[2023-06-28 14:06:29,903] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:06:29,909] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:06:29,909] [INFO] DQC Reference Directory: /var/lib/cwl/stg4741bdd1-a8dd-4948-869e-9b46c7f7b949/dqc_reference
[2023-06-28 14:06:31,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:06:31,143] [INFO] Task started: Prodigal
[2023-06-28 14:06:31,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg52716496-38bb-4418-9a54-1f1b8827279a/GCA_015232685.1_ASM1523268v1_genomic.fna.gz | prodigal -d GCA_015232685.1_ASM1523268v1_genomic.fna/cds.fna -a GCA_015232685.1_ASM1523268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:06:40,976] [INFO] Task succeeded: Prodigal
[2023-06-28 14:06:40,977] [INFO] Task started: HMMsearch
[2023-06-28 14:06:40,977] [INFO] Running command: hmmsearch --tblout GCA_015232685.1_ASM1523268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4741bdd1-a8dd-4948-869e-9b46c7f7b949/dqc_reference/reference_markers.hmm GCA_015232685.1_ASM1523268v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:06:41,168] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:06:41,169] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg52716496-38bb-4418-9a54-1f1b8827279a/GCA_015232685.1_ASM1523268v1_genomic.fna.gz]
[2023-06-28 14:06:41,204] [INFO] Query marker FASTA was written to GCA_015232685.1_ASM1523268v1_genomic.fna/markers.fasta
[2023-06-28 14:06:41,204] [INFO] Task started: Blastn
[2023-06-28 14:06:41,204] [INFO] Running command: blastn -query GCA_015232685.1_ASM1523268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4741bdd1-a8dd-4948-869e-9b46c7f7b949/dqc_reference/reference_markers.fasta -out GCA_015232685.1_ASM1523268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:06:41,934] [INFO] Task succeeded: Blastn
[2023-06-28 14:06:41,938] [INFO] Selected 21 target genomes.
[2023-06-28 14:06:41,939] [INFO] Target genome list was writen to GCA_015232685.1_ASM1523268v1_genomic.fna/target_genomes.txt
[2023-06-28 14:06:41,940] [INFO] Task started: fastANI
[2023-06-28 14:06:41,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg52716496-38bb-4418-9a54-1f1b8827279a/GCA_015232685.1_ASM1523268v1_genomic.fna.gz --refList GCA_015232685.1_ASM1523268v1_genomic.fna/target_genomes.txt --output GCA_015232685.1_ASM1523268v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:06:51,928] [INFO] Task succeeded: fastANI
[2023-06-28 14:06:51,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4741bdd1-a8dd-4948-869e-9b46c7f7b949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:06:51,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4741bdd1-a8dd-4948-869e-9b46c7f7b949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:06:51,931] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:06:51,931] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 14:06:51,932] [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 14:06:51,934] [INFO] DFAST Taxonomy check result was written to GCA_015232685.1_ASM1523268v1_genomic.fna/tc_result.tsv
[2023-06-28 14:06:51,934] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:06:51,935] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:06:51,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4741bdd1-a8dd-4948-869e-9b46c7f7b949/dqc_reference/checkm_data
[2023-06-28 14:06:51,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:06:51,970] [INFO] Task started: CheckM
[2023-06-28 14:06:51,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015232685.1_ASM1523268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015232685.1_ASM1523268v1_genomic.fna/checkm_input GCA_015232685.1_ASM1523268v1_genomic.fna/checkm_result
[2023-06-28 14:07:24,674] [INFO] Task succeeded: CheckM
[2023-06-28 14:07:24,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:07:24,695] [INFO] ===== Completeness check finished =====
[2023-06-28 14:07:24,695] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:07:24,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015232685.1_ASM1523268v1_genomic.fna/markers.fasta)
[2023-06-28 14:07:24,696] [INFO] Task started: Blastn
[2023-06-28 14:07:24,696] [INFO] Running command: blastn -query GCA_015232685.1_ASM1523268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4741bdd1-a8dd-4948-869e-9b46c7f7b949/dqc_reference/reference_markers_gtdb.fasta -out GCA_015232685.1_ASM1523268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:07:25,830] [INFO] Task succeeded: Blastn
[2023-06-28 14:07:25,835] [INFO] Selected 15 target genomes.
[2023-06-28 14:07:25,835] [INFO] Target genome list was writen to GCA_015232685.1_ASM1523268v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:07:25,841] [INFO] Task started: fastANI
[2023-06-28 14:07:25,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg52716496-38bb-4418-9a54-1f1b8827279a/GCA_015232685.1_ASM1523268v1_genomic.fna.gz --refList GCA_015232685.1_ASM1523268v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015232685.1_ASM1523268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:07:35,693] [INFO] Task succeeded: fastANI
[2023-06-28 14:07:35,700] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 14:07:35,701] [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_002753515.1	s__UBA8363 sp002753515	95.6784	784	959	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__UBA8363;g__UBA8363	95.0	97.02	95.52	0.84	0.80	4	inconclusive
GCA_015228975.1	s__UBA8363 sp015228975	95.5665	642	959	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__UBA8363;g__UBA8363	95.0	95.91	95.91	0.77	0.77	2	inconclusive
GCA_002753735.1	s__UBA8363 sp002753735	77.6885	217	959	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__UBA8363;g__UBA8363	95.0	99.34	98.94	0.91	0.90	7	-
GCA_015228925.1	s__UBA8363 sp015228925	77.362	164	959	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__UBA8363;g__UBA8363	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660855.1	s__UBA8363 sp013349385	77.2355	209	959	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__UBA8363;g__UBA8363	95.0	99.80	99.80	0.97	0.97	2	-
GCA_015232645.1	s__UBA8363 sp015232645	77.2263	167	959	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__UBA8363;g__UBA8363	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002753615.1	s__UBA8363 sp002753615	77.0141	128	959	d__Bacteria;p__Proteobacteria;c__Magnetococcia;o__Magnetococcales;f__UBA8363;g__UBA8363	95.0	99.68	99.58	0.84	0.78	3	-
--------------------------------------------------------------------------------
[2023-06-28 14:07:35,702] [INFO] GTDB search result was written to GCA_015232685.1_ASM1523268v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:07:35,703] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:07:35,706] [INFO] DFAST_QC result json was written to GCA_015232685.1_ASM1523268v1_genomic.fna/dqc_result.json
[2023-06-28 14:07:35,707] [INFO] DFAST_QC completed!
[2023-06-28 14:07:35,707] [INFO] Total running time: 0h1m6s