[2023-06-07 18:15:05,587] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:15:05,592] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:15:05,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg99d74e65-8de1-4b04-9dfc-827011f2a3ec/dqc_reference
[2023-06-07 18:15:07,055] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:15:07,056] [INFO] Task started: Prodigal
[2023-06-07 18:15:07,056] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3d4df67-152f-407e-91ed-53e7f86950d0/GCA_902614515.1_AG-891-L09_genomic.fna.gz | prodigal -d GCA_902614515.1_AG-891-L09_genomic.fna/cds.fna -a GCA_902614515.1_AG-891-L09_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:15:10,831] [INFO] Task succeeded: Prodigal
[2023-06-07 18:15:10,831] [INFO] Task started: HMMsearch
[2023-06-07 18:15:10,831] [INFO] Running command: hmmsearch --tblout GCA_902614515.1_AG-891-L09_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99d74e65-8de1-4b04-9dfc-827011f2a3ec/dqc_reference/reference_markers.hmm GCA_902614515.1_AG-891-L09_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:15:11,009] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:15:11,011] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb3d4df67-152f-407e-91ed-53e7f86950d0/GCA_902614515.1_AG-891-L09_genomic.fna.gz]
[2023-06-07 18:15:11,032] [INFO] Query marker FASTA was written to GCA_902614515.1_AG-891-L09_genomic.fna/markers.fasta
[2023-06-07 18:15:11,033] [INFO] Task started: Blastn
[2023-06-07 18:15:11,033] [INFO] Running command: blastn -query GCA_902614515.1_AG-891-L09_genomic.fna/markers.fasta -db /var/lib/cwl/stg99d74e65-8de1-4b04-9dfc-827011f2a3ec/dqc_reference/reference_markers.fasta -out GCA_902614515.1_AG-891-L09_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:11,543] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:11,552] [INFO] Selected 9 target genomes.
[2023-06-07 18:15:11,552] [INFO] Target genome list was writen to GCA_902614515.1_AG-891-L09_genomic.fna/target_genomes.txt
[2023-06-07 18:15:11,555] [INFO] Task started: fastANI
[2023-06-07 18:15:11,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3d4df67-152f-407e-91ed-53e7f86950d0/GCA_902614515.1_AG-891-L09_genomic.fna.gz --refList GCA_902614515.1_AG-891-L09_genomic.fna/target_genomes.txt --output GCA_902614515.1_AG-891-L09_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:15:17,722] [INFO] Task succeeded: fastANI
[2023-06-07 18:15:17,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99d74e65-8de1-4b04-9dfc-827011f2a3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:15:17,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99d74e65-8de1-4b04-9dfc-827011f2a3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:15:17,726] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:15:17,726] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 18:15:17,726] [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
--------------------------------------------------------------------------------
[2023-06-07 18:15:17,729] [INFO] DFAST Taxonomy check result was written to GCA_902614515.1_AG-891-L09_genomic.fna/tc_result.tsv
[2023-06-07 18:15:17,729] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:15:17,730] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:15:17,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99d74e65-8de1-4b04-9dfc-827011f2a3ec/dqc_reference/checkm_data
[2023-06-07 18:15:17,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:15:17,759] [INFO] Task started: CheckM
[2023-06-07 18:15:17,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614515.1_AG-891-L09_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614515.1_AG-891-L09_genomic.fna/checkm_input GCA_902614515.1_AG-891-L09_genomic.fna/checkm_result
[2023-06-07 18:15:36,897] [INFO] Task succeeded: CheckM
[2023-06-07 18:15:36,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 10.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:15:36,926] [INFO] ===== Completeness check finished =====
[2023-06-07 18:15:36,926] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:15:36,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614515.1_AG-891-L09_genomic.fna/markers.fasta)
[2023-06-07 18:15:36,927] [INFO] Task started: Blastn
[2023-06-07 18:15:36,927] [INFO] Running command: blastn -query GCA_902614515.1_AG-891-L09_genomic.fna/markers.fasta -db /var/lib/cwl/stg99d74e65-8de1-4b04-9dfc-827011f2a3ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614515.1_AG-891-L09_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:37,459] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:37,464] [INFO] Selected 7 target genomes.
[2023-06-07 18:15:37,464] [INFO] Target genome list was writen to GCA_902614515.1_AG-891-L09_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:15:37,470] [INFO] Task started: fastANI
[2023-06-07 18:15:37,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3d4df67-152f-407e-91ed-53e7f86950d0/GCA_902614515.1_AG-891-L09_genomic.fna.gz --refList GCA_902614515.1_AG-891-L09_genomic.fna/target_genomes_gtdb.txt --output GCA_902614515.1_AG-891-L09_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:15:40,636] [INFO] Task succeeded: fastANI
[2023-06-07 18:15:40,646] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 18:15:40,646] [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_011522845.1	s__JCVI-SCAAA005 sp011522845	94.9036	279	496	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730365.1	s__JCVI-SCAAA005 sp002730365	92.164	130	496	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450295.1	s__JCVI-SCAAA005 sp002450295	88.8303	246	496	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	96.73	95.52	0.71	0.67	8	-
GCA_002683655.1	s__JCVI-SCAAA005 sp002683655	87.3764	268	496	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	98.22	98.15	0.75	0.71	3	-
GCA_003541985.1	s__JCVI-SCAAA005 sp003541985	85.0676	167	496	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 18:15:40,649] [INFO] GTDB search result was written to GCA_902614515.1_AG-891-L09_genomic.fna/result_gtdb.tsv
[2023-06-07 18:15:40,650] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:15:40,653] [INFO] DFAST_QC result json was written to GCA_902614515.1_AG-891-L09_genomic.fna/dqc_result.json
[2023-06-07 18:15:40,653] [INFO] DFAST_QC completed!
[2023-06-07 18:15:40,653] [INFO] Total running time: 0h0m35s