[2024-01-24 15:14:46,932] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:46,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:46,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg73ef7036-dba6-465c-be96-c2fcd5ac80c3/dqc_reference
[2024-01-24 15:14:48,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:48,126] [INFO] Task started: Prodigal
[2024-01-24 15:14:48,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg96854048-4160-4412-af9e-a17d32bb0a82/GCF_009711415.1_ASM971141v1_genomic.fna.gz | prodigal -d GCF_009711415.1_ASM971141v1_genomic.fna/cds.fna -a GCF_009711415.1_ASM971141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:02,741] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:02,742] [INFO] Task started: HMMsearch
[2024-01-24 15:15:02,742] [INFO] Running command: hmmsearch --tblout GCF_009711415.1_ASM971141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73ef7036-dba6-465c-be96-c2fcd5ac80c3/dqc_reference/reference_markers.hmm GCF_009711415.1_ASM971141v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:03,018] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:03,019] [INFO] Found 6/6 markers.
[2024-01-24 15:15:03,062] [INFO] Query marker FASTA was written to GCF_009711415.1_ASM971141v1_genomic.fna/markers.fasta
[2024-01-24 15:15:03,063] [INFO] Task started: Blastn
[2024-01-24 15:15:03,063] [INFO] Running command: blastn -query GCF_009711415.1_ASM971141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73ef7036-dba6-465c-be96-c2fcd5ac80c3/dqc_reference/reference_markers.fasta -out GCF_009711415.1_ASM971141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:03,896] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:03,901] [INFO] Selected 21 target genomes.
[2024-01-24 15:15:03,901] [INFO] Target genome list was writen to GCF_009711415.1_ASM971141v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:03,926] [INFO] Task started: fastANI
[2024-01-24 15:15:03,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg96854048-4160-4412-af9e-a17d32bb0a82/GCF_009711415.1_ASM971141v1_genomic.fna.gz --refList GCF_009711415.1_ASM971141v1_genomic.fna/target_genomes.txt --output GCF_009711415.1_ASM971141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:21,828] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:21,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73ef7036-dba6-465c-be96-c2fcd5ac80c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:21,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73ef7036-dba6-465c-be96-c2fcd5ac80c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:21,845] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:21,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:21,846] [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
Roseibium denhamense	strain=JCM 10543	GCA_009711415.1	76305	76305	type	True	100.0	1556	1560	95	conclusive
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	79.9411	542	1560	95	below_threshold
Roseibium hamelinense	strain=NBRC 16783	GCA_009711505.1	150831	150831	type	True	79.3001	347	1560	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	78.4698	535	1560	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	78.3318	472	1560	95	below_threshold
Roseibium aquae	strain=CGMCC 1.12426	GCA_008711285.1	1323746	1323746	type	True	78.2002	293	1560	95	below_threshold
Roseibium aquae	strain=CGMCC 1.12426	GCA_014637575.1	1323746	1323746	type	True	78.1798	292	1560	95	below_threshold
Roseibium album	strain=CECT 5095	GCA_001404515.1	311410	311410	type	True	77.7635	417	1560	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	77.6759	295	1560	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	77.6009	238	1560	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	77.5697	296	1560	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	77.3684	252	1560	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	76.3399	72	1560	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	76.2559	100	1560	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	76.1378	68	1560	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	76.0991	121	1560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:21,848] [INFO] DFAST Taxonomy check result was written to GCF_009711415.1_ASM971141v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:21,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:21,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:21,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73ef7036-dba6-465c-be96-c2fcd5ac80c3/dqc_reference/checkm_data
[2024-01-24 15:15:21,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:21,898] [INFO] Task started: CheckM
[2024-01-24 15:15:21,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711415.1_ASM971141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711415.1_ASM971141v1_genomic.fna/checkm_input GCF_009711415.1_ASM971141v1_genomic.fna/checkm_result
[2024-01-24 15:16:06,636] [INFO] Task succeeded: CheckM
[2024-01-24 15:16:06,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:16:06,659] [INFO] ===== Completeness check finished =====
[2024-01-24 15:16:06,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:16:06,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711415.1_ASM971141v1_genomic.fna/markers.fasta)
[2024-01-24 15:16:06,660] [INFO] Task started: Blastn
[2024-01-24 15:16:06,660] [INFO] Running command: blastn -query GCF_009711415.1_ASM971141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73ef7036-dba6-465c-be96-c2fcd5ac80c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711415.1_ASM971141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:16:08,074] [INFO] Task succeeded: Blastn
[2024-01-24 15:16:08,079] [INFO] Selected 18 target genomes.
[2024-01-24 15:16:08,080] [INFO] Target genome list was writen to GCF_009711415.1_ASM971141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:16:08,097] [INFO] Task started: fastANI
[2024-01-24 15:16:08,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg96854048-4160-4412-af9e-a17d32bb0a82/GCF_009711415.1_ASM971141v1_genomic.fna.gz --refList GCF_009711415.1_ASM971141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711415.1_ASM971141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:28,353] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:28,367] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:28,367] [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_009711415.1	s__Roseibium denhamense	100.0	1556	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000158095.2	s__Roseibium alexandrii	79.9464	541	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.43	97.43	0.93	0.93	2	-
GCA_001890945.1	s__Roseibium sp001890945	79.7813	534	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	95.65	95.54	0.93	0.91	4	-
GCF_002237595.1	s__Roseibium sp002237595	78.7553	605	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517275.1	s__Roseibium sp006517275	78.6739	455	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107695.1	s__Roseibium sp008107695	78.6218	504	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	78.4626	536	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	78.3558	542	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_002906165.1	s__Roseibium marinum	78.3397	471	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075075.1	s__Roseibium sp003075075	78.229	486	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711285.1	s__Roseibium aquae	78.2041	292	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_008107755.1	s__Roseibium sp008107755	78.1794	451	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309185.1	s__Roseibium aggregatum_B	78.113	468	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	77.9789	354	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	77.1719	186	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_014534685.1	s__Aminobacter sp014534685	76.4858	75	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	76.0991	121	1560	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:28,368] [INFO] GTDB search result was written to GCF_009711415.1_ASM971141v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:28,369] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:28,372] [INFO] DFAST_QC result json was written to GCF_009711415.1_ASM971141v1_genomic.fna/dqc_result.json
[2024-01-24 15:16:28,372] [INFO] DFAST_QC completed!
[2024-01-24 15:16:28,373] [INFO] Total running time: 0h1m41s