[2024-01-24 12:47:11,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:11,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:11,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2c38c78-f8c0-47e3-8536-71bcda75216c/dqc_reference
[2024-01-24 12:47:13,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,043] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,044] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5d91695-60c0-46c9-b123-1794320a6df0/GCF_011516875.1_ASM1151687v1_genomic.fna.gz | prodigal -d GCF_011516875.1_ASM1151687v1_genomic.fna/cds.fna -a GCF_011516875.1_ASM1151687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:24,614] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:24,615] [INFO] Task started: HMMsearch
[2024-01-24 12:47:24,615] [INFO] Running command: hmmsearch --tblout GCF_011516875.1_ASM1151687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2c38c78-f8c0-47e3-8536-71bcda75216c/dqc_reference/reference_markers.hmm GCF_011516875.1_ASM1151687v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:24,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:24,868] [INFO] Found 6/6 markers.
[2024-01-24 12:47:24,904] [INFO] Query marker FASTA was written to GCF_011516875.1_ASM1151687v1_genomic.fna/markers.fasta
[2024-01-24 12:47:24,904] [INFO] Task started: Blastn
[2024-01-24 12:47:24,904] [INFO] Running command: blastn -query GCF_011516875.1_ASM1151687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2c38c78-f8c0-47e3-8536-71bcda75216c/dqc_reference/reference_markers.fasta -out GCF_011516875.1_ASM1151687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:25,694] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:25,698] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:25,698] [INFO] Target genome list was writen to GCF_011516875.1_ASM1151687v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:25,703] [INFO] Task started: fastANI
[2024-01-24 12:47:25,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d91695-60c0-46c9-b123-1794320a6df0/GCF_011516875.1_ASM1151687v1_genomic.fna.gz --refList GCF_011516875.1_ASM1151687v1_genomic.fna/target_genomes.txt --output GCF_011516875.1_ASM1151687v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:34,970] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:34,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2c38c78-f8c0-47e3-8536-71bcda75216c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:34,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2c38c78-f8c0-47e3-8536-71bcda75216c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:34,980] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:34,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:34,981] [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 lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	100.0	1122	1125	95	conclusive
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	99.9957	1112	1125	95	conclusive
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	93.7412	804	1125	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	87.3883	786	1125	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	85.6537	701	1125	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	85.2987	690	1125	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	85.1845	687	1125	95	below_threshold
Acetobacter syzygii	strain=9H-2	GCA_000964225.1	146476	146476	type	True	84.1033	680	1125	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.7714	459	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:34,985] [INFO] DFAST Taxonomy check result was written to GCF_011516875.1_ASM1151687v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:34,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:34,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:34,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2c38c78-f8c0-47e3-8536-71bcda75216c/dqc_reference/checkm_data
[2024-01-24 12:47:34,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:35,027] [INFO] Task started: CheckM
[2024-01-24 12:47:35,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011516875.1_ASM1151687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011516875.1_ASM1151687v1_genomic.fna/checkm_input GCF_011516875.1_ASM1151687v1_genomic.fna/checkm_result
[2024-01-24 12:48:12,240] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:12,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:12,266] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:12,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:12,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011516875.1_ASM1151687v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:12,268] [INFO] Task started: Blastn
[2024-01-24 12:48:12,268] [INFO] Running command: blastn -query GCF_011516875.1_ASM1151687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2c38c78-f8c0-47e3-8536-71bcda75216c/dqc_reference/reference_markers_gtdb.fasta -out GCF_011516875.1_ASM1151687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:13,528] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:13,531] [INFO] Selected 7 target genomes.
[2024-01-24 12:48:13,532] [INFO] Target genome list was writen to GCF_011516875.1_ASM1151687v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:13,537] [INFO] Task started: fastANI
[2024-01-24 12:48:13,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5d91695-60c0-46c9-b123-1794320a6df0/GCF_011516875.1_ASM1151687v1_genomic.fna.gz --refList GCF_011516875.1_ASM1151687v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011516875.1_ASM1151687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:18,740] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:18,750] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:18,750] [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_014207635.1	s__Acetobacter lovaniensis	99.9957	1112	1125	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_011516925.1	s__Acetobacter fabarum	93.7465	804	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_011516885.1	s__Acetobacter lambici	87.3867	786	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613865.1	s__Acetobacter okinawensis	85.6537	701	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	-
GCF_002153655.1	s__Acetobacter okinawensis_A	85.613	684	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499675.1	s__Acetobacter ghanensis	85.299	691	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000964225.1	s__Acetobacter syzygii	84.0879	681	1125	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.87	98.22	0.97	0.90	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:18,752] [INFO] GTDB search result was written to GCF_011516875.1_ASM1151687v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:18,752] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:18,755] [INFO] DFAST_QC result json was written to GCF_011516875.1_ASM1151687v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:18,755] [INFO] DFAST_QC completed!
[2024-01-24 12:48:18,756] [INFO] Total running time: 0h1m7s