/cwl/stgc532444b-b057-4a10-9167-ce69d94ff51f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46541/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:30:59,300] [INFO] Task succeeded: Blastn
[2023-03-18 04:30:59,301] [INFO] Selected 16 target genomes.
[2023-03-18 04:30:59,301] [INFO] Target genome list was writen to OceanDNA-b46541/target_genomes_gtdb.txt
[2023-03-18 04:30:59,317] [INFO] Task started: fastANI
[2023-03-18 04:30:59,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe4fc396-9fc3-402a-8abd-f95006f756e3/OceanDNA-b46541.fa --refList OceanDNA-b46541/target_genomes_gtdb.txt --output OceanDNA-b46541/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:31:07,685] [INFO] Task succeeded: fastANI
[2023-03-18 04:31:07,688] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:31:07,688] [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_015660155.1	s__JACNJL01 sp015660155	82.7788	90	162	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239365.1	s__JACNJL01 sp014239365	82.033	121	162	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382585.1	s__JACNJL01 sp014382585	81.527	114	162	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:31:07,688] [INFO] GTDB search result was written to OceanDNA-b46541/result_gtdb.tsv
[2023-03-18 04:31:07,688] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:31:07,689] [INFO] DFAST_QC result json was written to OceanDNA-b46541/dqc_result.json
[2023-03-18 04:31:07,689] [INFO] DFAST_QC completed!
[2023-03-18 04:31:07,689] [INFO] Total running time: 0h1m5s