[2024-01-25 18:41:20,739] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:20,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:20,741] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4db69d5-e5d0-4b26-b15b-45694bfe3abd/dqc_reference
[2024-01-25 18:41:21,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:21,909] [INFO] Task started: Prodigal
[2024-01-25 18:41:21,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgc96d38f4-ef09-4bb9-8891-1879c10df21b/GCF_014878255.1_ASM1487825v1_genomic.fna.gz | prodigal -d GCF_014878255.1_ASM1487825v1_genomic.fna/cds.fna -a GCF_014878255.1_ASM1487825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:27,606] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:27,607] [INFO] Task started: HMMsearch
[2024-01-25 18:41:27,607] [INFO] Running command: hmmsearch --tblout GCF_014878255.1_ASM1487825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4db69d5-e5d0-4b26-b15b-45694bfe3abd/dqc_reference/reference_markers.hmm GCF_014878255.1_ASM1487825v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:27,820] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:27,821] [INFO] Found 6/6 markers.
[2024-01-25 18:41:27,842] [INFO] Query marker FASTA was written to GCF_014878255.1_ASM1487825v1_genomic.fna/markers.fasta
[2024-01-25 18:41:27,842] [INFO] Task started: Blastn
[2024-01-25 18:41:27,843] [INFO] Running command: blastn -query GCF_014878255.1_ASM1487825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4db69d5-e5d0-4b26-b15b-45694bfe3abd/dqc_reference/reference_markers.fasta -out GCF_014878255.1_ASM1487825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:28,576] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:28,580] [INFO] Selected 17 target genomes.
[2024-01-25 18:41:28,580] [INFO] Target genome list was writen to GCF_014878255.1_ASM1487825v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:28,603] [INFO] Task started: fastANI
[2024-01-25 18:41:28,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgc96d38f4-ef09-4bb9-8891-1879c10df21b/GCF_014878255.1_ASM1487825v1_genomic.fna.gz --refList GCF_014878255.1_ASM1487825v1_genomic.fna/target_genomes.txt --output GCF_014878255.1_ASM1487825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:38,087] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:38,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4db69d5-e5d0-4b26-b15b-45694bfe3abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:38,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4db69d5-e5d0-4b26-b15b-45694bfe3abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:38,096] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:41:38,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:38,096] [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
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	100.0	674	674	95	conclusive
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	99.9898	672	674	95	conclusive
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	83.4151	556	674	95	below_threshold
Bombella intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	83.1948	538	674	95	below_threshold
Acidomonas methanolica	strain=NBRC 104435	GCA_007988925.1	437	437	type	True	78.222	98	674	95	below_threshold
Gluconobacter vitians	strain=LMG 31484	GCA_015244565.1	2728102	2728102	type	True	77.6553	128	674	95	below_threshold
Gluconobacter japonicus	strain=NBRC 3271	GCA_002723975.1	376620	376620	type	True	77.3386	108	674	95	below_threshold
Oecophyllibacter saccharovorans	strain=Ha5	GCA_006542375.1	2558360	2558360	type	True	77.085	124	674	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	76.9898	107	674	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	76.1436	61	674	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.0497	55	674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:38,099] [INFO] DFAST Taxonomy check result was written to GCF_014878255.1_ASM1487825v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:38,100] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:38,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:38,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4db69d5-e5d0-4b26-b15b-45694bfe3abd/dqc_reference/checkm_data
[2024-01-25 18:41:38,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:38,126] [INFO] Task started: CheckM
[2024-01-25 18:41:38,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014878255.1_ASM1487825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014878255.1_ASM1487825v1_genomic.fna/checkm_input GCF_014878255.1_ASM1487825v1_genomic.fna/checkm_result
[2024-01-25 18:42:00,692] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:00,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:00,707] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:00,707] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:00,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014878255.1_ASM1487825v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:00,708] [INFO] Task started: Blastn
[2024-01-25 18:42:00,708] [INFO] Running command: blastn -query GCF_014878255.1_ASM1487825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4db69d5-e5d0-4b26-b15b-45694bfe3abd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014878255.1_ASM1487825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:01,968] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:01,970] [INFO] Selected 12 target genomes.
[2024-01-25 18:42:01,970] [INFO] Target genome list was writen to GCF_014878255.1_ASM1487825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:01,976] [INFO] Task started: fastANI
[2024-01-25 18:42:01,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgc96d38f4-ef09-4bb9-8891-1879c10df21b/GCF_014878255.1_ASM1487825v1_genomic.fna.gz --refList GCF_014878255.1_ASM1487825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014878255.1_ASM1487825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:08,418] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:08,425] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:08,425] [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_018221685.1	s__Bombella apis	99.9898	672	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	conclusive
GCF_014048465.1	s__Bombella mellum	87.9668	564	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014048475.1	s__Bombella favorum	83.4151	556	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002003665.1	s__Bombella intestini	83.1948	538	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725755.1	s__Bombella sp009725755	78.4437	249	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.22	99.22	0.99	0.99	2	-
GCF_002592045.1	s__Bombella apium_A	78.3216	228	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346035.1	s__Acidomonas methanolica	78.1303	97	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidomonas	95.0	99.93	99.80	0.99	0.98	4	-
GCF_000234355.1	s__Gluconobacter_C morbifer	77.4633	130	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403295.1	s__Komagataeibacter melaceti	76.9689	108	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764365.1	s__Roseococcus sp014764365	76.0795	54	674	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:08,426] [INFO] GTDB search result was written to GCF_014878255.1_ASM1487825v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:08,427] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:08,429] [INFO] DFAST_QC result json was written to GCF_014878255.1_ASM1487825v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:08,429] [INFO] DFAST_QC completed!
[2024-01-25 18:42:08,429] [INFO] Total running time: 0h0m48s