[2024-01-24 12:52:51,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg545f430b-a3c9-4e56-b4ff-46f4dd981b3c/dqc_reference
[2024-01-24 12:52:53,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,763] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg49ccf1ff-a91c-4f8b-ae11-5b827607c321/GCF_000963945.1_ASM96394v1_genomic.fna.gz | prodigal -d GCF_000963945.1_ASM96394v1_genomic.fna/cds.fna -a GCF_000963945.1_ASM96394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:03,654] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:03,655] [INFO] Task started: HMMsearch
[2024-01-24 12:53:03,655] [INFO] Running command: hmmsearch --tblout GCF_000963945.1_ASM96394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg545f430b-a3c9-4e56-b4ff-46f4dd981b3c/dqc_reference/reference_markers.hmm GCF_000963945.1_ASM96394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:03,892] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:03,894] [INFO] Found 6/6 markers.
[2024-01-24 12:53:03,926] [INFO] Query marker FASTA was written to GCF_000963945.1_ASM96394v1_genomic.fna/markers.fasta
[2024-01-24 12:53:03,927] [INFO] Task started: Blastn
[2024-01-24 12:53:03,927] [INFO] Running command: blastn -query GCF_000963945.1_ASM96394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg545f430b-a3c9-4e56-b4ff-46f4dd981b3c/dqc_reference/reference_markers.fasta -out GCF_000963945.1_ASM96394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:04,620] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:04,625] [INFO] Selected 16 target genomes.
[2024-01-24 12:53:04,626] [INFO] Target genome list was writen to GCF_000963945.1_ASM96394v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:04,713] [INFO] Task started: fastANI
[2024-01-24 12:53:04,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ccf1ff-a91c-4f8b-ae11-5b827607c321/GCF_000963945.1_ASM96394v1_genomic.fna.gz --refList GCF_000963945.1_ASM96394v1_genomic.fna/target_genomes.txt --output GCF_000963945.1_ASM96394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:14,861] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:14,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg545f430b-a3c9-4e56-b4ff-46f4dd981b3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:14,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg545f430b-a3c9-4e56-b4ff-46f4dd981b3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:14,875] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:53:14,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:14,876] [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 indonesiensis	strain=5H-1	GCA_000963945.1	104101	104101	type	True	100.0	1087	1088	95	conclusive
Acetobacter indonesiensis	strain=NBRC 16471	GCA_007991075.1	104101	104101	type	True	99.9977	1077	1088	95	conclusive
Acetobacter tropicalis	strain=NBRC 16470	GCA_000787635.2	104102	104102	type	True	81.61	595	1088	95	below_threshold
Acetobacter tropicalis	strain=LMG 19825	GCA_001580915.1	104102	104102	type	True	81.6	595	1088	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_007989245.1	104102	104102	type	True	81.5292	602	1088	95	below_threshold
Acetobacter senegalensis	strain=LMG 23690	GCA_001580995.1	446692	446692	type	True	81.4535	582	1088	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	79.9591	425	1088	95	below_threshold
Acetobacter malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	79.6099	411	1088	95	below_threshold
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	79.5975	411	1088	95	below_threshold
Acetobacter orleanensis	strain=NBRC 13752	GCA_006539325.1	104099	104099	type	True	79.569	405	1088	95	below_threshold
Acetobacter orleanensis	strain=JCM 7639T	GCA_000964205.1	104099	104099	type	True	79.5421	404	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:14,877] [INFO] DFAST Taxonomy check result was written to GCF_000963945.1_ASM96394v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:14,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:14,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:14,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg545f430b-a3c9-4e56-b4ff-46f4dd981b3c/dqc_reference/checkm_data
[2024-01-24 12:53:14,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:14,913] [INFO] Task started: CheckM
[2024-01-24 12:53:14,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000963945.1_ASM96394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000963945.1_ASM96394v1_genomic.fna/checkm_input GCF_000963945.1_ASM96394v1_genomic.fna/checkm_result
[2024-01-24 12:53:48,391] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:48,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:48,413] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:48,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:48,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000963945.1_ASM96394v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:48,414] [INFO] Task started: Blastn
[2024-01-24 12:53:48,414] [INFO] Running command: blastn -query GCF_000963945.1_ASM96394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg545f430b-a3c9-4e56-b4ff-46f4dd981b3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000963945.1_ASM96394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:49,544] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:49,549] [INFO] Selected 11 target genomes.
[2024-01-24 12:53:49,549] [INFO] Target genome list was writen to GCF_000963945.1_ASM96394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:49,568] [INFO] Task started: fastANI
[2024-01-24 12:53:49,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ccf1ff-a91c-4f8b-ae11-5b827607c321/GCF_000963945.1_ASM96394v1_genomic.fna.gz --refList GCF_000963945.1_ASM96394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000963945.1_ASM96394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:56,343] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:56,365] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:56,366] [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_000963945.1	s__Acetobacter indonesiensis	100.0	1087	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	96.85	0.92	0.88	4	conclusive
GCF_001580915.1	s__Acetobacter tropicalis	81.6	595	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.32	97.71	0.90	0.87	9	-
GCF_001580995.1	s__Acetobacter senegalensis	81.4496	583	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.25	96.97	0.85	0.80	6	-
GCF_002153605.1	s__Acetobacter malorum_A	80.1443	416	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_001580535.1	s__Acetobacter cerevisiae	79.9652	425	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_001580615.1	s__Acetobacter malorum	79.6069	412	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_001581005.1	s__Acetobacter orleanensis	79.5849	412	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
GCF_011516935.1	s__Acetobacter farinalis	79.4226	405	1088	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	78.851	128	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.82	96.47	0.96	0.89	7	-
GCF_002005445.1	s__Acetobacter aceti_B	77.4863	122	1088	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:56,369] [INFO] GTDB search result was written to GCF_000963945.1_ASM96394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:56,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:56,374] [INFO] DFAST_QC result json was written to GCF_000963945.1_ASM96394v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:56,374] [INFO] DFAST_QC completed!
[2024-01-24 12:53:56,374] [INFO] Total running time: 0h1m5s