[2023-03-16 18:18:12,618] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:18:12,618] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:18:12,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg3328fe6f-0eb5-48e4-972a-3027f81717c6/dqc_reference
[2023-03-16 18:18:13,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:18:13,719] [INFO] Task started: Prodigal
[2023-03-16 18:18:13,719] [INFO] Running command: cat /var/lib/cwl/stg150c3659-eba6-4087-8e35-3d2fdb235e86/OceanDNA-b13291.fa | prodigal -d OceanDNA-b13291/cds.fna -a OceanDNA-b13291/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:18:36,064] [INFO] Task succeeded: Prodigal
[2023-03-16 18:18:36,064] [INFO] Task started: HMMsearch
[2023-03-16 18:18:36,065] [INFO] Running command: hmmsearch --tblout OceanDNA-b13291/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3328fe6f-0eb5-48e4-972a-3027f81717c6/dqc_reference/reference_markers.hmm OceanDNA-b13291/protein.faa > /dev/null
[2023-03-16 18:18:36,491] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:18:36,491] [INFO] Found 6/6 markers.
[2023-03-16 18:18:36,513] [INFO] Query marker FASTA was written to OceanDNA-b13291/markers.fasta
[2023-03-16 18:18:36,522] [INFO] Task started: Blastn
[2023-03-16 18:18:36,522] [INFO] Running command: blastn -query OceanDNA-b13291/markers.fasta -db /var/lib/cwl/stg3328fe6f-0eb5-48e4-972a-3027f81717c6/dqc_reference/reference_markers.fasta -out OceanDNA-b13291/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:18:37,782] [INFO] Task succeeded: Blastn
[2023-03-16 18:18:37,783] [INFO] Selected 22 target genomes.
[2023-03-16 18:18:37,784] [INFO] Target genome list was writen to OceanDNA-b13291/target_genomes.txt
[2023-03-16 18:18:37,795] [INFO] Task started: fastANI
[2023-03-16 18:18:37,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg150c3659-eba6-4087-8e35-3d2fdb235e86/OceanDNA-b13291.fa --refList OceanDNA-b13291/target_genomes.txt --output OceanDNA-b13291/fastani_result.tsv --threads 1
[2023-03-16 18:18:53,563] [INFO] Task succeeded: fastANI
[2023-03-16 18:18:53,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3328fe6f-0eb5-48e4-972a-3027f81717c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:18:53,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3328fe6f-0eb5-48e4-972a-3027f81717c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:18:53,567] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:18:53,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:18:53,567] [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
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8555	64	801	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:18:53,568] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13291/tc_result.tsv
[2023-03-16 18:18:53,568] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:18:53,568] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:18:53,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3328fe6f-0eb5-48e4-972a-3027f81717c6/dqc_reference/checkm_data
[2023-03-16 18:18:53,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:18:53,611] [INFO] Task started: CheckM
[2023-03-16 18:18:53,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13291/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13291/checkm_input OceanDNA-b13291/checkm_result
[2023-03-16 18:19:32,463] [INFO] Task succeeded: CheckM
[2023-03-16 18:19:32,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:19:32,466] [INFO] ===== Completeness check finished =====
[2023-03-16 18:19:32,466] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:19:32,466] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13291/markers.fasta)
[2023-03-16 18:19:32,467] [INFO] Task started: Blastn
[2023-03-16 18:19:32,467] [INFO] Running command: blastn -query OceanDNA-b13291/markers.fasta -db /var/lib/cwl/stg3328fe6f-0eb5-48e4-972a-3027f81717c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13291/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:19:33,322] [INFO] Task succeeded: Blastn
[2023-03-16 18:19:33,323] [INFO] Selected 12 target genomes.
[2023-03-16 18:19:33,323] [INFO] Target genome list was writen to OceanDNA-b13291/target_genomes_gtdb.txt
[2023-03-16 18:19:33,442] [INFO] Task started: fastANI
[2023-03-16 18:19:33,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg150c3659-eba6-4087-8e35-3d2fdb235e86/OceanDNA-b13291.fa --refList OceanDNA-b13291/target_genomes_gtdb.txt --output OceanDNA-b13291/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:19:41,284] [INFO] Task succeeded: fastANI
[2023-03-16 18:19:41,287] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:19:41,288] [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_002311335.1	s__UBA1149 sp002311335	94.3019	695	801	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__UBA1149	95.0	98.21	98.21	0.88	0.88	2	-
GCA_012960245.1	s__UBA1149 sp012960245	93.2402	757	801	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__UBA1149	95.0	99.91	99.91	0.97	0.97	2	-
GCA_014382245.1	s__UBA1149 sp014382245	92.4603	706	801	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__UBA1149	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218925.1	s__CAITLU01 sp016218925	76.2549	60	801	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA1149;f__UBA1149;g__CAITLU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:19:41,288] [INFO] GTDB search result was written to OceanDNA-b13291/result_gtdb.tsv
[2023-03-16 18:19:41,288] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:19:41,289] [INFO] DFAST_QC result json was written to OceanDNA-b13291/dqc_result.json
[2023-03-16 18:19:41,289] [INFO] DFAST_QC completed!
[2023-03-16 18:19:41,289] [INFO] Total running time: 0h1m29s