[2023-06-08 10:40:55,906] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:40:55,908] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:40:55,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6ee3c72-ada6-4552-ad44-45a20865f6cb/dqc_reference
[2023-06-08 10:40:57,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:40:57,266] [INFO] Task started: Prodigal
[2023-06-08 10:40:57,266] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8c1fc40-0df9-4909-baab-451d0551662f/GCA_902520295.1_AG-333-I09_genomic.fna.gz | prodigal -d GCA_902520295.1_AG-333-I09_genomic.fna/cds.fna -a GCA_902520295.1_AG-333-I09_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:40:58,410] [INFO] Task succeeded: Prodigal
[2023-06-08 10:40:58,410] [INFO] Task started: HMMsearch
[2023-06-08 10:40:58,410] [INFO] Running command: hmmsearch --tblout GCA_902520295.1_AG-333-I09_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6ee3c72-ada6-4552-ad44-45a20865f6cb/dqc_reference/reference_markers.hmm GCA_902520295.1_AG-333-I09_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:40:58,601] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:40:58,607] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgf8c1fc40-0df9-4909-baab-451d0551662f/GCA_902520295.1_AG-333-I09_genomic.fna.gz]
[2023-06-08 10:40:58,617] [INFO] Query marker FASTA was written to GCA_902520295.1_AG-333-I09_genomic.fna/markers.fasta
[2023-06-08 10:40:58,618] [INFO] Task started: Blastn
[2023-06-08 10:40:58,618] [INFO] Running command: blastn -query GCA_902520295.1_AG-333-I09_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6ee3c72-ada6-4552-ad44-45a20865f6cb/dqc_reference/reference_markers.fasta -out GCA_902520295.1_AG-333-I09_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:40:59,339] [INFO] Task succeeded: Blastn
[2023-06-08 10:40:59,344] [INFO] Selected 0 target genomes.
[2023-06-08 10:40:59,344] [INFO] Target genome list was writen to GCA_902520295.1_AG-333-I09_genomic.fna/target_genomes.txt
[2023-06-08 10:40:59,344] [ERROR] File is empty. [GCA_902520295.1_AG-333-I09_genomic.fna/target_genomes.txt]
[2023-06-08 10:40:59,344] [ERROR] Task failed. No target genome found.
[2023-06-08 10:40:59,344] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:40:59,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6ee3c72-ada6-4552-ad44-45a20865f6cb/dqc_reference/checkm_data
[2023-06-08 10:40:59,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:40:59,354] [INFO] Task started: CheckM
[2023-06-08 10:40:59,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902520295.1_AG-333-I09_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902520295.1_AG-333-I09_genomic.fna/checkm_input GCA_902520295.1_AG-333-I09_genomic.fna/checkm_result
[2023-06-08 10:41:12,792] [INFO] Task succeeded: CheckM
[2023-06-08 10:41:12,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:41:12,828] [INFO] ===== Completeness check finished =====
[2023-06-08 10:41:12,829] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:41:12,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902520295.1_AG-333-I09_genomic.fna/markers.fasta)
[2023-06-08 10:41:12,829] [INFO] Task started: Blastn
[2023-06-08 10:41:12,829] [INFO] Running command: blastn -query GCA_902520295.1_AG-333-I09_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6ee3c72-ada6-4552-ad44-45a20865f6cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_902520295.1_AG-333-I09_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:41:13,403] [INFO] Task succeeded: Blastn
[2023-06-08 10:41:13,407] [INFO] Selected 5 target genomes.
[2023-06-08 10:41:13,407] [INFO] Target genome list was writen to GCA_902520295.1_AG-333-I09_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:41:13,411] [INFO] Task started: fastANI
[2023-06-08 10:41:13,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8c1fc40-0df9-4909-baab-451d0551662f/GCA_902520295.1_AG-333-I09_genomic.fna.gz --refList GCA_902520295.1_AG-333-I09_genomic.fna/target_genomes_gtdb.txt --output GCA_902520295.1_AG-333-I09_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:41:14,320] [INFO] Task succeeded: fastANI
[2023-06-08 10:41:14,333] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 10:41:14,334] [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_902574725.1	s__Pelagibacter sp902574725	80.9577	54	121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611145.1	s__Pelagibacter sp902611145	80.673	88	121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.26	99.26	0.79	0.79	2	-
GCA_902588255.1	s__Pelagibacter sp902588255	79.3013	58	121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902636025.1	s__Pelagibacter sp902636025	78.6528	55	121	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.39	99.39	0.68	0.68	2	-
--------------------------------------------------------------------------------
[2023-06-08 10:41:14,342] [INFO] GTDB search result was written to GCA_902520295.1_AG-333-I09_genomic.fna/result_gtdb.tsv
[2023-06-08 10:41:14,343] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:41:14,346] [INFO] DFAST_QC result json was written to GCA_902520295.1_AG-333-I09_genomic.fna/dqc_result.json
[2023-06-08 10:41:14,346] [INFO] DFAST_QC completed!
[2023-06-08 10:41:14,346] [INFO] Total running time: 0h0m18s