[2023-03-14 13:37:57,149] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:37:57,149] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:37:57,149] [INFO] DQC Reference Directory: /var/lib/cwl/stgeae95976-73f0-41c9-8323-0c734942b363/dqc_reference
[2023-03-14 13:37:58,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:37:58,315] [INFO] Task started: Prodigal
[2023-03-14 13:37:58,315] [INFO] Running command: cat /var/lib/cwl/stg32e28fc2-87cd-403e-90f3-7c059005ca5e/OceanDNA-b42657.fa | prodigal -d OceanDNA-b42657/cds.fna -a OceanDNA-b42657/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:38:03,098] [INFO] Task succeeded: Prodigal
[2023-03-14 13:38:03,098] [INFO] Task started: HMMsearch
[2023-03-14 13:38:03,098] [INFO] Running command: hmmsearch --tblout OceanDNA-b42657/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeae95976-73f0-41c9-8323-0c734942b363/dqc_reference/reference_markers.hmm OceanDNA-b42657/protein.faa > /dev/null
[2023-03-14 13:38:03,242] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:38:03,243] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32e28fc2-87cd-403e-90f3-7c059005ca5e/OceanDNA-b42657.fa]
[2023-03-14 13:38:03,250] [INFO] Query marker FASTA was written to OceanDNA-b42657/markers.fasta
[2023-03-14 13:38:03,252] [INFO] Task started: Blastn
[2023-03-14 13:38:03,252] [INFO] Running command: blastn -query OceanDNA-b42657/markers.fasta -db /var/lib/cwl/stgeae95976-73f0-41c9-8323-0c734942b363/dqc_reference/reference_markers.fasta -out OceanDNA-b42657/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:03,789] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:03,791] [INFO] Selected 10 target genomes.
[2023-03-14 13:38:03,791] [INFO] Target genome list was writen to OceanDNA-b42657/target_genomes.txt
[2023-03-14 13:38:03,795] [INFO] Task started: fastANI
[2023-03-14 13:38:03,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e28fc2-87cd-403e-90f3-7c059005ca5e/OceanDNA-b42657.fa --refList OceanDNA-b42657/target_genomes.txt --output OceanDNA-b42657/fastani_result.tsv --threads 1
[2023-03-14 13:38:08,305] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:08,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeae95976-73f0-41c9-8323-0c734942b363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:38:08,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeae95976-73f0-41c9-8323-0c734942b363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:38:08,306] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:38:08,306] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:38:08,306] [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
--------------------------------------------------------------------------------
[2023-03-14 13:38:08,307] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42657/tc_result.tsv
[2023-03-14 13:38:08,307] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:38:08,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:38:08,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeae95976-73f0-41c9-8323-0c734942b363/dqc_reference/checkm_data
[2023-03-14 13:38:08,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:38:08,313] [INFO] Task started: CheckM
[2023-03-14 13:38:08,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42657/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42657/checkm_input OceanDNA-b42657/checkm_result
[2023-03-14 13:38:26,221] [INFO] Task succeeded: CheckM
[2023-03-14 13:38:26,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:38:26,223] [INFO] ===== Completeness check finished =====
[2023-03-14 13:38:26,223] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:38:26,224] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42657/markers.fasta)
[2023-03-14 13:38:26,224] [INFO] Task started: Blastn
[2023-03-14 13:38:26,224] [INFO] Running command: blastn -query OceanDNA-b42657/markers.fasta -db /var/lib/cwl/stgeae95976-73f0-41c9-8323-0c734942b363/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42657/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:26,879] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:26,880] [INFO] Selected 14 target genomes.
[2023-03-14 13:38:26,880] [INFO] Target genome list was writen to OceanDNA-b42657/target_genomes_gtdb.txt
[2023-03-14 13:38:26,910] [INFO] Task started: fastANI
[2023-03-14 13:38:26,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e28fc2-87cd-403e-90f3-7c059005ca5e/OceanDNA-b42657.fa --refList OceanDNA-b42657/target_genomes_gtdb.txt --output OceanDNA-b42657/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:38:29,303] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:29,308] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:38:29,309] [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_902535365.1	s__TMED112 sp902535365	95.1496	256	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.49	95.14	0.87	0.82	7	conclusive
GCA_902585315.1	s__TMED112 sp902585315	78.1229	75	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.21	96.04	0.78	0.78	6	-
GCA_902619265.1	s__TMED112 sp902619265	77.7734	87	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.88	96.64	0.91	0.88	6	-
GCA_002683115.1	s__TMED112 sp002683115	77.472	63	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213455.1	s__TMED112 sp003213455	77.2997	63	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002170245.2	s__TMED112 sp002170245	77.2393	89	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004321845.1	s__TMED112 sp004321845	77.2127	61	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:38:29,309] [INFO] GTDB search result was written to OceanDNA-b42657/result_gtdb.tsv
[2023-03-14 13:38:29,309] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:38:29,310] [INFO] DFAST_QC result json was written to OceanDNA-b42657/dqc_result.json
[2023-03-14 13:38:29,310] [INFO] DFAST_QC completed!
[2023-03-14 13:38:29,310] [INFO] Total running time: 0h0m32s