[2023-03-16 05:52:41,089] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,090] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,090] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb5494fa-3e22-45d6-a2a5-8167edbe830e/dqc_reference
[2023-03-16 05:52:42,230] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,230] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,230] [INFO] Running command: cat /var/lib/cwl/stg595d4813-4794-4846-aca7-ccf044adf23f/OceanDNA-b12088.fa | prodigal -d OceanDNA-b12088/cds.fna -a OceanDNA-b12088/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:56,388] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:56,388] [INFO] Task started: HMMsearch
[2023-03-16 05:52:56,388] [INFO] Running command: hmmsearch --tblout OceanDNA-b12088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb5494fa-3e22-45d6-a2a5-8167edbe830e/dqc_reference/reference_markers.hmm OceanDNA-b12088/protein.faa > /dev/null
[2023-03-16 05:52:56,561] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:56,561] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg595d4813-4794-4846-aca7-ccf044adf23f/OceanDNA-b12088.fa]
[2023-03-16 05:52:56,578] [INFO] Query marker FASTA was written to OceanDNA-b12088/markers.fasta
[2023-03-16 05:52:56,579] [INFO] Task started: Blastn
[2023-03-16 05:52:56,579] [INFO] Running command: blastn -query OceanDNA-b12088/markers.fasta -db /var/lib/cwl/stgbb5494fa-3e22-45d6-a2a5-8167edbe830e/dqc_reference/reference_markers.fasta -out OceanDNA-b12088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:57,121] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:57,122] [INFO] Selected 23 target genomes.
[2023-03-16 05:52:57,122] [INFO] Target genome list was writen to OceanDNA-b12088/target_genomes.txt
[2023-03-16 05:52:57,140] [INFO] Task started: fastANI
[2023-03-16 05:52:57,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg595d4813-4794-4846-aca7-ccf044adf23f/OceanDNA-b12088.fa --refList OceanDNA-b12088/target_genomes.txt --output OceanDNA-b12088/fastani_result.tsv --threads 1
[2023-03-16 05:53:12,719] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:12,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb5494fa-3e22-45d6-a2a5-8167edbe830e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:53:12,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb5494fa-3e22-45d6-a2a5-8167edbe830e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:53:12,720] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:53:12,720] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:53:12,720] [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
--------------------------------------------------------------------------------
[2023-03-16 05:53:12,721] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12088/tc_result.tsv
[2023-03-16 05:53:12,721] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:53:12,721] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:53:12,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb5494fa-3e22-45d6-a2a5-8167edbe830e/dqc_reference/checkm_data
[2023-03-16 05:53:12,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:53:12,760] [INFO] Task started: CheckM
[2023-03-16 05:53:12,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12088/checkm_input OceanDNA-b12088/checkm_result
[2023-03-16 05:53:53,271] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:53,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:53:53,284] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:53,284] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:53,284] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12088/markers.fasta)
[2023-03-16 05:53:53,285] [INFO] Task started: Blastn
[2023-03-16 05:53:53,285] [INFO] Running command: blastn -query OceanDNA-b12088/markers.fasta -db /var/lib/cwl/stgbb5494fa-3e22-45d6-a2a5-8167edbe830e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:53,961] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:53,963] [INFO] Selected 17 target genomes.
[2023-03-16 05:53:53,963] [INFO] Target genome list was writen to OceanDNA-b12088/target_genomes_gtdb.txt
[2023-03-16 05:53:53,980] [INFO] Task started: fastANI
[2023-03-16 05:53:53,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg595d4813-4794-4846-aca7-ccf044adf23f/OceanDNA-b12088.fa --refList OceanDNA-b12088/target_genomes_gtdb.txt --output OceanDNA-b12088/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:54:00,737] [INFO] Task succeeded: fastANI
[2023-03-16 05:54:00,742] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:54:00,742] [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_002339135.1	s__UBA974 sp002339135	99.6473	527	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015660615.1	s__UBA974 sp015660615	80.1987	260	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292405.1	s__UBA974 sp002292405	79.8225	291	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	99.64	99.64	0.67	0.67	2	-
GCA_018700255.1	s__UBA974 sp018700255	79.6074	260	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336655.1	s__UBA974 sp002336655	78.1234	93	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015663855.1	s__UBA974 sp012963975	77.5323	64	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	99.32	99.24	0.89	0.87	4	-
GCA_002700285.1	s__UBA974 sp002700285	77.3481	122	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA974	95.0	99.89	99.89	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-16 05:54:00,743] [INFO] GTDB search result was written to OceanDNA-b12088/result_gtdb.tsv
[2023-03-16 05:54:00,743] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:54:00,745] [INFO] DFAST_QC result json was written to OceanDNA-b12088/dqc_result.json
[2023-03-16 05:54:00,745] [INFO] DFAST_QC completed!
[2023-03-16 05:54:00,745] [INFO] Total running time: 0h1m20s