[2024-01-24 12:29:28,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,083] [INFO] DQC Reference Directory: /var/lib/cwl/stgda6f7925-7705-47a9-941c-ea8d24017100/dqc_reference
[2024-01-24 12:29:29,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:29,476] [INFO] Task started: Prodigal
[2024-01-24 12:29:29,477] [INFO] Running command: gunzip -c /var/lib/cwl/stg0546fb4a-a114-42ab-82db-351b9496dc35/GCF_017377735.1_ASM1737773v1_genomic.fna.gz | prodigal -d GCF_017377735.1_ASM1737773v1_genomic.fna/cds.fna -a GCF_017377735.1_ASM1737773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:41,949] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:41,950] [INFO] Task started: HMMsearch
[2024-01-24 12:29:41,950] [INFO] Running command: hmmsearch --tblout GCF_017377735.1_ASM1737773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda6f7925-7705-47a9-941c-ea8d24017100/dqc_reference/reference_markers.hmm GCF_017377735.1_ASM1737773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:42,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:42,324] [INFO] Found 6/6 markers.
[2024-01-24 12:29:42,355] [INFO] Query marker FASTA was written to GCF_017377735.1_ASM1737773v1_genomic.fna/markers.fasta
[2024-01-24 12:29:42,355] [INFO] Task started: Blastn
[2024-01-24 12:29:42,356] [INFO] Running command: blastn -query GCF_017377735.1_ASM1737773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda6f7925-7705-47a9-941c-ea8d24017100/dqc_reference/reference_markers.fasta -out GCF_017377735.1_ASM1737773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:43,043] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:43,046] [INFO] Selected 22 target genomes.
[2024-01-24 12:29:43,047] [INFO] Target genome list was writen to GCF_017377735.1_ASM1737773v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:43,057] [INFO] Task started: fastANI
[2024-01-24 12:29:43,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg0546fb4a-a114-42ab-82db-351b9496dc35/GCF_017377735.1_ASM1737773v1_genomic.fna.gz --refList GCF_017377735.1_ASM1737773v1_genomic.fna/target_genomes.txt --output GCF_017377735.1_ASM1737773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:56,795] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:56,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda6f7925-7705-47a9-941c-ea8d24017100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:56,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda6f7925-7705-47a9-941c-ea8d24017100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:56,813] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:56,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:56,813] [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 garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	100.0	1246	1247	95	conclusive
Acetobacter papayae	strain=JCM 25143	GCA_000613285.1	1076592	1076592	type	True	80.3205	422	1247	95	below_threshold
Acetobacter peroxydans	strain=NBRC 13755	GCA_006539345.1	104098	104098	type	True	79.9726	430	1247	95	below_threshold
Acetobacter peroxydans	strain=LMG 1635	GCA_011516745.1	104098	104098	type	True	79.9268	432	1247	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	79.8097	455	1247	95	below_threshold
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	79.7908	449	1247	95	below_threshold
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	79.5253	421	1247	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	79.3666	383	1247	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	79.3086	353	1247	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	79.3007	412	1247	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	78.4689	294	1247	95	below_threshold
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	78.4398	298	1247	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.4344	300	1247	95	below_threshold
Acetobacter syzygii	strain=NBRC 16604	GCA_007989285.1	146476	146476	type	True	78.4313	320	1247	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	78.4176	327	1247	95	below_threshold
Acetobacter syzygii	strain=9H-2	GCA_000964225.1	146476	146476	type	True	78.3445	324	1247	95	below_threshold
Acetobacter pasteurianus subsp. pasteurianus	strain=IFO 3191	GCA_000241625.2	481145	438	type	True	78.3106	275	1247	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	77.9438	308	1247	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.6321	159	1247	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.5386	154	1247	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1528	87	1247	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.0685	97	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:56,815] [INFO] DFAST Taxonomy check result was written to GCF_017377735.1_ASM1737773v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:56,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:56,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:56,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda6f7925-7705-47a9-941c-ea8d24017100/dqc_reference/checkm_data
[2024-01-24 12:29:56,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:56,860] [INFO] Task started: CheckM
[2024-01-24 12:29:56,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017377735.1_ASM1737773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017377735.1_ASM1737773v1_genomic.fna/checkm_input GCF_017377735.1_ASM1737773v1_genomic.fna/checkm_result
[2024-01-24 12:30:37,951] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:37,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,977] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:37,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:37,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017377735.1_ASM1737773v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:37,978] [INFO] Task started: Blastn
[2024-01-24 12:30:37,978] [INFO] Running command: blastn -query GCF_017377735.1_ASM1737773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda6f7925-7705-47a9-941c-ea8d24017100/dqc_reference/reference_markers_gtdb.fasta -out GCF_017377735.1_ASM1737773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:39,051] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:39,055] [INFO] Selected 16 target genomes.
[2024-01-24 12:30:39,055] [INFO] Target genome list was writen to GCF_017377735.1_ASM1737773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:39,077] [INFO] Task started: fastANI
[2024-01-24 12:30:39,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg0546fb4a-a114-42ab-82db-351b9496dc35/GCF_017377735.1_ASM1737773v1_genomic.fna.gz --refList GCF_017377735.1_ASM1737773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017377735.1_ASM1737773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:49,668] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:49,687] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:49,688] [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_017377735.1	s__Acetobacter sp017377735	100.0	1246	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000613285.1	s__Acetobacter papayae	80.3205	422	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377745.1	s__Acetobacter suratthaniensis	80.0155	454	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539345.1	s__Acetobacter peroxydans	79.9596	431	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008365315.1	s__Acetobacter sp008365315	79.8399	447	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207635.1	s__Acetobacter lovaniensis	79.8344	454	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011516925.1	s__Acetobacter fabarum	79.5374	420	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_000613865.1	s__Acetobacter okinawensis	79.3605	384	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	-
GCF_001499675.1	s__Acetobacter ghanensis	79.344	347	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011516885.1	s__Acetobacter lambici	79.2895	413	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153655.1	s__Acetobacter okinawensis_A	79.2124	369	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206495.1	s__Komagataeibacter entanii	79.1563	322	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.26	98.23	0.88	0.87	3	-
GCF_004014775.2	s__Acetobacter oryzoeni	78.9755	304	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.72	97.29	0.89	0.84	4	-
GCF_014174165.1	s__Gluconacetobacter dulcium	78.45	326	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	78.4402	298	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	78.2416	335	1247	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 12:30:49,690] [INFO] GTDB search result was written to GCF_017377735.1_ASM1737773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:49,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:49,695] [INFO] DFAST_QC result json was written to GCF_017377735.1_ASM1737773v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:49,695] [INFO] DFAST_QC completed!
[2024-01-24 12:30:49,695] [INFO] Total running time: 0h1m22s