[2023-06-08 07:43:24,510] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:43:24,514] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:43:24,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg3db20a78-bbd4-4357-9005-3bfff57447d2/dqc_reference
[2023-06-08 07:43:25,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:43:25,860] [INFO] Task started: Prodigal
[2023-06-08 07:43:25,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg0764bac9-16b8-4ee5-9b42-a044c852ad1d/GCA_902620815.1_AG-920-M16_genomic.fna.gz | prodigal -d GCA_902620815.1_AG-920-M16_genomic.fna/cds.fna -a GCA_902620815.1_AG-920-M16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:43:27,012] [INFO] Task succeeded: Prodigal
[2023-06-08 07:43:27,013] [INFO] Task started: HMMsearch
[2023-06-08 07:43:27,013] [INFO] Running command: hmmsearch --tblout GCA_902620815.1_AG-920-M16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3db20a78-bbd4-4357-9005-3bfff57447d2/dqc_reference/reference_markers.hmm GCA_902620815.1_AG-920-M16_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:43:27,177] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:43:27,178] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0764bac9-16b8-4ee5-9b42-a044c852ad1d/GCA_902620815.1_AG-920-M16_genomic.fna.gz]
[2023-06-08 07:43:27,191] [INFO] Query marker FASTA was written to GCA_902620815.1_AG-920-M16_genomic.fna/markers.fasta
[2023-06-08 07:43:27,191] [INFO] Task started: Blastn
[2023-06-08 07:43:27,191] [INFO] Running command: blastn -query GCA_902620815.1_AG-920-M16_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db20a78-bbd4-4357-9005-3bfff57447d2/dqc_reference/reference_markers.fasta -out GCA_902620815.1_AG-920-M16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:27,706] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:27,710] [INFO] Selected 0 target genomes.
[2023-06-08 07:43:27,711] [INFO] Target genome list was writen to GCA_902620815.1_AG-920-M16_genomic.fna/target_genomes.txt
[2023-06-08 07:43:27,711] [ERROR] File is empty. [GCA_902620815.1_AG-920-M16_genomic.fna/target_genomes.txt]
[2023-06-08 07:43:27,711] [ERROR] Task failed. No target genome found.
[2023-06-08 07:43:27,711] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:43:27,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3db20a78-bbd4-4357-9005-3bfff57447d2/dqc_reference/checkm_data
[2023-06-08 07:43:27,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:43:27,729] [INFO] Task started: CheckM
[2023-06-08 07:43:27,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902620815.1_AG-920-M16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902620815.1_AG-920-M16_genomic.fna/checkm_input GCA_902620815.1_AG-920-M16_genomic.fna/checkm_result
[2023-06-08 07:43:39,644] [INFO] Task succeeded: CheckM
[2023-06-08 07:43:39,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:43:39,684] [INFO] ===== Completeness check finished =====
[2023-06-08 07:43:39,684] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:43:39,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902620815.1_AG-920-M16_genomic.fna/markers.fasta)
[2023-06-08 07:43:39,685] [INFO] Task started: Blastn
[2023-06-08 07:43:39,686] [INFO] Running command: blastn -query GCA_902620815.1_AG-920-M16_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db20a78-bbd4-4357-9005-3bfff57447d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902620815.1_AG-920-M16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:40,281] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:40,284] [INFO] Selected 6 target genomes.
[2023-06-08 07:43:40,285] [INFO] Target genome list was writen to GCA_902620815.1_AG-920-M16_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:43:40,286] [INFO] Task started: fastANI
[2023-06-08 07:43:40,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg0764bac9-16b8-4ee5-9b42-a044c852ad1d/GCA_902620815.1_AG-920-M16_genomic.fna.gz --refList GCA_902620815.1_AG-920-M16_genomic.fna/target_genomes_gtdb.txt --output GCA_902620815.1_AG-920-M16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:43:41,679] [INFO] Task succeeded: fastANI
[2023-06-08 07:43:41,686] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:43:41,686] [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_902612915.1	s__SAR86A sp902612915	99.8444	166	197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	conclusive
GCA_902617045.1	s__SAR86A sp902617045	94.4054	170	197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902547295.1	s__SAR86A sp902547295	94.2869	149	197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541175.1	s__SAR86A sp902541175	94.2781	170	197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902591925.1	s__SAR86A sp902591925	91.1874	155	197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_000252525.1	s__SAR86A sp000252525	81.9402	95	197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
--------------------------------------------------------------------------------
[2023-06-08 07:43:41,688] [INFO] GTDB search result was written to GCA_902620815.1_AG-920-M16_genomic.fna/result_gtdb.tsv
[2023-06-08 07:43:41,689] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:43:41,692] [INFO] DFAST_QC result json was written to GCA_902620815.1_AG-920-M16_genomic.fna/dqc_result.json
[2023-06-08 07:43:41,692] [INFO] DFAST_QC completed!
[2023-06-08 07:43:41,692] [INFO] Total running time: 0h0m17s