[2023-03-16 23:55:45,757] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:55:45,763] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:55:45,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg588777a2-7874-484a-ab8c-0023cd4b2098/dqc_reference
[2023-03-16 23:55:46,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:55:46,852] [INFO] Task started: Prodigal
[2023-03-16 23:55:46,852] [INFO] Running command: cat /var/lib/cwl/stgb3b0e272-4210-4b17-a630-ea689a6b9cc7/OceanDNA-b41333.fa | prodigal -d OceanDNA-b41333/cds.fna -a OceanDNA-b41333/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:55:59,599] [INFO] Task succeeded: Prodigal
[2023-03-16 23:55:59,599] [INFO] Task started: HMMsearch
[2023-03-16 23:55:59,599] [INFO] Running command: hmmsearch --tblout OceanDNA-b41333/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg588777a2-7874-484a-ab8c-0023cd4b2098/dqc_reference/reference_markers.hmm OceanDNA-b41333/protein.faa > /dev/null
[2023-03-16 23:55:59,788] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:55:59,789] [INFO] Found 6/6 markers.
[2023-03-16 23:55:59,834] [INFO] Query marker FASTA was written to OceanDNA-b41333/markers.fasta
[2023-03-16 23:55:59,835] [INFO] Task started: Blastn
[2023-03-16 23:55:59,836] [INFO] Running command: blastn -query OceanDNA-b41333/markers.fasta -db /var/lib/cwl/stg588777a2-7874-484a-ab8c-0023cd4b2098/dqc_reference/reference_markers.fasta -out OceanDNA-b41333/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:56:00,457] [INFO] Task succeeded: Blastn
[2023-03-16 23:56:00,466] [INFO] Selected 38 target genomes.
[2023-03-16 23:56:00,466] [INFO] Target genome list was writen to OceanDNA-b41333/target_genomes.txt
[2023-03-16 23:56:00,491] [INFO] Task started: fastANI
[2023-03-16 23:56:00,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3b0e272-4210-4b17-a630-ea689a6b9cc7/OceanDNA-b41333.fa --refList OceanDNA-b41333/target_genomes.txt --output OceanDNA-b41333/fastani_result.tsv --threads 1
[2023-03-16 23:56:28,084] [INFO] Task succeeded: fastANI
[2023-03-16 23:56:28,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg588777a2-7874-484a-ab8c-0023cd4b2098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:56:28,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg588777a2-7874-484a-ab8c-0023cd4b2098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:56:28,089] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:56:28,089] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:56:28,089] [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
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.227	73	655	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	76.9933	79	655	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:56:28,107] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41333/tc_result.tsv
[2023-03-16 23:56:28,142] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:56:28,142] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:56:28,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg588777a2-7874-484a-ab8c-0023cd4b2098/dqc_reference/checkm_data
[2023-03-16 23:56:28,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:56:28,183] [INFO] Task started: CheckM
[2023-03-16 23:56:28,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41333/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41333/checkm_input OceanDNA-b41333/checkm_result
[2023-03-16 23:57:04,487] [INFO] Task succeeded: CheckM
[2023-03-16 23:57:04,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:57:04,897] [INFO] ===== Completeness check finished =====
[2023-03-16 23:57:04,897] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:57:04,897] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41333/markers.fasta)
[2023-03-16 23:57:04,898] [INFO] Task started: Blastn
[2023-03-16 23:57:04,898] [INFO] Running command: blastn -query OceanDNA-b41333/markers.fasta -db /var/lib/cwl/stg588777a2-7874-484a-ab8c-0023cd4b2098/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41333/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:57:05,899] [INFO] Task succeeded: Blastn
[2023-03-16 23:57:05,957] [INFO] Selected 35 target genomes.
[2023-03-16 23:57:05,957] [INFO] Target genome list was writen to OceanDNA-b41333/target_genomes_gtdb.txt
[2023-03-16 23:57:06,759] [INFO] Task started: fastANI
[2023-03-16 23:57:06,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3b0e272-4210-4b17-a630-ea689a6b9cc7/OceanDNA-b41333.fa --refList OceanDNA-b41333/target_genomes_gtdb.txt --output OceanDNA-b41333/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:57:29,912] [INFO] Task succeeded: fastANI
[2023-03-16 23:57:29,915] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:57:29,915] [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_002723385.1	s__Oceanobacter sp002723385	79.8707	272	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	99.82	99.82	0.84	0.84	2	-
GCF_000422845.1	s__Oceanobacter kriegii	76.9933	79	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785795.1	s__UBA2009 sp002335285	76.5816	52	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
--------------------------------------------------------------------------------
[2023-03-16 23:57:29,920] [INFO] GTDB search result was written to OceanDNA-b41333/result_gtdb.tsv
[2023-03-16 23:57:29,926] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:57:29,932] [INFO] DFAST_QC result json was written to OceanDNA-b41333/dqc_result.json
[2023-03-16 23:57:29,932] [INFO] DFAST_QC completed!
[2023-03-16 23:57:29,932] [INFO] Total running time: 0h1m44s