[2023-03-14 11:33:34,937] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,937] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c64f50f-7827-40bf-97fc-c394a49d7d19/dqc_reference
[2023-03-14 11:33:36,225] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,225] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,225] [INFO] Running command: cat /var/lib/cwl/stg32b6cc6b-df8d-44b0-a1c9-875c3a10092a/OceanDNA-b21560.fa | prodigal -d OceanDNA-b21560/cds.fna -a OceanDNA-b21560/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:43,315] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:43,315] [INFO] Task started: HMMsearch
[2023-03-14 11:33:43,315] [INFO] Running command: hmmsearch --tblout OceanDNA-b21560/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c64f50f-7827-40bf-97fc-c394a49d7d19/dqc_reference/reference_markers.hmm OceanDNA-b21560/protein.faa > /dev/null
[2023-03-14 11:33:43,506] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:43,506] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32b6cc6b-df8d-44b0-a1c9-875c3a10092a/OceanDNA-b21560.fa]
[2023-03-14 11:33:43,514] [INFO] Query marker FASTA was written to OceanDNA-b21560/markers.fasta
[2023-03-14 11:33:43,514] [INFO] Task started: Blastn
[2023-03-14 11:33:43,514] [INFO] Running command: blastn -query OceanDNA-b21560/markers.fasta -db /var/lib/cwl/stg9c64f50f-7827-40bf-97fc-c394a49d7d19/dqc_reference/reference_markers.fasta -out OceanDNA-b21560/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:44,024] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:44,025] [INFO] Selected 14 target genomes.
[2023-03-14 11:33:44,025] [INFO] Target genome list was writen to OceanDNA-b21560/target_genomes.txt
[2023-03-14 11:33:44,033] [INFO] Task started: fastANI
[2023-03-14 11:33:44,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b6cc6b-df8d-44b0-a1c9-875c3a10092a/OceanDNA-b21560.fa --refList OceanDNA-b21560/target_genomes.txt --output OceanDNA-b21560/fastani_result.tsv --threads 1
[2023-03-14 11:33:50,595] [INFO] Task succeeded: fastANI
[2023-03-14 11:33:50,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c64f50f-7827-40bf-97fc-c394a49d7d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:33:50,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c64f50f-7827-40bf-97fc-c394a49d7d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:33:50,596] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:33:50,596] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:33:50,596] [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 11:33:50,596] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21560/tc_result.tsv
[2023-03-14 11:33:50,597] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:33:50,597] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:33:50,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c64f50f-7827-40bf-97fc-c394a49d7d19/dqc_reference/checkm_data
[2023-03-14 11:33:50,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:33:50,603] [INFO] Task started: CheckM
[2023-03-14 11:33:50,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21560/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21560/checkm_input OceanDNA-b21560/checkm_result
[2023-03-14 11:34:14,570] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:14,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:14,572] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:14,573] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:14,573] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21560/markers.fasta)
[2023-03-14 11:34:14,573] [INFO] Task started: Blastn
[2023-03-14 11:34:14,573] [INFO] Running command: blastn -query OceanDNA-b21560/markers.fasta -db /var/lib/cwl/stg9c64f50f-7827-40bf-97fc-c394a49d7d19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21560/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:15,230] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:15,231] [INFO] Selected 13 target genomes.
[2023-03-14 11:34:15,231] [INFO] Target genome list was writen to OceanDNA-b21560/target_genomes_gtdb.txt
[2023-03-14 11:34:15,269] [INFO] Task started: fastANI
[2023-03-14 11:34:15,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b6cc6b-df8d-44b0-a1c9-875c3a10092a/OceanDNA-b21560.fa --refList OceanDNA-b21560/target_genomes_gtdb.txt --output OceanDNA-b21560/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:34:19,028] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:19,030] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:34:19,031] [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_018662075.1	s__UBA2170 sp018662075	99.5387	223	285	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Peribacterales;f__Peribacteraceae;g__UBA2170	95.0	99.68	99.68	0.85	0.85	2	conclusive
GCA_002772815.1	s__UBA2170 sp002772815	79.7526	136	285	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Peribacterales;f__Peribacteraceae;g__UBA2170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018652955.1	s__UBA2170 sp018652955	78.2992	65	285	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__Peribacterales;f__Peribacteraceae;g__UBA2170	95.0	99.95	99.94	0.98	0.97	8	-
--------------------------------------------------------------------------------
[2023-03-14 11:34:19,031] [INFO] GTDB search result was written to OceanDNA-b21560/result_gtdb.tsv
[2023-03-14 11:34:19,031] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:34:19,031] [INFO] DFAST_QC result json was written to OceanDNA-b21560/dqc_result.json
[2023-03-14 11:34:19,032] [INFO] DFAST_QC completed!
[2023-03-14 11:34:19,032] [INFO] Total running time: 0h0m44s