[2023-06-17 01:28:46,961] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:28:46,963] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:28:46,963] [INFO] DQC Reference Directory: /var/lib/cwl/stgd454e3d8-0908-4255-bf03-6185f6ae33b0/dqc_reference
[2023-06-17 01:28:48,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:28:48,871] [INFO] Task started: Prodigal
[2023-06-17 01:28:48,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c68b2a6-36cb-489c-a463-36fbe18ff5de/GCA_013545935.1_ASM1354593v1_genomic.fna.gz | prodigal -d GCA_013545935.1_ASM1354593v1_genomic.fna/cds.fna -a GCA_013545935.1_ASM1354593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:28:49,960] [INFO] Task succeeded: Prodigal
[2023-06-17 01:28:49,961] [INFO] Task started: HMMsearch
[2023-06-17 01:28:49,961] [INFO] Running command: hmmsearch --tblout GCA_013545935.1_ASM1354593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd454e3d8-0908-4255-bf03-6185f6ae33b0/dqc_reference/reference_markers.hmm GCA_013545935.1_ASM1354593v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:28:50,187] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:28:50,188] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg4c68b2a6-36cb-489c-a463-36fbe18ff5de/GCA_013545935.1_ASM1354593v1_genomic.fna.gz]
[2023-06-17 01:28:50,199] [INFO] Query marker FASTA was written to GCA_013545935.1_ASM1354593v1_genomic.fna/markers.fasta
[2023-06-17 01:28:50,200] [INFO] Task started: Blastn
[2023-06-17 01:28:50,200] [INFO] Running command: blastn -query GCA_013545935.1_ASM1354593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd454e3d8-0908-4255-bf03-6185f6ae33b0/dqc_reference/reference_markers.fasta -out GCA_013545935.1_ASM1354593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:28:53,233] [INFO] Task succeeded: Blastn
[2023-06-17 01:28:53,237] [INFO] Selected 0 target genomes.
[2023-06-17 01:28:53,238] [INFO] Target genome list was writen to GCA_013545935.1_ASM1354593v1_genomic.fna/target_genomes.txt
[2023-06-17 01:28:53,238] [ERROR] File is empty. [GCA_013545935.1_ASM1354593v1_genomic.fna/target_genomes.txt]
[2023-06-17 01:28:53,238] [ERROR] Task failed. No target genome found.
[2023-06-17 01:28:53,239] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:28:53,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd454e3d8-0908-4255-bf03-6185f6ae33b0/dqc_reference/checkm_data
[2023-06-17 01:28:53,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:28:53,253] [INFO] Task started: CheckM
[2023-06-17 01:28:53,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013545935.1_ASM1354593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013545935.1_ASM1354593v1_genomic.fna/checkm_input GCA_013545935.1_ASM1354593v1_genomic.fna/checkm_result
[2023-06-17 01:29:07,614] [INFO] Task succeeded: CheckM
[2023-06-17 01:29:07,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:29:07,645] [INFO] ===== Completeness check finished =====
[2023-06-17 01:29:07,645] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:29:07,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013545935.1_ASM1354593v1_genomic.fna/markers.fasta)
[2023-06-17 01:29:07,646] [INFO] Task started: Blastn
[2023-06-17 01:29:07,647] [INFO] Running command: blastn -query GCA_013545935.1_ASM1354593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd454e3d8-0908-4255-bf03-6185f6ae33b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_013545935.1_ASM1354593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:08,141] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:08,144] [INFO] Selected 5 target genomes.
[2023-06-17 01:29:08,145] [INFO] Target genome list was writen to GCA_013545935.1_ASM1354593v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:29:08,150] [INFO] Task started: fastANI
[2023-06-17 01:29:08,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c68b2a6-36cb-489c-a463-36fbe18ff5de/GCA_013545935.1_ASM1354593v1_genomic.fna.gz --refList GCA_013545935.1_ASM1354593v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013545935.1_ASM1354593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:29:08,927] [INFO] Task succeeded: fastANI
[2023-06-17 01:29:08,932] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 01:29:08,933] [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_902607525.1	s__AG-414-E02 sp902607525	78.3089	54	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589505.1	s__AG-414-E02 sp902589505	77.6473	53	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764285.1	s__AG-414-E02 sp016764285	77.3316	50	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:29:08,935] [INFO] GTDB search result was written to GCA_013545935.1_ASM1354593v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:29:08,936] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:29:08,939] [INFO] DFAST_QC result json was written to GCA_013545935.1_ASM1354593v1_genomic.fna/dqc_result.json
[2023-06-17 01:29:08,939] [INFO] DFAST_QC completed!
[2023-06-17 01:29:08,939] [INFO] Total running time: 0h0m22s