[2023-03-18 01:59:39,785] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,786] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,786] [INFO] DQC Reference Directory: /var/lib/cwl/stga44f04df-914e-4c57-a355-ad7f5e043828/dqc_reference
[2023-03-18 01:59:40,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,952] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,952] [INFO] Running command: cat /var/lib/cwl/stge819acc4-b4bd-4b1a-ab06-c551a202d3d1/OceanDNA-b46556.fa | prodigal -d OceanDNA-b46556/cds.fna -a OceanDNA-b46556/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:51,798] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:51,798] [INFO] Task started: HMMsearch
[2023-03-18 01:59:51,799] [INFO] Running command: hmmsearch --tblout OceanDNA-b46556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga44f04df-914e-4c57-a355-ad7f5e043828/dqc_reference/reference_markers.hmm OceanDNA-b46556/protein.faa > /dev/null
[2023-03-18 01:59:51,940] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:51,941] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge819acc4-b4bd-4b1a-ab06-c551a202d3d1/OceanDNA-b46556.fa]
[2023-03-18 01:59:51,973] [INFO] Query marker FASTA was written to OceanDNA-b46556/markers.fasta
[2023-03-18 01:59:51,973] [INFO] Task started: Blastn
[2023-03-18 01:59:51,973] [INFO] Running command: blastn -query OceanDNA-b46556/markers.fasta -db /var/lib/cwl/stga44f04df-914e-4c57-a355-ad7f5e043828/dqc_reference/reference_markers.fasta -out OceanDNA-b46556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:52,421] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:52,424] [INFO] Selected 16 target genomes.
[2023-03-18 01:59:52,425] [INFO] Target genome list was writen to OceanDNA-b46556/target_genomes.txt
[2023-03-18 01:59:52,436] [INFO] Task started: fastANI
[2023-03-18 01:59:52,436] [INFO] Running command: fastANI --query /var/lib/cwl/stge819acc4-b4bd-4b1a-ab06-c551a202d3d1/OceanDNA-b46556.fa --refList OceanDNA-b46556/target_genomes.txt --output OceanDNA-b46556/fastani_result.tsv --threads 1
[2023-03-18 02:00:02,233] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:02,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga44f04df-914e-4c57-a355-ad7f5e043828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:02,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga44f04df-914e-4c57-a355-ad7f5e043828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:02,234] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:02,234] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:00:02,234] [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 02:00:02,235] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46556/tc_result.tsv
[2023-03-18 02:00:02,240] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:02,240] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:02,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga44f04df-914e-4c57-a355-ad7f5e043828/dqc_reference/checkm_data
[2023-03-18 02:00:02,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:02,276] [INFO] Task started: CheckM
[2023-03-18 02:00:02,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46556/checkm_input OceanDNA-b46556/checkm_result
[2023-03-18 02:00:35,371] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:35,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 9.26%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:35,402] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:35,403] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:35,403] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46556/markers.fasta)
[2023-03-18 02:00:35,404] [INFO] Task started: Blastn
[2023-03-18 02:00:35,404] [INFO] Running command: blastn -query OceanDNA-b46556/markers.fasta -db /var/lib/cwl/stga44f04df-914e-4c57-a355-ad7f5e043828/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:35,856] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:35,860] [INFO] Selected 16 target genomes.
[2023-03-18 02:00:35,860] [INFO] Target genome list was writen to OceanDNA-b46556/target_genomes_gtdb.txt
[2023-03-18 02:00:35,884] [INFO] Task started: fastANI
[2023-03-18 02:00:35,884] [INFO] Running command: fastANI --query /var/lib/cwl/stge819acc4-b4bd-4b1a-ab06-c551a202d3d1/OceanDNA-b46556.fa --refList OceanDNA-b46556/target_genomes_gtdb.txt --output OceanDNA-b46556/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:00:43,478] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:43,481] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:00:43,481] [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_014239365.1	s__JACNJL01 sp014239365	77.7593	75	199	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	77.6455	68	199	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 02:00:43,482] [INFO] GTDB search result was written to OceanDNA-b46556/result_gtdb.tsv
[2023-03-18 02:00:43,484] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:00:43,486] [INFO] DFAST_QC result json was written to OceanDNA-b46556/dqc_result.json
[2023-03-18 02:00:43,486] [INFO] DFAST_QC completed!
[2023-03-18 02:00:43,486] [INFO] Total running time: 0h1m4s