[2023-06-28 13:31:39,994] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:39,996] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:39,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg42333d60-d23b-4eb4-8372-665a571e0c94/dqc_reference
[2023-06-28 13:31:41,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:41,756] [INFO] Task started: Prodigal
[2023-06-28 13:31:41,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg65316d3d-f131-46e5-9c35-c02a2f32d4c8/GCA_002708525.1_ASM270852v1_genomic.fna.gz | prodigal -d GCA_002708525.1_ASM270852v1_genomic.fna/cds.fna -a GCA_002708525.1_ASM270852v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:31:43,301] [INFO] Task succeeded: Prodigal
[2023-06-28 13:31:43,301] [INFO] Task started: HMMsearch
[2023-06-28 13:31:43,301] [INFO] Running command: hmmsearch --tblout GCA_002708525.1_ASM270852v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42333d60-d23b-4eb4-8372-665a571e0c94/dqc_reference/reference_markers.hmm GCA_002708525.1_ASM270852v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:31:43,474] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:31:43,475] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg65316d3d-f131-46e5-9c35-c02a2f32d4c8/GCA_002708525.1_ASM270852v1_genomic.fna.gz]
[2023-06-28 13:31:43,489] [INFO] Query marker FASTA was written to GCA_002708525.1_ASM270852v1_genomic.fna/markers.fasta
[2023-06-28 13:31:43,489] [INFO] Task started: Blastn
[2023-06-28 13:31:43,489] [INFO] Running command: blastn -query GCA_002708525.1_ASM270852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42333d60-d23b-4eb4-8372-665a571e0c94/dqc_reference/reference_markers.fasta -out GCA_002708525.1_ASM270852v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:45,195] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:45,199] [INFO] Selected 11 target genomes.
[2023-06-28 13:31:45,200] [INFO] Target genome list was writen to GCA_002708525.1_ASM270852v1_genomic.fna/target_genomes.txt
[2023-06-28 13:31:45,204] [INFO] Task started: fastANI
[2023-06-28 13:31:45,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg65316d3d-f131-46e5-9c35-c02a2f32d4c8/GCA_002708525.1_ASM270852v1_genomic.fna.gz --refList GCA_002708525.1_ASM270852v1_genomic.fna/target_genomes.txt --output GCA_002708525.1_ASM270852v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:31:50,231] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:50,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42333d60-d23b-4eb4-8372-665a571e0c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:31:50,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42333d60-d23b-4eb4-8372-665a571e0c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:31:50,233] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:31:50,234] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:31:50,234] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-28 13:31:50,281] [INFO] DFAST Taxonomy check result was written to GCA_002708525.1_ASM270852v1_genomic.fna/tc_result.tsv
[2023-06-28 13:31:50,282] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:31:50,283] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:31:50,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42333d60-d23b-4eb4-8372-665a571e0c94/dqc_reference/checkm_data
[2023-06-28 13:31:50,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:31:50,302] [INFO] Task started: CheckM
[2023-06-28 13:31:50,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708525.1_ASM270852v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708525.1_ASM270852v1_genomic.fna/checkm_input GCA_002708525.1_ASM270852v1_genomic.fna/checkm_result
[2023-06-28 13:32:07,896] [INFO] Task succeeded: CheckM
[2023-06-28 13:32:07,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:32:07,914] [INFO] ===== Completeness check finished =====
[2023-06-28 13:32:07,914] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:32:07,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708525.1_ASM270852v1_genomic.fna/markers.fasta)
[2023-06-28 13:32:07,915] [INFO] Task started: Blastn
[2023-06-28 13:32:07,915] [INFO] Running command: blastn -query GCA_002708525.1_ASM270852v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42333d60-d23b-4eb4-8372-665a571e0c94/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708525.1_ASM270852v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:32:08,437] [INFO] Task succeeded: Blastn
[2023-06-28 13:32:08,444] [INFO] Selected 15 target genomes.
[2023-06-28 13:32:08,444] [INFO] Target genome list was writen to GCA_002708525.1_ASM270852v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:32:08,484] [INFO] Task started: fastANI
[2023-06-28 13:32:08,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg65316d3d-f131-46e5-9c35-c02a2f32d4c8/GCA_002708525.1_ASM270852v1_genomic.fna.gz --refList GCA_002708525.1_ASM270852v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708525.1_ASM270852v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:32:11,846] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:11,856] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:32:11,857] [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_002708525.1	s__Pelagibacter sp002708525	100.0	169	171	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_902634885.1	s__Pelagibacter sp902634885	78.5611	51	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.47	97.62	0.77	0.76	3	-
GCA_011526385.1	s__Pelagibacter sp011526385	78.2373	56	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.04	98.04	0.83	0.83	2	-
GCA_902596915.1	s__Pelagibacter sp902596915	77.927	50	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625715.1	s__Pelagibacter sp902625715	77.9024	61	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.20	95.77	0.80	0.79	3	-
GCA_902576045.1	s__Pelagibacter sp902576045	77.8787	57	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.81	95.50	0.75	0.71	6	-
GCF_002101295.1	s__Pelagibacter sp002101295	77.6466	63	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.97	95.60	0.92	0.90	4	-
GCA_902551985.1	s__Pelagibacter sp902551985	77.6359	63	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579105.1	s__Pelagibacter sp902579105	77.4316	58	171	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.93	95.75	0.80	0.79	5	-
--------------------------------------------------------------------------------
[2023-06-28 13:32:11,861] [INFO] GTDB search result was written to GCA_002708525.1_ASM270852v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:32:11,862] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:32:11,866] [INFO] DFAST_QC result json was written to GCA_002708525.1_ASM270852v1_genomic.fna/dqc_result.json
[2023-06-28 13:32:11,866] [INFO] DFAST_QC completed!
[2023-06-28 13:32:11,866] [INFO] Total running time: 0h0m32s