[2023-03-18 00:58:44,624] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg044dc6f5-552e-4ba8-9203-4a8f1dc0d21b/dqc_reference
[2023-03-18 00:58:46,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,296] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,296] [INFO] Running command: cat /var/lib/cwl/stg4019e75e-1d7c-4761-911e-38f4fd93231e/OceanDNA-b40853.fa | prodigal -d OceanDNA-b40853/cds.fna -a OceanDNA-b40853/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:59:01,311] [INFO] Task succeeded: Prodigal
[2023-03-18 00:59:01,312] [INFO] Task started: HMMsearch
[2023-03-18 00:59:01,312] [INFO] Running command: hmmsearch --tblout OceanDNA-b40853/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg044dc6f5-552e-4ba8-9203-4a8f1dc0d21b/dqc_reference/reference_markers.hmm OceanDNA-b40853/protein.faa > /dev/null
[2023-03-18 00:59:01,494] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:59:01,495] [INFO] Found 6/6 markers.
[2023-03-18 00:59:01,514] [INFO] Query marker FASTA was written to OceanDNA-b40853/markers.fasta
[2023-03-18 00:59:01,515] [INFO] Task started: Blastn
[2023-03-18 00:59:01,515] [INFO] Running command: blastn -query OceanDNA-b40853/markers.fasta -db /var/lib/cwl/stg044dc6f5-552e-4ba8-9203-4a8f1dc0d21b/dqc_reference/reference_markers.fasta -out OceanDNA-b40853/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:02,081] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:02,082] [INFO] Selected 19 target genomes.
[2023-03-18 00:59:02,082] [INFO] Target genome list was writen to OceanDNA-b40853/target_genomes.txt
[2023-03-18 00:59:02,092] [INFO] Task started: fastANI
[2023-03-18 00:59:02,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg4019e75e-1d7c-4761-911e-38f4fd93231e/OceanDNA-b40853.fa --refList OceanDNA-b40853/target_genomes.txt --output OceanDNA-b40853/fastani_result.tsv --threads 1
[2023-03-18 00:59:11,572] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:11,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg044dc6f5-552e-4ba8-9203-4a8f1dc0d21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:11,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg044dc6f5-552e-4ba8-9203-4a8f1dc0d21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:11,573] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:59:11,573] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:59:11,573] [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 00:59:11,574] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40853/tc_result.tsv
[2023-03-18 00:59:11,574] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:11,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:11,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg044dc6f5-552e-4ba8-9203-4a8f1dc0d21b/dqc_reference/checkm_data
[2023-03-18 00:59:11,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:11,619] [INFO] Task started: CheckM
[2023-03-18 00:59:11,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40853/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40853/checkm_input OceanDNA-b40853/checkm_result
[2023-03-18 00:59:51,880] [INFO] Task succeeded: CheckM
[2023-03-18 00:59:51,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:59:51,884] [INFO] ===== Completeness check finished =====
[2023-03-18 00:59:51,884] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:59:51,884] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40853/markers.fasta)
[2023-03-18 00:59:51,885] [INFO] Task started: Blastn
[2023-03-18 00:59:51,885] [INFO] Running command: blastn -query OceanDNA-b40853/markers.fasta -db /var/lib/cwl/stg044dc6f5-552e-4ba8-9203-4a8f1dc0d21b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40853/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:52,830] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:52,832] [INFO] Selected 25 target genomes.
[2023-03-18 00:59:52,832] [INFO] Target genome list was writen to OceanDNA-b40853/target_genomes_gtdb.txt
[2023-03-18 00:59:52,914] [INFO] Task started: fastANI
[2023-03-18 00:59:52,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg4019e75e-1d7c-4761-911e-38f4fd93231e/OceanDNA-b40853.fa --refList OceanDNA-b40853/target_genomes_gtdb.txt --output OceanDNA-b40853/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:00:06,440] [INFO] Task succeeded: fastANI
[2023-03-18 01:00:06,443] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:00:06,443] [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_002694855.1	s__UBA9145 sp002694855	97.381	621	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.18	97.28	0.74	0.66	6	conclusive
GCA_002712055.1	s__UBA9145 sp002712055	81.9344	456	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.31	99.25	0.77	0.70	5	-
GCA_012103535.1	s__UBA9145 sp012103535	76.716	67	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:00:06,444] [INFO] GTDB search result was written to OceanDNA-b40853/result_gtdb.tsv
[2023-03-18 01:00:06,444] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:00:06,445] [INFO] DFAST_QC result json was written to OceanDNA-b40853/dqc_result.json
[2023-03-18 01:00:06,445] [INFO] DFAST_QC completed!
[2023-03-18 01:00:06,445] [INFO] Total running time: 0h1m22s