[2024-01-24 13:12:39,033] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:39,038] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:39,038] [INFO] DQC Reference Directory: /var/lib/cwl/stgcea5a674-56d8-4dc4-a266-cd6eef280983/dqc_reference
[2024-01-24 13:12:40,370] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,371] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,371] [INFO] Running command: gunzip -c /var/lib/cwl/stg11514b96-8e0a-4360-8b20-bfc62b86438f/GCF_003207955.1_ASM320795v1_genomic.fna.gz | prodigal -d GCF_003207955.1_ASM320795v1_genomic.fna/cds.fna -a GCF_003207955.1_ASM320795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:51,320] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:51,320] [INFO] Task started: HMMsearch
[2024-01-24 13:12:51,320] [INFO] Running command: hmmsearch --tblout GCF_003207955.1_ASM320795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcea5a674-56d8-4dc4-a266-cd6eef280983/dqc_reference/reference_markers.hmm GCF_003207955.1_ASM320795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:51,627] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:51,628] [INFO] Found 6/6 markers.
[2024-01-24 13:12:51,660] [INFO] Query marker FASTA was written to GCF_003207955.1_ASM320795v1_genomic.fna/markers.fasta
[2024-01-24 13:12:51,661] [INFO] Task started: Blastn
[2024-01-24 13:12:51,661] [INFO] Running command: blastn -query GCF_003207955.1_ASM320795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcea5a674-56d8-4dc4-a266-cd6eef280983/dqc_reference/reference_markers.fasta -out GCF_003207955.1_ASM320795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:52,496] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:52,500] [INFO] Selected 11 target genomes.
[2024-01-24 13:12:52,501] [INFO] Target genome list was writen to GCF_003207955.1_ASM320795v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:52,506] [INFO] Task started: fastANI
[2024-01-24 13:12:52,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg11514b96-8e0a-4360-8b20-bfc62b86438f/GCF_003207955.1_ASM320795v1_genomic.fna.gz --refList GCF_003207955.1_ASM320795v1_genomic.fna/target_genomes.txt --output GCF_003207955.1_ASM320795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:00,767] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:00,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcea5a674-56d8-4dc4-a266-cd6eef280983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:00,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcea5a674-56d8-4dc4-a266-cd6eef280983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:00,777] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:00,777] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:13:00,777] [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
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	100.0	1086	1092	95	inconclusive
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	95.1375	981	1092	95	inconclusive
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	86.6869	832	1092	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	86.6428	848	1092	95	below_threshold
Novacetimonas hansenii	strain=JCM 7643	GCA_000964405.1	436	436	type	True	84.4127	677	1092	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	79.3717	458	1092	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.2488	297	1092	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.1861	62	1092	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	75.9113	70	1092	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	75.7643	54	1092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:00,779] [INFO] DFAST Taxonomy check result was written to GCF_003207955.1_ASM320795v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:00,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:00,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:00,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcea5a674-56d8-4dc4-a266-cd6eef280983/dqc_reference/checkm_data
[2024-01-24 13:13:00,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:00,816] [INFO] Task started: CheckM
[2024-01-24 13:13:00,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003207955.1_ASM320795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003207955.1_ASM320795v1_genomic.fna/checkm_input GCF_003207955.1_ASM320795v1_genomic.fna/checkm_result
[2024-01-24 13:13:38,484] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:38,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,505] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:38,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:38,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003207955.1_ASM320795v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:38,507] [INFO] Task started: Blastn
[2024-01-24 13:13:38,507] [INFO] Running command: blastn -query GCF_003207955.1_ASM320795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcea5a674-56d8-4dc4-a266-cd6eef280983/dqc_reference/reference_markers_gtdb.fasta -out GCF_003207955.1_ASM320795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:39,928] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:39,932] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:39,932] [INFO] Target genome list was writen to GCF_003207955.1_ASM320795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:39,949] [INFO] Task started: fastANI
[2024-01-24 13:13:39,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg11514b96-8e0a-4360-8b20-bfc62b86438f/GCF_003207955.1_ASM320795v1_genomic.fna.gz --refList GCF_003207955.1_ASM320795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003207955.1_ASM320795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:49,045] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:49,061] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:49,062] [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_003311635.1	s__Komagataeibacter cocois	95.1375	981	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	95.20	95.16	0.89	0.89	4	conclusive
GCF_002906255.1	s__Komagataeibacter maltaceti	86.6997	831	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.99	99.99	0.97	0.97	2	-
GCF_003206495.1	s__Komagataeibacter entanii	86.5742	816	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.26	98.23	0.88	0.87	3	-
GCF_000964405.1	s__Komagataeibacter hansenii	84.3868	679	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.02	97.76	0.88	0.75	12	-
GCF_003207895.1	s__Komagataeibacter swingsii	82.4837	647	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_000285295.1	s__Komagataeibacter europaeus	82.1335	621	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_014199155.1	s__Komagataeibacter kakiaceti	81.5097	575	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_003207855.1	s__Komagataeibacter rhaeticus	81.0336	550	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.08	98.72	0.93	0.91	8	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	79.1587	432	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	79.0281	417	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174255.1	s__Gluconacetobacter sacchari	78.9839	423	1092	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:49,064] [INFO] GTDB search result was written to GCF_003207955.1_ASM320795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:49,065] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:49,070] [INFO] DFAST_QC result json was written to GCF_003207955.1_ASM320795v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:49,070] [INFO] DFAST_QC completed!
[2024-01-24 13:13:49,070] [INFO] Total running time: 0h1m10s