[2023-03-16 01:12:29,294] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,304] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,304] [INFO] DQC Reference Directory: /var/lib/cwl/stge67ff1e9-3e22-41e0-bc04-c0251ab1a334/dqc_reference
[2023-03-16 01:12:30,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,461] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stgcacfccff-875b-4dc4-b0d7-0eff3ecd1336/OceanDNA-b11706.fa | prodigal -d OceanDNA-b11706/cds.fna -a OceanDNA-b11706/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:49,588] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:49,588] [INFO] Task started: HMMsearch
[2023-03-16 01:12:49,588] [INFO] Running command: hmmsearch --tblout OceanDNA-b11706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge67ff1e9-3e22-41e0-bc04-c0251ab1a334/dqc_reference/reference_markers.hmm OceanDNA-b11706/protein.faa > /dev/null
[2023-03-16 01:12:49,764] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:49,765] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcacfccff-875b-4dc4-b0d7-0eff3ecd1336/OceanDNA-b11706.fa]
[2023-03-16 01:12:49,778] [INFO] Query marker FASTA was written to OceanDNA-b11706/markers.fasta
[2023-03-16 01:12:49,779] [INFO] Task started: Blastn
[2023-03-16 01:12:49,779] [INFO] Running command: blastn -query OceanDNA-b11706/markers.fasta -db /var/lib/cwl/stge67ff1e9-3e22-41e0-bc04-c0251ab1a334/dqc_reference/reference_markers.fasta -out OceanDNA-b11706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:50,329] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:50,329] [INFO] Selected 25 target genomes.
[2023-03-16 01:12:50,330] [INFO] Target genome list was writen to OceanDNA-b11706/target_genomes.txt
[2023-03-16 01:12:50,428] [INFO] Task started: fastANI
[2023-03-16 01:12:50,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacfccff-875b-4dc4-b0d7-0eff3ecd1336/OceanDNA-b11706.fa --refList OceanDNA-b11706/target_genomes.txt --output OceanDNA-b11706/fastani_result.tsv --threads 1
[2023-03-16 01:13:05,886] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:05,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge67ff1e9-3e22-41e0-bc04-c0251ab1a334/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:13:05,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge67ff1e9-3e22-41e0-bc04-c0251ab1a334/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:13:05,887] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:13:05,887] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:13:05,887] [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 01:13:05,887] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11706/tc_result.tsv
[2023-03-16 01:13:05,887] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:13:05,887] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:13:05,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge67ff1e9-3e22-41e0-bc04-c0251ab1a334/dqc_reference/checkm_data
[2023-03-16 01:13:05,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:13:05,894] [INFO] Task started: CheckM
[2023-03-16 01:13:05,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11706/checkm_input OceanDNA-b11706/checkm_result
[2023-03-16 01:13:58,842] [INFO] Task succeeded: CheckM
[2023-03-16 01:13:58,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:13:58,845] [INFO] ===== Completeness check finished =====
[2023-03-16 01:13:58,846] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:13:58,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11706/markers.fasta)
[2023-03-16 01:13:58,847] [INFO] Task started: Blastn
[2023-03-16 01:13:58,847] [INFO] Running command: blastn -query OceanDNA-b11706/markers.fasta -db /var/lib/cwl/stge67ff1e9-3e22-41e0-bc04-c0251ab1a334/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:13:59,702] [INFO] Task succeeded: Blastn
[2023-03-16 01:13:59,703] [INFO] Selected 16 target genomes.
[2023-03-16 01:13:59,703] [INFO] Target genome list was writen to OceanDNA-b11706/target_genomes_gtdb.txt
[2023-03-16 01:13:59,928] [INFO] Task started: fastANI
[2023-03-16 01:13:59,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacfccff-875b-4dc4-b0d7-0eff3ecd1336/OceanDNA-b11706.fa --refList OceanDNA-b11706/target_genomes_gtdb.txt --output OceanDNA-b11706/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:14:06,882] [INFO] Task succeeded: fastANI
[2023-03-16 01:14:06,887] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:14:06,887] [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_002323795.1	s__UA16 sp002323795	83.0052	532	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.84	99.84	0.86	0.86	2	-
GCA_905479395.1	s__UA16 sp905479395	79.8415	348	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.40	98.40	0.84	0.84	2	-
GCA_016777435.1	s__UA16 sp016777435	78.6867	204	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477505.1	s__UA16 sp002477505	78.4477	212	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.58	99.42	0.88	0.80	7	-
GCA_905478895.1	s__UA16 sp905478895	77.9016	130	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478325.1	s__UA16 sp002390615	76.7536	58	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.70	99.69	0.88	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-16 01:14:06,887] [INFO] GTDB search result was written to OceanDNA-b11706/result_gtdb.tsv
[2023-03-16 01:14:06,887] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:14:06,888] [INFO] DFAST_QC result json was written to OceanDNA-b11706/dqc_result.json
[2023-03-16 01:14:06,888] [INFO] DFAST_QC completed!
[2023-03-16 01:14:06,888] [INFO] Total running time: 0h1m38s