[2024-01-24 10:58:17,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:17,089] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:17,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dbffcf7-f323-483e-b6d1-261f2d524a08/dqc_reference
[2024-01-24 10:58:18,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:18,376] [INFO] Task started: Prodigal
[2024-01-24 10:58:18,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ee8fefa-94ad-4b94-8fd4-e74820724ab2/GCF_001677435.1_ASM167743v1_genomic.fna.gz | prodigal -d GCF_001677435.1_ASM167743v1_genomic.fna/cds.fna -a GCF_001677435.1_ASM167743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:31,267] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:31,268] [INFO] Task started: HMMsearch
[2024-01-24 10:58:31,268] [INFO] Running command: hmmsearch --tblout GCF_001677435.1_ASM167743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dbffcf7-f323-483e-b6d1-261f2d524a08/dqc_reference/reference_markers.hmm GCF_001677435.1_ASM167743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:31,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:31,543] [INFO] Found 6/6 markers.
[2024-01-24 10:58:31,581] [INFO] Query marker FASTA was written to GCF_001677435.1_ASM167743v1_genomic.fna/markers.fasta
[2024-01-24 10:58:31,582] [INFO] Task started: Blastn
[2024-01-24 10:58:31,582] [INFO] Running command: blastn -query GCF_001677435.1_ASM167743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dbffcf7-f323-483e-b6d1-261f2d524a08/dqc_reference/reference_markers.fasta -out GCF_001677435.1_ASM167743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:32,328] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:32,331] [INFO] Selected 27 target genomes.
[2024-01-24 10:58:32,331] [INFO] Target genome list was writen to GCF_001677435.1_ASM167743v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:32,352] [INFO] Task started: fastANI
[2024-01-24 10:58:32,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ee8fefa-94ad-4b94-8fd4-e74820724ab2/GCF_001677435.1_ASM167743v1_genomic.fna.gz --refList GCF_001677435.1_ASM167743v1_genomic.fna/target_genomes.txt --output GCF_001677435.1_ASM167743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:51,476] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:51,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dbffcf7-f323-483e-b6d1-261f2d524a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:51,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dbffcf7-f323-483e-b6d1-261f2d524a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:51,482] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:51,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:51,482] [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
Woeseia oceani	strain=XK5	GCA_001677435.1	1548547	1548547	type	True	100.0	1353	1353	95	conclusive
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	75.953	51	1353	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	75.7085	58	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:51,484] [INFO] DFAST Taxonomy check result was written to GCF_001677435.1_ASM167743v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:51,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:51,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:51,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dbffcf7-f323-483e-b6d1-261f2d524a08/dqc_reference/checkm_data
[2024-01-24 10:58:51,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:51,530] [INFO] Task started: CheckM
[2024-01-24 10:58:51,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001677435.1_ASM167743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001677435.1_ASM167743v1_genomic.fna/checkm_input GCF_001677435.1_ASM167743v1_genomic.fna/checkm_result
[2024-01-24 10:59:31,436] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:31,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:31,462] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:31,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:31,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001677435.1_ASM167743v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:31,464] [INFO] Task started: Blastn
[2024-01-24 10:59:31,464] [INFO] Running command: blastn -query GCF_001677435.1_ASM167743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dbffcf7-f323-483e-b6d1-261f2d524a08/dqc_reference/reference_markers_gtdb.fasta -out GCF_001677435.1_ASM167743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:32,782] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:32,788] [INFO] Selected 25 target genomes.
[2024-01-24 10:59:32,788] [INFO] Target genome list was writen to GCF_001677435.1_ASM167743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:32,827] [INFO] Task started: fastANI
[2024-01-24 10:59:32,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ee8fefa-94ad-4b94-8fd4-e74820724ab2/GCF_001677435.1_ASM167743v1_genomic.fna.gz --refList GCF_001677435.1_ASM167743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001677435.1_ASM167743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:47,865] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:47,882] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:47,883] [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
GCF_001677435.1	s__Woeseia oceani	100.0	1353	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013003155.1	s__Woeseia sp013003155	76.8994	124	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	99.53	99.50	0.81	0.79	4	-
GCA_009937615.1	s__JAACFB01 sp009937615	76.5394	62	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151645.1	s__JAADHU01 sp013151645	76.5356	84	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAADHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138675.1	s__JAACFB01 sp013138675	76.4558	57	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043165.1	s__UBA1847 sp013043165	76.4126	80	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_013042375.1	s__UBA1847 sp013042375	76.2385	80	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_004282875.1	s__UBA1847 sp004282875	76.1735	69	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018677555.1	s__IDS-8 sp018677555	75.9776	90	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__IDS-8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937505.1	s__JAACFE01 sp009937505	75.9592	76	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790065.1	s__Steroidobacter_A sp016790065	75.831	51	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937445.1	s__UBA1847 sp009937445	75.7789	55	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:47,884] [INFO] GTDB search result was written to GCF_001677435.1_ASM167743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:47,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:47,888] [INFO] DFAST_QC result json was written to GCF_001677435.1_ASM167743v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:47,888] [INFO] DFAST_QC completed!
[2024-01-24 10:59:47,888] [INFO] Total running time: 0h1m31s