[2023-06-30 06:10:54,403] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:10:54,407] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:10:54,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg06990963-f7c0-4f80-9a47-963794a321ac/dqc_reference
[2023-06-30 06:10:55,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:10:55,832] [INFO] Task started: Prodigal
[2023-06-30 06:10:55,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg1970bb30-4648-4154-b281-6458c544306a/GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna.gz | prodigal -d GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/cds.fna -a GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:10:57,007] [INFO] Task succeeded: Prodigal
[2023-06-30 06:10:57,008] [INFO] Task started: HMMsearch
[2023-06-30 06:10:57,008] [INFO] Running command: hmmsearch --tblout GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06990963-f7c0-4f80-9a47-963794a321ac/dqc_reference/reference_markers.hmm GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:10:57,155] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:10:57,156] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1970bb30-4648-4154-b281-6458c544306a/GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna.gz]
[2023-06-30 06:10:57,166] [INFO] Query marker FASTA was written to GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/markers.fasta
[2023-06-30 06:10:57,166] [INFO] Task started: Blastn
[2023-06-30 06:10:57,166] [INFO] Running command: blastn -query GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/markers.fasta -db /var/lib/cwl/stg06990963-f7c0-4f80-9a47-963794a321ac/dqc_reference/reference_markers.fasta -out GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:10:59,576] [INFO] Task succeeded: Blastn
[2023-06-30 06:10:59,580] [INFO] Selected 0 target genomes.
[2023-06-30 06:10:59,581] [INFO] Target genome list was writen to GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/target_genomes.txt
[2023-06-30 06:10:59,581] [ERROR] File is empty. [GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/target_genomes.txt]
[2023-06-30 06:10:59,581] [ERROR] Task failed. No target genome found.
[2023-06-30 06:10:59,581] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:10:59,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06990963-f7c0-4f80-9a47-963794a321ac/dqc_reference/checkm_data
[2023-06-30 06:10:59,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:10:59,592] [INFO] Task started: CheckM
[2023-06-30 06:10:59,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/checkm_input GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/checkm_result
[2023-06-30 06:11:13,118] [INFO] Task succeeded: CheckM
[2023-06-30 06:11:13,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:11:13,134] [INFO] ===== Completeness check finished =====
[2023-06-30 06:11:13,135] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:11:13,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/markers.fasta)
[2023-06-30 06:11:13,135] [INFO] Task started: Blastn
[2023-06-30 06:11:13,135] [INFO] Running command: blastn -query GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/markers.fasta -db /var/lib/cwl/stg06990963-f7c0-4f80-9a47-963794a321ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:11:13,659] [INFO] Task succeeded: Blastn
[2023-06-30 06:11:13,662] [INFO] Selected 9 target genomes.
[2023-06-30 06:11:13,662] [INFO] Target genome list was writen to GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:11:13,664] [INFO] Task started: fastANI
[2023-06-30 06:11:13,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg1970bb30-4648-4154-b281-6458c544306a/GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna.gz --refList GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/target_genomes_gtdb.txt --output GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:11:15,697] [INFO] Task succeeded: fastANI
[2023-06-30 06:11:15,701] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 06:11:15,701] [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_903897155.1	s__PALSA-747 sp903897155	97.4619	85	142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.95	98.34	0.84	0.73	51	conclusive
GCA_903899145.1	s__PALSA-747 sp903899145	88.3583	65	142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:11:15,703] [INFO] GTDB search result was written to GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/result_gtdb.tsv
[2023-06-30 06:11:15,704] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:11:15,706] [INFO] DFAST_QC result json was written to GCA_903995075.1_freshwater_SAG_---_SB-2103-996-D15_genomic.fna/dqc_result.json
[2023-06-30 06:11:15,706] [INFO] DFAST_QC completed!
[2023-06-30 06:11:15,706] [INFO] Total running time: 0h0m21s