[2024-01-25 18:02:05,836] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:05,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:05,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg34097dfe-bba1-4dbd-a51a-7ba9b0d896ef/dqc_reference
[2024-01-25 18:02:07,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:07,020] [INFO] Task started: Prodigal
[2024-01-25 18:02:07,020] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6ec5f94-19fb-4d87-b55a-3bc33d3d8f90/GCF_000375425.1_ASM37542v1_genomic.fna.gz | prodigal -d GCF_000375425.1_ASM37542v1_genomic.fna/cds.fna -a GCF_000375425.1_ASM37542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:21,863] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:21,863] [INFO] Task started: HMMsearch
[2024-01-25 18:02:21,863] [INFO] Running command: hmmsearch --tblout GCF_000375425.1_ASM37542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34097dfe-bba1-4dbd-a51a-7ba9b0d896ef/dqc_reference/reference_markers.hmm GCF_000375425.1_ASM37542v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:22,085] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:22,087] [INFO] Found 6/6 markers.
[2024-01-25 18:02:22,117] [INFO] Query marker FASTA was written to GCF_000375425.1_ASM37542v1_genomic.fna/markers.fasta
[2024-01-25 18:02:22,118] [INFO] Task started: Blastn
[2024-01-25 18:02:22,118] [INFO] Running command: blastn -query GCF_000375425.1_ASM37542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34097dfe-bba1-4dbd-a51a-7ba9b0d896ef/dqc_reference/reference_markers.fasta -out GCF_000375425.1_ASM37542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:22,653] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:22,656] [INFO] Selected 16 target genomes.
[2024-01-25 18:02:22,657] [INFO] Target genome list was writen to GCF_000375425.1_ASM37542v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:22,661] [INFO] Task started: fastANI
[2024-01-25 18:02:22,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6ec5f94-19fb-4d87-b55a-3bc33d3d8f90/GCF_000375425.1_ASM37542v1_genomic.fna.gz --refList GCF_000375425.1_ASM37542v1_genomic.fna/target_genomes.txt --output GCF_000375425.1_ASM37542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:34,514] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:34,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34097dfe-bba1-4dbd-a51a-7ba9b0d896ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:34,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34097dfe-bba1-4dbd-a51a-7ba9b0d896ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:34,519] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:34,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:34,519] [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
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	100.0	1248	1250	95	conclusive
Gracilimonas amylolytica	strain=LA399	GCA_002911695.1	1749045	1749045	type	True	79.0744	294	1250	95	below_threshold
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	77.7316	245	1250	95	below_threshold
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	76.5596	57	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:34,520] [INFO] DFAST Taxonomy check result was written to GCF_000375425.1_ASM37542v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:34,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:34,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:34,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34097dfe-bba1-4dbd-a51a-7ba9b0d896ef/dqc_reference/checkm_data
[2024-01-25 18:02:34,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:34,570] [INFO] Task started: CheckM
[2024-01-25 18:02:34,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000375425.1_ASM37542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000375425.1_ASM37542v1_genomic.fna/checkm_input GCF_000375425.1_ASM37542v1_genomic.fna/checkm_result
[2024-01-25 18:03:20,000] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:20,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:20,021] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:20,021] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:20,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000375425.1_ASM37542v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:20,022] [INFO] Task started: Blastn
[2024-01-25 18:03:20,022] [INFO] Running command: blastn -query GCF_000375425.1_ASM37542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34097dfe-bba1-4dbd-a51a-7ba9b0d896ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_000375425.1_ASM37542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:20,822] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:20,824] [INFO] Selected 16 target genomes.
[2024-01-25 18:03:20,825] [INFO] Target genome list was writen to GCF_000375425.1_ASM37542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:20,832] [INFO] Task started: fastANI
[2024-01-25 18:03:20,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6ec5f94-19fb-4d87-b55a-3bc33d3d8f90/GCF_000375425.1_ASM37542v1_genomic.fna.gz --refList GCF_000375425.1_ASM37542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000375425.1_ASM37542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:31,818] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:31,824] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:31,825] [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_000375425.1	s__Gracilimonas tropica	100.0	1248	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002696035.1	s__Gracilimonas sp002696035	79.2393	537	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002911695.1	s__Gracilimonas amylolytica	79.0183	293	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017641085.1	s__Gracilimonas sp017641085	78.6082	326	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014762685.1	s__Gracilimonas sp014762685	78.4867	282	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694685.1	s__Gracilimonas sp002694685	78.386	270	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCF_900182705.1	s__Gracilimonas mengyeensis	77.7453	244	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364085.1	s__Balneola sp002364085	76.5359	78	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	-
GCA_009711805.1	s__MES10 sp009711805	76.517	107	1250	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__MES10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:31,826] [INFO] GTDB search result was written to GCF_000375425.1_ASM37542v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:31,826] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:31,829] [INFO] DFAST_QC result json was written to GCF_000375425.1_ASM37542v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:31,829] [INFO] DFAST_QC completed!
[2024-01-25 18:03:31,829] [INFO] Total running time: 0h1m26s