[2023-06-08 17:09:34,078] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:34,084] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:34,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f75cfca-b117-42ab-8644-ee7eb2c3fb61/dqc_reference
[2023-06-08 17:09:35,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:35,540] [INFO] Task started: Prodigal
[2023-06-08 17:09:35,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b11a34-8dc8-4f1b-a2ca-2cf746bcf475/GCA_902620205.1_AG-920-K03_genomic.fna.gz | prodigal -d GCA_902620205.1_AG-920-K03_genomic.fna/cds.fna -a GCA_902620205.1_AG-920-K03_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:36,900] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:36,901] [INFO] Task started: HMMsearch
[2023-06-08 17:09:36,901] [INFO] Running command: hmmsearch --tblout GCA_902620205.1_AG-920-K03_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f75cfca-b117-42ab-8644-ee7eb2c3fb61/dqc_reference/reference_markers.hmm GCA_902620205.1_AG-920-K03_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:37,040] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:37,041] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg53b11a34-8dc8-4f1b-a2ca-2cf746bcf475/GCA_902620205.1_AG-920-K03_genomic.fna.gz]
[2023-06-08 17:09:37,051] [INFO] Query marker FASTA was written to GCA_902620205.1_AG-920-K03_genomic.fna/markers.fasta
[2023-06-08 17:09:37,052] [INFO] Task started: Blastn
[2023-06-08 17:09:37,052] [INFO] Running command: blastn -query GCA_902620205.1_AG-920-K03_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f75cfca-b117-42ab-8644-ee7eb2c3fb61/dqc_reference/reference_markers.fasta -out GCA_902620205.1_AG-920-K03_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:37,602] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:37,605] [INFO] Selected 0 target genomes.
[2023-06-08 17:09:37,605] [INFO] Target genome list was writen to GCA_902620205.1_AG-920-K03_genomic.fna/target_genomes.txt
[2023-06-08 17:09:37,605] [ERROR] File is empty. [GCA_902620205.1_AG-920-K03_genomic.fna/target_genomes.txt]
[2023-06-08 17:09:37,606] [ERROR] Task failed. No target genome found.
[2023-06-08 17:09:37,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:37,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f75cfca-b117-42ab-8644-ee7eb2c3fb61/dqc_reference/checkm_data
[2023-06-08 17:09:37,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:37,618] [INFO] Task started: CheckM
[2023-06-08 17:09:37,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902620205.1_AG-920-K03_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902620205.1_AG-920-K03_genomic.fna/checkm_input GCA_902620205.1_AG-920-K03_genomic.fna/checkm_result
[2023-06-08 17:09:50,372] [INFO] Task succeeded: CheckM
[2023-06-08 17:09:50,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 20.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:09:50,393] [INFO] ===== Completeness check finished =====
[2023-06-08 17:09:50,393] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:09:50,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902620205.1_AG-920-K03_genomic.fna/markers.fasta)
[2023-06-08 17:09:50,394] [INFO] Task started: Blastn
[2023-06-08 17:09:50,394] [INFO] Running command: blastn -query GCA_902620205.1_AG-920-K03_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f75cfca-b117-42ab-8644-ee7eb2c3fb61/dqc_reference/reference_markers_gtdb.fasta -out GCA_902620205.1_AG-920-K03_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:50,936] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:50,941] [INFO] Selected 3 target genomes.
[2023-06-08 17:09:50,941] [INFO] Target genome list was writen to GCA_902620205.1_AG-920-K03_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:09:50,946] [INFO] Task started: fastANI
[2023-06-08 17:09:50,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b11a34-8dc8-4f1b-a2ca-2cf746bcf475/GCA_902620205.1_AG-920-K03_genomic.fna.gz --refList GCA_902620205.1_AG-920-K03_genomic.fna/target_genomes_gtdb.txt --output GCA_902620205.1_AG-920-K03_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:09:51,607] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:51,612] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:09:51,612] [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_902586025.1	s__Pelagibacter sp902586025	99.3239	103	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.23	95.42	0.77	0.69	3	conclusive
GCA_902570695.1	s__Pelagibacter sp902570695	93.6255	111	141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.72	99.69	0.89	0.86	4	-
GCA_902576815.1	s__Pelagibacter sp902576815	92.0251	87	141	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 17:09:51,614] [INFO] GTDB search result was written to GCA_902620205.1_AG-920-K03_genomic.fna/result_gtdb.tsv
[2023-06-08 17:09:51,615] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:09:51,623] [INFO] DFAST_QC result json was written to GCA_902620205.1_AG-920-K03_genomic.fna/dqc_result.json
[2023-06-08 17:09:51,624] [INFO] DFAST_QC completed!
[2023-06-08 17:09:51,624] [INFO] Total running time: 0h0m18s