[2023-06-28 14:28:10,685] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:28:10,688] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:28:10,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg3796eed8-9d95-4ba4-8613-f46f90378841/dqc_reference
[2023-06-28 14:28:11,834] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:28:11,835] [INFO] Task started: Prodigal
[2023-06-28 14:28:11,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg99dd59f2-d4d5-46dc-bfed-8cea975d765a/GCA_002708115.1_ASM270811v1_genomic.fna.gz | prodigal -d GCA_002708115.1_ASM270811v1_genomic.fna/cds.fna -a GCA_002708115.1_ASM270811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:28:12,755] [INFO] Task succeeded: Prodigal
[2023-06-28 14:28:12,755] [INFO] Task started: HMMsearch
[2023-06-28 14:28:12,755] [INFO] Running command: hmmsearch --tblout GCA_002708115.1_ASM270811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3796eed8-9d95-4ba4-8613-f46f90378841/dqc_reference/reference_markers.hmm GCA_002708115.1_ASM270811v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:28:12,869] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:28:12,870] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg99dd59f2-d4d5-46dc-bfed-8cea975d765a/GCA_002708115.1_ASM270811v1_genomic.fna.gz]
[2023-06-28 14:28:12,883] [INFO] Query marker FASTA was written to GCA_002708115.1_ASM270811v1_genomic.fna/markers.fasta
[2023-06-28 14:28:12,883] [INFO] Task started: Blastn
[2023-06-28 14:28:12,883] [INFO] Running command: blastn -query GCA_002708115.1_ASM270811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3796eed8-9d95-4ba4-8613-f46f90378841/dqc_reference/reference_markers.fasta -out GCA_002708115.1_ASM270811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:28:13,340] [INFO] Task succeeded: Blastn
[2023-06-28 14:28:13,345] [INFO] Selected 0 target genomes.
[2023-06-28 14:28:13,345] [INFO] Target genome list was writen to GCA_002708115.1_ASM270811v1_genomic.fna/target_genomes.txt
[2023-06-28 14:28:13,346] [ERROR] File is empty. [GCA_002708115.1_ASM270811v1_genomic.fna/target_genomes.txt]
[2023-06-28 14:28:13,346] [ERROR] Task failed. No target genome found.
[2023-06-28 14:28:13,346] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:28:13,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3796eed8-9d95-4ba4-8613-f46f90378841/dqc_reference/checkm_data
[2023-06-28 14:28:13,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:28:13,358] [INFO] Task started: CheckM
[2023-06-28 14:28:13,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708115.1_ASM270811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708115.1_ASM270811v1_genomic.fna/checkm_input GCA_002708115.1_ASM270811v1_genomic.fna/checkm_result
[2023-06-28 14:28:23,636] [INFO] Task succeeded: CheckM
[2023-06-28 14:28:23,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:28:23,651] [INFO] ===== Completeness check finished =====
[2023-06-28 14:28:23,651] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:28:23,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708115.1_ASM270811v1_genomic.fna/markers.fasta)
[2023-06-28 14:28:23,652] [INFO] Task started: Blastn
[2023-06-28 14:28:23,652] [INFO] Running command: blastn -query GCA_002708115.1_ASM270811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3796eed8-9d95-4ba4-8613-f46f90378841/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708115.1_ASM270811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:28:24,083] [INFO] Task succeeded: Blastn
[2023-06-28 14:28:24,087] [INFO] Selected 8 target genomes.
[2023-06-28 14:28:24,087] [INFO] Target genome list was writen to GCA_002708115.1_ASM270811v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:28:24,089] [INFO] Task started: fastANI
[2023-06-28 14:28:24,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg99dd59f2-d4d5-46dc-bfed-8cea975d765a/GCA_002708115.1_ASM270811v1_genomic.fna.gz --refList GCA_002708115.1_ASM270811v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708115.1_ASM270811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:28:26,761] [INFO] Task succeeded: fastANI
[2023-06-28 14:28:26,769] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:28:26,769] [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_002720535.1	s__TMED109 sp002720535	96.498	177	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	conclusive
GCA_002171375.1	s__TMED109 sp002171375	83.0226	163	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002937655.1	s__TMED109 sp002937655	81.8662	153	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	99.81	99.81	0.91	0.91	2	-
GCA_015660425.1	s__TMED109 sp015660425	78.0527	79	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684605.1	s__TMED109 sp002684605	77.7792	94	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715265.1	s__GCA-002727615 sp002715265	77.5275	66	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-002727615	95.0	98.23	98.23	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-28 14:28:26,771] [INFO] GTDB search result was written to GCA_002708115.1_ASM270811v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:28:26,772] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:28:26,775] [INFO] DFAST_QC result json was written to GCA_002708115.1_ASM270811v1_genomic.fna/dqc_result.json
[2023-06-28 14:28:26,775] [INFO] DFAST_QC completed!
[2023-06-28 14:28:26,775] [INFO] Total running time: 0h0m16s