[2024-01-24 11:12:39,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg09db04d3-fa09-4f73-86f8-101e6a82fb26/dqc_reference
[2024-01-24 11:12:41,282] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,283] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,283] [INFO] Running command: gunzip -c /var/lib/cwl/stg92abe78b-a4ad-4aea-8ed4-7122c471e2f6/GCF_001189235.2_ASM118923v2_genomic.fna.gz | prodigal -d GCF_001189235.2_ASM118923v2_genomic.fna/cds.fna -a GCF_001189235.2_ASM118923v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:05,761] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:05,762] [INFO] Task started: HMMsearch
[2024-01-24 11:13:05,762] [INFO] Running command: hmmsearch --tblout GCF_001189235.2_ASM118923v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09db04d3-fa09-4f73-86f8-101e6a82fb26/dqc_reference/reference_markers.hmm GCF_001189235.2_ASM118923v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:06,144] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:06,146] [INFO] Found 6/6 markers.
[2024-01-24 11:13:06,213] [INFO] Query marker FASTA was written to GCF_001189235.2_ASM118923v2_genomic.fna/markers.fasta
[2024-01-24 11:13:06,214] [INFO] Task started: Blastn
[2024-01-24 11:13:06,214] [INFO] Running command: blastn -query GCF_001189235.2_ASM118923v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09db04d3-fa09-4f73-86f8-101e6a82fb26/dqc_reference/reference_markers.fasta -out GCF_001189235.2_ASM118923v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:07,297] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:07,301] [INFO] Selected 12 target genomes.
[2024-01-24 11:13:07,301] [INFO] Target genome list was writen to GCF_001189235.2_ASM118923v2_genomic.fna/target_genomes.txt
[2024-01-24 11:13:07,306] [INFO] Task started: fastANI
[2024-01-24 11:13:07,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg92abe78b-a4ad-4aea-8ed4-7122c471e2f6/GCF_001189235.2_ASM118923v2_genomic.fna.gz --refList GCF_001189235.2_ASM118923v2_genomic.fna/target_genomes.txt --output GCF_001189235.2_ASM118923v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:37,041] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:37,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09db04d3-fa09-4f73-86f8-101e6a82fb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:37,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09db04d3-fa09-4f73-86f8-101e6a82fb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:37,054] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:37,055] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:37,055] [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
Bradyrhizobium embrapense	strain=SEMIA 6208	GCA_001189235.2	630921	630921	type	True	100.0	2736	2739	95	conclusive
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	92.0594	2174	2739	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	91.8912	2091	2739	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	91.5953	2214	2739	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	91.4069	2228	2739	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	90.9225	2135	2739	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	90.8296	2032	2739	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	90.6352	2040	2739	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	90.2906	2150	2739	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	90.2678	2134	2739	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	90.0905	2093	2739	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	89.9992	2078	2739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:37,056] [INFO] DFAST Taxonomy check result was written to GCF_001189235.2_ASM118923v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:37,057] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:37,057] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:37,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09db04d3-fa09-4f73-86f8-101e6a82fb26/dqc_reference/checkm_data
[2024-01-24 11:13:37,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:37,133] [INFO] Task started: CheckM
[2024-01-24 11:13:37,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001189235.2_ASM118923v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001189235.2_ASM118923v2_genomic.fna/checkm_input GCF_001189235.2_ASM118923v2_genomic.fna/checkm_result
[2024-01-24 11:14:46,651] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:46,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:46,679] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:46,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:46,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001189235.2_ASM118923v2_genomic.fna/markers.fasta)
[2024-01-24 11:14:46,681] [INFO] Task started: Blastn
[2024-01-24 11:14:46,681] [INFO] Running command: blastn -query GCF_001189235.2_ASM118923v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg09db04d3-fa09-4f73-86f8-101e6a82fb26/dqc_reference/reference_markers_gtdb.fasta -out GCF_001189235.2_ASM118923v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:48,848] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:48,853] [INFO] Selected 11 target genomes.
[2024-01-24 11:14:48,853] [INFO] Target genome list was writen to GCF_001189235.2_ASM118923v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:48,863] [INFO] Task started: fastANI
[2024-01-24 11:14:48,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg92abe78b-a4ad-4aea-8ed4-7122c471e2f6/GCF_001189235.2_ASM118923v2_genomic.fna.gz --refList GCF_001189235.2_ASM118923v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001189235.2_ASM118923v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:15,096] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:15,111] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:15,111] [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_001189235.2	s__Bradyrhizobium embrapense	100.0	2736	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002532045.1	s__Bradyrhizobium sp002532045	92.4657	2206	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105845.1	s__Bradyrhizobium erythrophlei_E	92.4583	2186	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	95.48	95.46	0.84	0.83	5	-
GCF_015291625.1	s__Bradyrhizobium sp015291625	92.1663	2275	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013373795.1	s__Bradyrhizobium quebecense	92.0842	2169	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.1616	96.90	95.60	0.87	0.83	3	-
GCA_001238275.1	s__Bradyrhizobium viridifuturi	91.6088	2212	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.73	98.73	0.92	0.92	2	-
GCF_001189845.1	s__Bradyrhizobium tropiciagri	91.4132	2227	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993935.1	s__Bradyrhizobium macuxiense_A	90.9532	2149	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839165.1	s__Bradyrhizobium sp003020075	90.8961	2042	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.93	99.86	0.97	0.95	16	-
GCF_001908235.1	s__Bradyrhizobium sp001908235	90.8233	2031	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516645.2	s__Bradyrhizobium septentrionale	89.9606	2080	2739	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:15,113] [INFO] GTDB search result was written to GCF_001189235.2_ASM118923v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:15,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:15,117] [INFO] DFAST_QC result json was written to GCF_001189235.2_ASM118923v2_genomic.fna/dqc_result.json
[2024-01-24 11:15:15,117] [INFO] DFAST_QC completed!
[2024-01-24 11:15:15,117] [INFO] Total running time: 0h2m35s