[2023-06-08 11:22:42,923] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:22:42,925] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:22:42,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg86727273-4302-44a0-ab5b-b719f9e3fbb8/dqc_reference
[2023-06-08 11:22:44,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:22:44,135] [INFO] Task started: Prodigal
[2023-06-08 11:22:44,135] [INFO] Running command: gunzip -c /var/lib/cwl/stgf736a745-c5c5-40aa-9206-2ae9ffd42c79/GCA_902635335.1_AG-915-C03_genomic.fna.gz | prodigal -d GCA_902635335.1_AG-915-C03_genomic.fna/cds.fna -a GCA_902635335.1_AG-915-C03_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:22:46,387] [INFO] Task succeeded: Prodigal
[2023-06-08 11:22:46,388] [INFO] Task started: HMMsearch
[2023-06-08 11:22:46,388] [INFO] Running command: hmmsearch --tblout GCA_902635335.1_AG-915-C03_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86727273-4302-44a0-ab5b-b719f9e3fbb8/dqc_reference/reference_markers.hmm GCA_902635335.1_AG-915-C03_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:22:46,567] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:22:46,569] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf736a745-c5c5-40aa-9206-2ae9ffd42c79/GCA_902635335.1_AG-915-C03_genomic.fna.gz]
[2023-06-08 11:22:46,587] [INFO] Query marker FASTA was written to GCA_902635335.1_AG-915-C03_genomic.fna/markers.fasta
[2023-06-08 11:22:46,587] [INFO] Task started: Blastn
[2023-06-08 11:22:46,587] [INFO] Running command: blastn -query GCA_902635335.1_AG-915-C03_genomic.fna/markers.fasta -db /var/lib/cwl/stg86727273-4302-44a0-ab5b-b719f9e3fbb8/dqc_reference/reference_markers.fasta -out GCA_902635335.1_AG-915-C03_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:22:47,085] [INFO] Task succeeded: Blastn
[2023-06-08 11:22:47,089] [INFO] Selected 0 target genomes.
[2023-06-08 11:22:47,089] [INFO] Target genome list was writen to GCA_902635335.1_AG-915-C03_genomic.fna/target_genomes.txt
[2023-06-08 11:22:47,090] [ERROR] File is empty. [GCA_902635335.1_AG-915-C03_genomic.fna/target_genomes.txt]
[2023-06-08 11:22:47,090] [ERROR] Task failed. No target genome found.
[2023-06-08 11:22:47,090] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:22:47,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86727273-4302-44a0-ab5b-b719f9e3fbb8/dqc_reference/checkm_data
[2023-06-08 11:22:47,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:22:47,111] [INFO] Task started: CheckM
[2023-06-08 11:22:47,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902635335.1_AG-915-C03_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902635335.1_AG-915-C03_genomic.fna/checkm_input GCA_902635335.1_AG-915-C03_genomic.fna/checkm_result
[2023-06-08 11:23:01,864] [INFO] Task succeeded: CheckM
[2023-06-08 11:23:01,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:23:01,885] [INFO] ===== Completeness check finished =====
[2023-06-08 11:23:01,886] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:23:01,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902635335.1_AG-915-C03_genomic.fna/markers.fasta)
[2023-06-08 11:23:01,887] [INFO] Task started: Blastn
[2023-06-08 11:23:01,887] [INFO] Running command: blastn -query GCA_902635335.1_AG-915-C03_genomic.fna/markers.fasta -db /var/lib/cwl/stg86727273-4302-44a0-ab5b-b719f9e3fbb8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902635335.1_AG-915-C03_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:23:02,466] [INFO] Task succeeded: Blastn
[2023-06-08 11:23:02,471] [INFO] Selected 11 target genomes.
[2023-06-08 11:23:02,471] [INFO] Target genome list was writen to GCA_902635335.1_AG-915-C03_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:23:02,477] [INFO] Task started: fastANI
[2023-06-08 11:23:02,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgf736a745-c5c5-40aa-9206-2ae9ffd42c79/GCA_902635335.1_AG-915-C03_genomic.fna.gz --refList GCA_902635335.1_AG-915-C03_genomic.fna/target_genomes_gtdb.txt --output GCA_902635335.1_AG-915-C03_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:23:04,933] [INFO] Task succeeded: fastANI
[2023-06-08 11:23:04,945] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:23:04,946] [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_902635335.1	s__Pelagibacter sp902635335	100.0	245	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902604975.1	s__Pelagibacter sp902604975	93.1699	148	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902549785.1	s__Pelagibacter sp902549785	90.8387	110	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.65	95.65	0.64	0.64	2	-
GCA_902520695.1	s__Pelagibacter sp902520695	89.9369	194	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599665.1	s__Pelagibacter sp902599665	89.354	165	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525355.1	s__Pelagibacter sp902525355	88.9487	167	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.77	97.77	0.74	0.74	2	-
GCA_902582765.1	s__Pelagibacter sp902582765	88.5471	132	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604245.1	s__Pelagibacter sp902604245	87.9498	151	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604795.1	s__Pelagibacter sp902604795	87.844	160	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571975.1	s__Pelagibacter sp902571975	87.6156	146	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594335.1	s__Pelagibacter sp902594335	87.3589	160	250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:23:04,948] [INFO] GTDB search result was written to GCA_902635335.1_AG-915-C03_genomic.fna/result_gtdb.tsv
[2023-06-08 11:23:04,948] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:23:04,951] [INFO] DFAST_QC result json was written to GCA_902635335.1_AG-915-C03_genomic.fna/dqc_result.json
[2023-06-08 11:23:04,951] [INFO] DFAST_QC completed!
[2023-06-08 11:23:04,952] [INFO] Total running time: 0h0m22s