[2023-06-17 11:26:05,712] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:05,720] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:05,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d6874c3-f9cf-4c0f-8c78-357be46d0156/dqc_reference
[2023-06-17 11:26:07,289] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:07,290] [INFO] Task started: Prodigal
[2023-06-17 11:26:07,290] [INFO] Running command: gunzip -c /var/lib/cwl/stgc92dbb95-e218-42ed-ad11-268724d75658/GCA_003449875.1_ASM344987v1_genomic.fna.gz | prodigal -d GCA_003449875.1_ASM344987v1_genomic.fna/cds.fna -a GCA_003449875.1_ASM344987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:26:18,060] [INFO] Task succeeded: Prodigal
[2023-06-17 11:26:18,060] [INFO] Task started: HMMsearch
[2023-06-17 11:26:18,060] [INFO] Running command: hmmsearch --tblout GCA_003449875.1_ASM344987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d6874c3-f9cf-4c0f-8c78-357be46d0156/dqc_reference/reference_markers.hmm GCA_003449875.1_ASM344987v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:26:18,367] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:26:18,369] [INFO] Found 6/6 markers.
[2023-06-17 11:26:18,419] [INFO] Query marker FASTA was written to GCA_003449875.1_ASM344987v1_genomic.fna/markers.fasta
[2023-06-17 11:26:18,420] [INFO] Task started: Blastn
[2023-06-17 11:26:18,420] [INFO] Running command: blastn -query GCA_003449875.1_ASM344987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d6874c3-f9cf-4c0f-8c78-357be46d0156/dqc_reference/reference_markers.fasta -out GCA_003449875.1_ASM344987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:19,047] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:19,051] [INFO] Selected 16 target genomes.
[2023-06-17 11:26:19,052] [INFO] Target genome list was writen to GCA_003449875.1_ASM344987v1_genomic.fna/target_genomes.txt
[2023-06-17 11:26:19,058] [INFO] Task started: fastANI
[2023-06-17 11:26:19,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92dbb95-e218-42ed-ad11-268724d75658/GCA_003449875.1_ASM344987v1_genomic.fna.gz --refList GCA_003449875.1_ASM344987v1_genomic.fna/target_genomes.txt --output GCA_003449875.1_ASM344987v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:26:29,907] [INFO] Task succeeded: fastANI
[2023-06-17 11:26:29,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d6874c3-f9cf-4c0f-8c78-357be46d0156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:26:29,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d6874c3-f9cf-4c0f-8c78-357be46d0156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:26:29,914] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:26:29,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:26:29,914] [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
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	77.5316	132	950	95	below_threshold
Gracilimonas amylolytica	strain=LA399	GCA_002911695.1	1749045	1749045	type	True	76.1715	62	950	95	below_threshold
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	75.9463	52	950	95	below_threshold
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	75.8314	74	950	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:26:29,916] [INFO] DFAST Taxonomy check result was written to GCA_003449875.1_ASM344987v1_genomic.fna/tc_result.tsv
[2023-06-17 11:26:29,917] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:26:29,917] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:26:29,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d6874c3-f9cf-4c0f-8c78-357be46d0156/dqc_reference/checkm_data
[2023-06-17 11:26:29,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:26:29,954] [INFO] Task started: CheckM
[2023-06-17 11:26:29,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003449875.1_ASM344987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003449875.1_ASM344987v1_genomic.fna/checkm_input GCA_003449875.1_ASM344987v1_genomic.fna/checkm_result
[2023-06-17 11:27:05,153] [INFO] Task succeeded: CheckM
[2023-06-17 11:27:05,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:27:05,174] [INFO] ===== Completeness check finished =====
[2023-06-17 11:27:05,174] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:27:05,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003449875.1_ASM344987v1_genomic.fna/markers.fasta)
[2023-06-17 11:27:05,175] [INFO] Task started: Blastn
[2023-06-17 11:27:05,175] [INFO] Running command: blastn -query GCA_003449875.1_ASM344987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d6874c3-f9cf-4c0f-8c78-357be46d0156/dqc_reference/reference_markers_gtdb.fasta -out GCA_003449875.1_ASM344987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:05,984] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:05,989] [INFO] Selected 9 target genomes.
[2023-06-17 11:27:05,989] [INFO] Target genome list was writen to GCA_003449875.1_ASM344987v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:27:05,996] [INFO] Task started: fastANI
[2023-06-17 11:27:05,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92dbb95-e218-42ed-ad11-268724d75658/GCA_003449875.1_ASM344987v1_genomic.fna.gz --refList GCA_003449875.1_ASM344987v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003449875.1_ASM344987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:27:12,023] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:12,037] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:27:12,037] [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_002364085.1	s__Balneola sp002364085	99.7944	903	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	conclusive
GCA_017643645.1	s__Balneola sp017643645	86.0389	689	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.99	99.98	1.00	0.99	5	-
GCA_017640785.1	s__Balneola sp017640785	85.9117	672	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650905.1	s__Balneola sp001650905	85.3326	664	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	96.92	96.92	0.89	0.89	2	-
GCF_000375465.1	s__Balneola vulgaris	77.5316	132	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712055.1	s__RHLJ01 sp003712055	76.2191	77	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694685.1	s__Gracilimonas sp002694685	76.0858	96	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCF_000375425.1	s__Gracilimonas tropica	75.8314	74	950	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:27:12,039] [INFO] GTDB search result was written to GCA_003449875.1_ASM344987v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:27:12,040] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:27:12,043] [INFO] DFAST_QC result json was written to GCA_003449875.1_ASM344987v1_genomic.fna/dqc_result.json
[2023-06-17 11:27:12,043] [INFO] DFAST_QC completed!
[2023-06-17 11:27:12,043] [INFO] Total running time: 0h1m6s