[2023-03-18 08:55:17,487] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:17,487] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:17,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg375ce120-1c64-40d5-9418-c9dc2280b6ba/dqc_reference
[2023-03-18 08:55:18,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:18,646] [INFO] Task started: Prodigal
[2023-03-18 08:55:18,646] [INFO] Running command: cat /var/lib/cwl/stg1b72aae3-a25f-4dcd-b749-f4c3b8e0f18a/OceanDNA-b40479.fa | prodigal -d OceanDNA-b40479/cds.fna -a OceanDNA-b40479/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:35,541] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:35,541] [INFO] Task started: HMMsearch
[2023-03-18 08:55:35,541] [INFO] Running command: hmmsearch --tblout OceanDNA-b40479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg375ce120-1c64-40d5-9418-c9dc2280b6ba/dqc_reference/reference_markers.hmm OceanDNA-b40479/protein.faa > /dev/null
[2023-03-18 08:55:35,724] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:35,724] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1b72aae3-a25f-4dcd-b749-f4c3b8e0f18a/OceanDNA-b40479.fa]
[2023-03-18 08:55:35,740] [INFO] Query marker FASTA was written to OceanDNA-b40479/markers.fasta
[2023-03-18 08:55:35,741] [INFO] Task started: Blastn
[2023-03-18 08:55:35,741] [INFO] Running command: blastn -query OceanDNA-b40479/markers.fasta -db /var/lib/cwl/stg375ce120-1c64-40d5-9418-c9dc2280b6ba/dqc_reference/reference_markers.fasta -out OceanDNA-b40479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:55:36,376] [INFO] Task succeeded: Blastn
[2023-03-18 08:55:36,377] [INFO] Selected 30 target genomes.
[2023-03-18 08:55:36,377] [INFO] Target genome list was writen to OceanDNA-b40479/target_genomes.txt
[2023-03-18 08:55:36,393] [INFO] Task started: fastANI
[2023-03-18 08:55:36,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b72aae3-a25f-4dcd-b749-f4c3b8e0f18a/OceanDNA-b40479.fa --refList OceanDNA-b40479/target_genomes.txt --output OceanDNA-b40479/fastani_result.tsv --threads 1
[2023-03-18 08:55:53,973] [INFO] Task succeeded: fastANI
[2023-03-18 08:55:53,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg375ce120-1c64-40d5-9418-c9dc2280b6ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:55:53,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg375ce120-1c64-40d5-9418-c9dc2280b6ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:55:53,974] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:55:53,974] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:55:53,974] [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 08:55:53,975] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40479/tc_result.tsv
[2023-03-18 08:55:53,975] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:55:53,975] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:55:53,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg375ce120-1c64-40d5-9418-c9dc2280b6ba/dqc_reference/checkm_data
[2023-03-18 08:55:53,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:55:53,983] [INFO] Task started: CheckM
[2023-03-18 08:55:53,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40479/checkm_input OceanDNA-b40479/checkm_result
[2023-03-18 08:56:37,680] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:37,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:38,145] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:38,145] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:38,145] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40479/markers.fasta)
[2023-03-18 08:56:38,146] [INFO] Task started: Blastn
[2023-03-18 08:56:38,146] [INFO] Running command: blastn -query OceanDNA-b40479/markers.fasta -db /var/lib/cwl/stg375ce120-1c64-40d5-9418-c9dc2280b6ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:39,215] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:39,217] [INFO] Selected 21 target genomes.
[2023-03-18 08:56:39,217] [INFO] Target genome list was writen to OceanDNA-b40479/target_genomes_gtdb.txt
[2023-03-18 08:56:39,306] [INFO] Task started: fastANI
[2023-03-18 08:56:39,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b72aae3-a25f-4dcd-b749-f4c3b8e0f18a/OceanDNA-b40479.fa --refList OceanDNA-b40479/target_genomes_gtdb.txt --output OceanDNA-b40479/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:51,250] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:51,254] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:56:51,254] [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_002416505.1	s__UBA5078 sp002416505	99.9909	916	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903862645.1	s__UBA5078 sp903862645	77.2816	137	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802565.1	s__UBA5078 sp001802565	77.2609	170	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876785.1	s__UBA5078 sp903876785	77.234	126	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	99.18	99.13	0.80	0.78	4	-
GCA_903889815.1	s__UBA5078 sp903889815	77.1778	104	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:51,255] [INFO] GTDB search result was written to OceanDNA-b40479/result_gtdb.tsv
[2023-03-18 08:56:51,255] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:51,256] [INFO] DFAST_QC result json was written to OceanDNA-b40479/dqc_result.json
[2023-03-18 08:56:51,256] [INFO] DFAST_QC completed!
[2023-03-18 08:56:51,256] [INFO] Total running time: 0h1m34s