[2023-03-17 04:15:14,747] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,747] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,747] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1705794-6599-4807-b994-4e0edb08737d/dqc_reference
[2023-03-17 04:15:16,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,097] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,097] [INFO] Running command: cat /var/lib/cwl/stg2ce9c03e-534a-435f-af73-e41ad9973d6b/OceanDNA-b28605.fa | prodigal -d OceanDNA-b28605/cds.fna -a OceanDNA-b28605/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:27,921] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:27,921] [INFO] Task started: HMMsearch
[2023-03-17 04:15:27,921] [INFO] Running command: hmmsearch --tblout OceanDNA-b28605/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1705794-6599-4807-b994-4e0edb08737d/dqc_reference/reference_markers.hmm OceanDNA-b28605/protein.faa > /dev/null
[2023-03-17 04:15:28,118] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:28,119] [INFO] Found 6/6 markers.
[2023-03-17 04:15:28,136] [INFO] Query marker FASTA was written to OceanDNA-b28605/markers.fasta
[2023-03-17 04:15:28,136] [INFO] Task started: Blastn
[2023-03-17 04:15:28,136] [INFO] Running command: blastn -query OceanDNA-b28605/markers.fasta -db /var/lib/cwl/stgd1705794-6599-4807-b994-4e0edb08737d/dqc_reference/reference_markers.fasta -out OceanDNA-b28605/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:28,712] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:28,713] [INFO] Selected 24 target genomes.
[2023-03-17 04:15:28,713] [INFO] Target genome list was writen to OceanDNA-b28605/target_genomes.txt
[2023-03-17 04:15:28,725] [INFO] Task started: fastANI
[2023-03-17 04:15:28,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce9c03e-534a-435f-af73-e41ad9973d6b/OceanDNA-b28605.fa --refList OceanDNA-b28605/target_genomes.txt --output OceanDNA-b28605/fastani_result.tsv --threads 1
[2023-03-17 04:15:43,108] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:43,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1705794-6599-4807-b994-4e0edb08737d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:43,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1705794-6599-4807-b994-4e0edb08737d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:43,112] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:43,112] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:43,112] [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
Pelagimonas varians	strain=DSM 23678	GCA_003208435.1	696760	696760	type	True	76.0958	50	588	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	76.0354	50	588	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	75.8542	59	588	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:43,112] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28605/tc_result.tsv
[2023-03-17 04:15:43,112] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:43,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:43,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1705794-6599-4807-b994-4e0edb08737d/dqc_reference/checkm_data
[2023-03-17 04:15:43,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:43,117] [INFO] Task started: CheckM
[2023-03-17 04:15:43,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28605/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28605/checkm_input OceanDNA-b28605/checkm_result
[2023-03-17 04:16:16,927] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:16,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.92%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:16,929] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:16,930] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:16,930] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28605/markers.fasta)
[2023-03-17 04:16:16,930] [INFO] Task started: Blastn
[2023-03-17 04:16:16,930] [INFO] Running command: blastn -query OceanDNA-b28605/markers.fasta -db /var/lib/cwl/stgd1705794-6599-4807-b994-4e0edb08737d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28605/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:17,803] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:17,804] [INFO] Selected 23 target genomes.
[2023-03-17 04:16:17,804] [INFO] Target genome list was writen to OceanDNA-b28605/target_genomes_gtdb.txt
[2023-03-17 04:16:18,056] [INFO] Task started: fastANI
[2023-03-17 04:16:18,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce9c03e-534a-435f-af73-e41ad9973d6b/OceanDNA-b28605.fa --refList OceanDNA-b28605/target_genomes_gtdb.txt --output OceanDNA-b28605/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:30,750] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:30,755] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:16:30,755] [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_009920815.1	s__HIMB11 sp009920815	97.6259	434	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009920225.1	s__HIMB11 sp009920225	79.0109	181	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852835.1	s__HIMB11 sp003486095	76.8652	86	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	98.02	97.17	0.82	0.75	18	-
GCA_018222665.1	s__HIMB11 sp018222665	76.8204	82	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000472185.1	s__HIMB11 sp000472185	76.6735	109	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	76.51	53	588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:30,755] [INFO] GTDB search result was written to OceanDNA-b28605/result_gtdb.tsv
[2023-03-17 04:16:30,755] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:30,756] [INFO] DFAST_QC result json was written to OceanDNA-b28605/dqc_result.json
[2023-03-17 04:16:30,756] [INFO] DFAST_QC completed!
[2023-03-17 04:16:30,756] [INFO] Total running time: 0h1m16s