[2023-06-19 09:52:10,878] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:52:10,882] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:52:10,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg31b85d41-e3ba-4a15-a5d3-0cc2e0091045/dqc_reference
[2023-06-19 09:52:12,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:52:12,228] [INFO] Task started: Prodigal
[2023-06-19 09:52:12,228] [INFO] Running command: gunzip -c /var/lib/cwl/stga66b0f55-17f6-450b-8723-76ed1bf03251/GCA_014304925.1_ASM1430492v1_genomic.fna.gz | prodigal -d GCA_014304925.1_ASM1430492v1_genomic.fna/cds.fna -a GCA_014304925.1_ASM1430492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:52:20,482] [INFO] Task succeeded: Prodigal
[2023-06-19 09:52:20,482] [INFO] Task started: HMMsearch
[2023-06-19 09:52:20,482] [INFO] Running command: hmmsearch --tblout GCA_014304925.1_ASM1430492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31b85d41-e3ba-4a15-a5d3-0cc2e0091045/dqc_reference/reference_markers.hmm GCA_014304925.1_ASM1430492v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:52:20,757] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:52:20,759] [INFO] Found 6/6 markers.
[2023-06-19 09:52:20,795] [INFO] Query marker FASTA was written to GCA_014304925.1_ASM1430492v1_genomic.fna/markers.fasta
[2023-06-19 09:52:20,795] [INFO] Task started: Blastn
[2023-06-19 09:52:20,795] [INFO] Running command: blastn -query GCA_014304925.1_ASM1430492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31b85d41-e3ba-4a15-a5d3-0cc2e0091045/dqc_reference/reference_markers.fasta -out GCA_014304925.1_ASM1430492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:52:21,452] [INFO] Task succeeded: Blastn
[2023-06-19 09:52:21,457] [INFO] Selected 25 target genomes.
[2023-06-19 09:52:21,457] [INFO] Target genome list was writen to GCA_014304925.1_ASM1430492v1_genomic.fna/target_genomes.txt
[2023-06-19 09:52:21,462] [INFO] Task started: fastANI
[2023-06-19 09:52:21,462] [INFO] Running command: fastANI --query /var/lib/cwl/stga66b0f55-17f6-450b-8723-76ed1bf03251/GCA_014304925.1_ASM1430492v1_genomic.fna.gz --refList GCA_014304925.1_ASM1430492v1_genomic.fna/target_genomes.txt --output GCA_014304925.1_ASM1430492v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:52:38,130] [INFO] Task succeeded: fastANI
[2023-06-19 09:52:38,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31b85d41-e3ba-4a15-a5d3-0cc2e0091045/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:52:38,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31b85d41-e3ba-4a15-a5d3-0cc2e0091045/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:52:38,135] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:52:38,135] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:52:38,135] [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
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	74.6909	52	931	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:52:38,138] [INFO] DFAST Taxonomy check result was written to GCA_014304925.1_ASM1430492v1_genomic.fna/tc_result.tsv
[2023-06-19 09:52:38,139] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:52:38,139] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:52:38,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31b85d41-e3ba-4a15-a5d3-0cc2e0091045/dqc_reference/checkm_data
[2023-06-19 09:52:38,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:52:38,178] [INFO] Task started: CheckM
[2023-06-19 09:52:38,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014304925.1_ASM1430492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014304925.1_ASM1430492v1_genomic.fna/checkm_input GCA_014304925.1_ASM1430492v1_genomic.fna/checkm_result
[2023-06-19 09:53:06,920] [INFO] Task succeeded: CheckM
[2023-06-19 09:53:06,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.49%
Contamintation: 2.55%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-19 09:53:06,951] [INFO] ===== Completeness check finished =====
[2023-06-19 09:53:06,951] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:53:06,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014304925.1_ASM1430492v1_genomic.fna/markers.fasta)
[2023-06-19 09:53:06,952] [INFO] Task started: Blastn
[2023-06-19 09:53:06,952] [INFO] Running command: blastn -query GCA_014304925.1_ASM1430492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31b85d41-e3ba-4a15-a5d3-0cc2e0091045/dqc_reference/reference_markers_gtdb.fasta -out GCA_014304925.1_ASM1430492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:53:07,947] [INFO] Task succeeded: Blastn
[2023-06-19 09:53:07,953] [INFO] Selected 16 target genomes.
[2023-06-19 09:53:07,953] [INFO] Target genome list was writen to GCA_014304925.1_ASM1430492v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:53:07,957] [INFO] Task started: fastANI
[2023-06-19 09:53:07,958] [INFO] Running command: fastANI --query /var/lib/cwl/stga66b0f55-17f6-450b-8723-76ed1bf03251/GCA_014304925.1_ASM1430492v1_genomic.fna.gz --refList GCA_014304925.1_ASM1430492v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014304925.1_ASM1430492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:53:16,396] [INFO] Task succeeded: fastANI
[2023-06-19 09:53:16,416] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:53:16,417] [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_014305025.1	s__Nyctobacter psychrophilus	99.9393	875	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Nyctobacter	95.0	99.96	99.94	0.96	0.94	3	conclusive
GCA_014304965.1	s__Cryoxeromicrobium davisii	77.7486	132	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Cryoxeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970385.1	s__Palsa-1515 sp903970385	77.3655	240	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Palsa-1515	95.0	97.40	97.40	0.78	0.78	2	-
GCA_003158195.1	s__Palsibacter borealis	77.0319	186	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Palsibacter	95.0	99.15	99.15	0.89	0.89	2	-
GCA_003136895.1	s__Erabacter solicola	76.7547	143	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Erabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003156715.1	s__Tityobacter terrigena	76.6913	158	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Tityobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134695.1	s__Zemynaea palustris	76.6003	150	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Zemynaea	95.0	99.68	99.42	0.94	0.92	6	-
GCA_003136655.1	s__Hesperobacter lustricola	76.5176	181	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Hesperobacter	95.0	99.53	99.53	0.92	0.92	2	-
GCA_002413145.1	s__Zemynaea sp002413145	76.4928	89	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Zemynaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168375.1	s__Elarobacter winogradskyi	76.3117	137	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Elarobacter	95.0	99.98	99.85	1.00	0.97	12	-
GCA_003164495.1	s__Lustribacter caenicola	75.8136	110	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Lustribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236975.1	s__JAFAHZ01 sp019236975	75.7707	79	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__JAFAHZ01	95.0	98.54	98.14	0.85	0.83	4	-
GCA_003167155.1	s__Cybelea tumulisoli	75.659	64	931	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Cybelea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 09:53:16,419] [INFO] GTDB search result was written to GCA_014304925.1_ASM1430492v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:53:16,422] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:53:16,426] [INFO] DFAST_QC result json was written to GCA_014304925.1_ASM1430492v1_genomic.fna/dqc_result.json
[2023-06-19 09:53:16,426] [INFO] DFAST_QC completed!
[2023-06-19 09:53:16,426] [INFO] Total running time: 0h1m6s