[2023-03-15 06:28:21,500] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,500] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgb209a2f8-6e5d-492d-bfd8-5b0c46c8f0fe/dqc_reference
[2023-03-15 06:28:22,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,594] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,595] [INFO] Running command: cat /var/lib/cwl/stg1f5590c5-4774-48fb-8b65-a4780aa79865/OceanDNA-b3836.fa | prodigal -d OceanDNA-b3836/cds.fna -a OceanDNA-b3836/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:35,178] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:35,178] [INFO] Task started: HMMsearch
[2023-03-15 06:28:35,178] [INFO] Running command: hmmsearch --tblout OceanDNA-b3836/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb209a2f8-6e5d-492d-bfd8-5b0c46c8f0fe/dqc_reference/reference_markers.hmm OceanDNA-b3836/protein.faa > /dev/null
[2023-03-15 06:28:35,384] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:35,384] [INFO] Found 6/6 markers.
[2023-03-15 06:28:35,399] [INFO] Query marker FASTA was written to OceanDNA-b3836/markers.fasta
[2023-03-15 06:28:35,400] [INFO] Task started: Blastn
[2023-03-15 06:28:35,400] [INFO] Running command: blastn -query OceanDNA-b3836/markers.fasta -db /var/lib/cwl/stgb209a2f8-6e5d-492d-bfd8-5b0c46c8f0fe/dqc_reference/reference_markers.fasta -out OceanDNA-b3836/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:35,923] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:35,924] [INFO] Selected 27 target genomes.
[2023-03-15 06:28:35,924] [INFO] Target genome list was writen to OceanDNA-b3836/target_genomes.txt
[2023-03-15 06:28:35,940] [INFO] Task started: fastANI
[2023-03-15 06:28:35,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5590c5-4774-48fb-8b65-a4780aa79865/OceanDNA-b3836.fa --refList OceanDNA-b3836/target_genomes.txt --output OceanDNA-b3836/fastani_result.tsv --threads 1
[2023-03-15 06:28:51,802] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:51,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb209a2f8-6e5d-492d-bfd8-5b0c46c8f0fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:51,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb209a2f8-6e5d-492d-bfd8-5b0c46c8f0fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:51,802] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:51,803] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:51,803] [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 06:28:51,803] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3836/tc_result.tsv
[2023-03-15 06:28:51,803] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:51,803] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:51,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb209a2f8-6e5d-492d-bfd8-5b0c46c8f0fe/dqc_reference/checkm_data
[2023-03-15 06:28:51,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:51,814] [INFO] Task started: CheckM
[2023-03-15 06:28:51,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3836/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3836/checkm_input OceanDNA-b3836/checkm_result
[2023-03-15 06:29:27,081] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:27,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:27,112] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:27,112] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:27,112] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3836/markers.fasta)
[2023-03-15 06:29:27,113] [INFO] Task started: Blastn
[2023-03-15 06:29:27,113] [INFO] Running command: blastn -query OceanDNA-b3836/markers.fasta -db /var/lib/cwl/stgb209a2f8-6e5d-492d-bfd8-5b0c46c8f0fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3836/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:27,814] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:27,820] [INFO] Selected 30 target genomes.
[2023-03-15 06:29:27,820] [INFO] Target genome list was writen to OceanDNA-b3836/target_genomes_gtdb.txt
[2023-03-15 06:29:27,841] [INFO] Task started: fastANI
[2023-03-15 06:29:27,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5590c5-4774-48fb-8b65-a4780aa79865/OceanDNA-b3836.fa --refList OceanDNA-b3836/target_genomes_gtdb.txt --output OceanDNA-b3836/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:42,022] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:42,025] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:29:42,025] [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_016777395.1	s__JAFMKE01 sp016777395	93.2668	363	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA8649;g__JAFMKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853115.1	s__JAFMKE01 sp017853115	76.6647	81	610	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__UBA8649;g__JAFMKE01	95.0	99.30	99.30	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:42,029] [INFO] GTDB search result was written to OceanDNA-b3836/result_gtdb.tsv
[2023-03-15 06:29:42,034] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:42,037] [INFO] DFAST_QC result json was written to OceanDNA-b3836/dqc_result.json
[2023-03-15 06:29:42,037] [INFO] DFAST_QC completed!
[2023-03-15 06:29:42,037] [INFO] Total running time: 0h1m21s