[2023-03-19 01:13:44,315] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,315] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg70164f16-25d1-4cc9-83fc-7dac381a7d7f/dqc_reference
[2023-03-19 01:13:45,455] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,455] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,455] [INFO] Running command: cat /var/lib/cwl/stg028b8c71-bbf1-4b25-9bd8-e66c767b4def/OceanDNA-b21323.fa | prodigal -d OceanDNA-b21323/cds.fna -a OceanDNA-b21323/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:50,336] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:50,337] [INFO] Task started: HMMsearch
[2023-03-19 01:13:50,337] [INFO] Running command: hmmsearch --tblout OceanDNA-b21323/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70164f16-25d1-4cc9-83fc-7dac381a7d7f/dqc_reference/reference_markers.hmm OceanDNA-b21323/protein.faa > /dev/null
[2023-03-19 01:13:50,514] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:50,514] [INFO] Found 6/6 markers.
[2023-03-19 01:13:50,525] [INFO] Query marker FASTA was written to OceanDNA-b21323/markers.fasta
[2023-03-19 01:13:50,527] [INFO] Task started: Blastn
[2023-03-19 01:13:50,527] [INFO] Running command: blastn -query OceanDNA-b21323/markers.fasta -db /var/lib/cwl/stg70164f16-25d1-4cc9-83fc-7dac381a7d7f/dqc_reference/reference_markers.fasta -out OceanDNA-b21323/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:51,082] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:51,083] [INFO] Selected 23 target genomes.
[2023-03-19 01:13:51,083] [INFO] Target genome list was writen to OceanDNA-b21323/target_genomes.txt
[2023-03-19 01:13:51,097] [INFO] Task started: fastANI
[2023-03-19 01:13:51,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg028b8c71-bbf1-4b25-9bd8-e66c767b4def/OceanDNA-b21323.fa --refList OceanDNA-b21323/target_genomes.txt --output OceanDNA-b21323/fastani_result.tsv --threads 1
[2023-03-19 01:14:02,706] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:02,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70164f16-25d1-4cc9-83fc-7dac381a7d7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:02,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70164f16-25d1-4cc9-83fc-7dac381a7d7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:02,707] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:02,707] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:14:02,707] [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
--------------------------------------------------------------------------------
[2023-03-19 01:14:02,707] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21323/tc_result.tsv
[2023-03-19 01:14:02,707] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:02,707] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:02,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70164f16-25d1-4cc9-83fc-7dac381a7d7f/dqc_reference/checkm_data
[2023-03-19 01:14:02,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:02,842] [INFO] Task started: CheckM
[2023-03-19 01:14:02,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21323/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21323/checkm_input OceanDNA-b21323/checkm_result
[2023-03-19 01:14:21,156] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:21,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.84%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:21,158] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:21,158] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:21,158] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21323/markers.fasta)
[2023-03-19 01:14:21,159] [INFO] Task started: Blastn
[2023-03-19 01:14:21,159] [INFO] Running command: blastn -query OceanDNA-b21323/markers.fasta -db /var/lib/cwl/stg70164f16-25d1-4cc9-83fc-7dac381a7d7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21323/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:22,096] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:22,096] [INFO] Selected 27 target genomes.
[2023-03-19 01:14:22,097] [INFO] Target genome list was writen to OceanDNA-b21323/target_genomes_gtdb.txt
[2023-03-19 01:14:22,775] [INFO] Task started: fastANI
[2023-03-19 01:14:22,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg028b8c71-bbf1-4b25-9bd8-e66c767b4def/OceanDNA-b21323.fa --refList OceanDNA-b21323/target_genomes_gtdb.txt --output OceanDNA-b21323/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:33,712] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:33,717] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:33,717] [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_002697825.1	s__UBA8687 sp002697825	78.7305	92	239	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665625.1	s__UBA8687 sp018665625	78.6379	119	239	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873655.1	s__UBA8687 sp009873655	78.5795	157	239	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	99.50	99.47	0.94	0.93	3	-
GCA_013349585.1	s__UBA8687 sp013349585	78.413	122	239	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763735.1	s__UBA8687 sp016763735	78.0981	81	239	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721515.1	s__UBA8687 sp002721515	77.0849	80	239	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:33,717] [INFO] GTDB search result was written to OceanDNA-b21323/result_gtdb.tsv
[2023-03-19 01:14:33,717] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:33,718] [INFO] DFAST_QC result json was written to OceanDNA-b21323/dqc_result.json
[2023-03-19 01:14:33,718] [INFO] DFAST_QC completed!
[2023-03-19 01:14:33,718] [INFO] Total running time: 0h0m49s