[2023-06-05 01:53:57,709] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:53:57,724] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:53:57,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg32baf083-cd79-47cf-a440-a126b0d89078/dqc_reference
[2023-06-05 01:53:59,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:53:59,410] [INFO] Task started: Prodigal
[2023-06-05 01:53:59,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e31588e-2082-46f0-8284-47080194cb4a/GCA_004377445.1_ASM437744v1_genomic.fna.gz | prodigal -d GCA_004377445.1_ASM437744v1_genomic.fna/cds.fna -a GCA_004377445.1_ASM437744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:54:00,752] [INFO] Task succeeded: Prodigal
[2023-06-05 01:54:00,752] [INFO] Task started: HMMsearch
[2023-06-05 01:54:00,752] [INFO] Running command: hmmsearch --tblout GCA_004377445.1_ASM437744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32baf083-cd79-47cf-a440-a126b0d89078/dqc_reference/reference_markers.hmm GCA_004377445.1_ASM437744v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:54:00,970] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:54:00,971] [INFO] Found 6/6 markers.
[2023-06-05 01:54:00,988] [INFO] Query marker FASTA was written to GCA_004377445.1_ASM437744v1_genomic.fna/markers.fasta
[2023-06-05 01:54:00,989] [INFO] Task started: Blastn
[2023-06-05 01:54:00,989] [INFO] Running command: blastn -query GCA_004377445.1_ASM437744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32baf083-cd79-47cf-a440-a126b0d89078/dqc_reference/reference_markers.fasta -out GCA_004377445.1_ASM437744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:54:02,405] [INFO] Task succeeded: Blastn
[2023-06-05 01:54:02,410] [INFO] Selected 26 target genomes.
[2023-06-05 01:54:02,411] [INFO] Target genome list was writen to GCA_004377445.1_ASM437744v1_genomic.fna/target_genomes.txt
[2023-06-05 01:54:02,595] [INFO] Task started: fastANI
[2023-06-05 01:54:02,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e31588e-2082-46f0-8284-47080194cb4a/GCA_004377445.1_ASM437744v1_genomic.fna.gz --refList GCA_004377445.1_ASM437744v1_genomic.fna/target_genomes.txt --output GCA_004377445.1_ASM437744v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:54:16,701] [INFO] Task succeeded: fastANI
[2023-06-05 01:54:16,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32baf083-cd79-47cf-a440-a126b0d89078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:54:16,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32baf083-cd79-47cf-a440-a126b0d89078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:54:16,704] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:54:16,704] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 01:54:16,704] [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
--------------------------------------------------------------------------------
[2023-06-05 01:54:16,706] [INFO] DFAST Taxonomy check result was written to GCA_004377445.1_ASM437744v1_genomic.fna/tc_result.tsv
[2023-06-05 01:54:16,707] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:54:16,707] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:54:16,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32baf083-cd79-47cf-a440-a126b0d89078/dqc_reference/checkm_data
[2023-06-05 01:54:16,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:54:16,725] [INFO] Task started: CheckM
[2023-06-05 01:54:16,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004377445.1_ASM437744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004377445.1_ASM437744v1_genomic.fna/checkm_input GCA_004377445.1_ASM437744v1_genomic.fna/checkm_result
[2023-06-05 01:54:29,784] [INFO] Task succeeded: CheckM
[2023-06-05 01:54:29,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.26%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 01:54:29,808] [INFO] ===== Completeness check finished =====
[2023-06-05 01:54:29,808] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:54:29,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004377445.1_ASM437744v1_genomic.fna/markers.fasta)
[2023-06-05 01:54:29,809] [INFO] Task started: Blastn
[2023-06-05 01:54:29,809] [INFO] Running command: blastn -query GCA_004377445.1_ASM437744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32baf083-cd79-47cf-a440-a126b0d89078/dqc_reference/reference_markers_gtdb.fasta -out GCA_004377445.1_ASM437744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:54:30,667] [INFO] Task succeeded: Blastn
[2023-06-05 01:54:30,672] [INFO] Selected 10 target genomes.
[2023-06-05 01:54:30,672] [INFO] Target genome list was writen to GCA_004377445.1_ASM437744v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:54:30,854] [INFO] Task started: fastANI
[2023-06-05 01:54:30,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e31588e-2082-46f0-8284-47080194cb4a/GCA_004377445.1_ASM437744v1_genomic.fna.gz --refList GCA_004377445.1_ASM437744v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004377445.1_ASM437744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:54:32,758] [INFO] Task succeeded: fastANI
[2023-06-05 01:54:32,766] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 01:54:32,766] [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_016845205.1	s__UBA2013 sp016845205	84.1977	83	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335045.1	s__UBA2013 sp002335045	84.1221	85	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_003978285.1	s__UBA2013 sp003978285	83.5468	67	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003489145.1	s__UBA2013 sp003489145	83.2975	77	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	99.21	98.78	0.83	0.78	42	-
GCA_003978185.1	s__UBA2013 sp003978185	82.987	55	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648985.1	s__UBA2013 sp018648985	82.9724	74	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910595805.1	s__UBA2013 sp910595805	81.6248	67	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658965.1	s__UBA2013 sp015658965	80.3028	68	95	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:54:32,768] [INFO] GTDB search result was written to GCA_004377445.1_ASM437744v1_genomic.fna/result_gtdb.tsv
[2023-06-05 01:54:32,769] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:54:32,771] [INFO] DFAST_QC result json was written to GCA_004377445.1_ASM437744v1_genomic.fna/dqc_result.json
[2023-06-05 01:54:32,772] [INFO] DFAST_QC completed!
[2023-06-05 01:54:32,772] [INFO] Total running time: 0h0m35s