[2024-01-24 13:28:44,485] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:44,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:44,488] [INFO] DQC Reference Directory: /var/lib/cwl/stgab5004e5-857a-4ceb-9706-54a968ade321/dqc_reference
[2024-01-24 13:28:45,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:45,744] [INFO] Task started: Prodigal
[2024-01-24 13:28:45,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg8612c169-7c77-4d95-986d-34f57fc0ba8a/GCF_000429165.1_ASM42916v1_genomic.fna.gz | prodigal -d GCF_000429165.1_ASM42916v1_genomic.fna/cds.fna -a GCF_000429165.1_ASM42916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:57,852] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:57,852] [INFO] Task started: HMMsearch
[2024-01-24 13:28:57,853] [INFO] Running command: hmmsearch --tblout GCF_000429165.1_ASM42916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab5004e5-857a-4ceb-9706-54a968ade321/dqc_reference/reference_markers.hmm GCF_000429165.1_ASM42916v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:58,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:58,174] [INFO] Found 6/6 markers.
[2024-01-24 13:28:58,212] [INFO] Query marker FASTA was written to GCF_000429165.1_ASM42916v1_genomic.fna/markers.fasta
[2024-01-24 13:28:58,213] [INFO] Task started: Blastn
[2024-01-24 13:28:58,213] [INFO] Running command: blastn -query GCF_000429165.1_ASM42916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab5004e5-857a-4ceb-9706-54a968ade321/dqc_reference/reference_markers.fasta -out GCF_000429165.1_ASM42916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:58,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:58,978] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:58,979] [INFO] Target genome list was writen to GCF_000429165.1_ASM42916v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:58,987] [INFO] Task started: fastANI
[2024-01-24 13:28:58,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg8612c169-7c77-4d95-986d-34f57fc0ba8a/GCF_000429165.1_ASM42916v1_genomic.fna.gz --refList GCF_000429165.1_ASM42916v1_genomic.fna/target_genomes.txt --output GCF_000429165.1_ASM42916v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:11,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:11,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab5004e5-857a-4ceb-9706-54a968ade321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:11,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab5004e5-857a-4ceb-9706-54a968ade321/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:11,398] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:11,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:11,399] [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
Acetobacter nitrogenifigens	strain=DSM 23921	GCA_000429165.1	285268	285268	type	True	100.0	1390	1393	95	conclusive
Acetobacter nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	99.9574	1347	1393	95	conclusive
Acetobacter sacchari	strain=TBRC 11175	GCA_017377715.1	2661687	2661687	type	True	92.7944	1194	1393	95	below_threshold
Acetobacter aceti	strain=DSM 3508	GCA_004341595.1	435	435	type	True	78.8727	245	1393	95	below_threshold
Acetobacter aceti	strain=NBRC 14818	GCA_000193495.2	435	435	type	True	78.7673	252	1393	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	78.4974	258	1393	95	below_threshold
Acetobacter fallax	strain=LMG 1636	GCA_011516735.1	1737473	1737473	type	True	78.4953	248	1393	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	78.4639	261	1393	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	78.0678	260	1393	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	78.045	138	1393	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.0171	265	1393	95	below_threshold
Komagataeibacter xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	77.9646	189	1393	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	77.8595	186	1393	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	77.6384	193	1393	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.0602	93	1393	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.6463	164	1393	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.5896	88	1393	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.5364	91	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:11,404] [INFO] DFAST Taxonomy check result was written to GCF_000429165.1_ASM42916v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:11,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:11,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:11,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab5004e5-857a-4ceb-9706-54a968ade321/dqc_reference/checkm_data
[2024-01-24 13:29:11,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:11,468] [INFO] Task started: CheckM
[2024-01-24 13:29:11,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429165.1_ASM42916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429165.1_ASM42916v1_genomic.fna/checkm_input GCF_000429165.1_ASM42916v1_genomic.fna/checkm_result
[2024-01-24 13:29:50,266] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:50,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:50,289] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:50,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:50,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429165.1_ASM42916v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:50,290] [INFO] Task started: Blastn
[2024-01-24 13:29:50,290] [INFO] Running command: blastn -query GCF_000429165.1_ASM42916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab5004e5-857a-4ceb-9706-54a968ade321/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429165.1_ASM42916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:51,433] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:51,436] [INFO] Selected 17 target genomes.
[2024-01-24 13:29:51,437] [INFO] Target genome list was writen to GCF_000429165.1_ASM42916v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:51,450] [INFO] Task started: fastANI
[2024-01-24 13:29:51,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg8612c169-7c77-4d95-986d-34f57fc0ba8a/GCF_000429165.1_ASM42916v1_genomic.fna.gz --refList GCF_000429165.1_ASM42916v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429165.1_ASM42916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:03,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:03,144] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:03,144] [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_000429165.1	s__Acetobacter nitrogenifigens	100.0	1390	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017377715.1	s__Acetobacter sacchari	92.8167	1192	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153745.1	s__Acetobacter sp002153745	91.799	790	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000193495.2	s__Acetobacter aceti	78.7666	251	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.82	96.47	0.96	0.89	7	-
GCF_011516765.1	s__Acetobacter sicerae	78.6322	273	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005445.1	s__Acetobacter aceti_B	78.6122	235	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516755.1	s__Acetobacter conturbans	78.597	264	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516735.1	s__Acetobacter fallax	78.4882	248	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	78.4488	262	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_013376175.1	s__Ameyamaea chiangmaiensis	78.4423	201	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	-
GCF_019083805.1	s__Acetobacter estunensis_A	78.3351	244	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002409645.1	s__Acetobacter sp002409645	78.1497	213	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	78.066	195	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	78.0494	263	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	78.0381	267	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001571345.1	s__Komagataeibacter xylinus	77.8658	185	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.56	99.15	0.93	0.88	3	-
GCF_003403295.1	s__Komagataeibacter melaceti	77.6538	192	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:03,146] [INFO] GTDB search result was written to GCF_000429165.1_ASM42916v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:03,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:03,157] [INFO] DFAST_QC result json was written to GCF_000429165.1_ASM42916v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:03,157] [INFO] DFAST_QC completed!
[2024-01-24 13:30:03,157] [INFO] Total running time: 0h1m19s