[2023-06-28 12:02:31,042] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:31,044] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:31,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg42837769-d247-417c-b0c6-7441490f56bb/dqc_reference
[2023-06-28 12:02:32,356] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:32,357] [INFO] Task started: Prodigal
[2023-06-28 12:02:32,357] [INFO] Running command: gunzip -c /var/lib/cwl/stg548ad7f4-6157-4ed5-8210-70b9eb718a34/GCA_027430935.1_ASM2743093v1_genomic.fna.gz | prodigal -d GCA_027430935.1_ASM2743093v1_genomic.fna/cds.fna -a GCA_027430935.1_ASM2743093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:46,195] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:46,196] [INFO] Task started: HMMsearch
[2023-06-28 12:02:46,196] [INFO] Running command: hmmsearch --tblout GCA_027430935.1_ASM2743093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42837769-d247-417c-b0c6-7441490f56bb/dqc_reference/reference_markers.hmm GCA_027430935.1_ASM2743093v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:46,518] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:46,519] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg548ad7f4-6157-4ed5-8210-70b9eb718a34/GCA_027430935.1_ASM2743093v1_genomic.fna.gz]
[2023-06-28 12:02:46,577] [INFO] Query marker FASTA was written to GCA_027430935.1_ASM2743093v1_genomic.fna/markers.fasta
[2023-06-28 12:02:46,578] [INFO] Task started: Blastn
[2023-06-28 12:02:46,578] [INFO] Running command: blastn -query GCA_027430935.1_ASM2743093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42837769-d247-417c-b0c6-7441490f56bb/dqc_reference/reference_markers.fasta -out GCA_027430935.1_ASM2743093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:47,375] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:47,379] [INFO] Selected 22 target genomes.
[2023-06-28 12:02:47,379] [INFO] Target genome list was writen to GCA_027430935.1_ASM2743093v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:47,382] [INFO] Task started: fastANI
[2023-06-28 12:02:47,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg548ad7f4-6157-4ed5-8210-70b9eb718a34/GCA_027430935.1_ASM2743093v1_genomic.fna.gz --refList GCA_027430935.1_ASM2743093v1_genomic.fna/target_genomes.txt --output GCA_027430935.1_ASM2743093v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:03:17,368] [INFO] Task succeeded: fastANI
[2023-06-28 12:03:17,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42837769-d247-417c-b0c6-7441490f56bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:03:17,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42837769-d247-417c-b0c6-7441490f56bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:03:17,386] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:03:17,387] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:03:17,387] [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 sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	80.2825	658	1461	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	80.0229	667	1461	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	79.953	713	1461	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	79.9458	717	1461	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	79.9245	664	1461	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	79.8774	675	1461	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	79.876	677	1461	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	79.7777	690	1461	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	79.6911	662	1461	95	below_threshold
Bradyrhizobium manausense	strain=BR 3351	GCA_001440035.1	989370	989370	suspected-type	True	79.6873	658	1461	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	79.647	659	1461	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	79.6465	662	1461	95	below_threshold
Bradyrhizobium retamae	strain=Ro19	GCA_001440415.1	1300035	1300035	type	True	79.6437	630	1461	95	below_threshold
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	79.6388	629	1461	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	79.6377	682	1461	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	79.5944	672	1461	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	79.5899	659	1461	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	79.5568	672	1461	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	79.5471	664	1461	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	79.2117	610	1461	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	79.0432	495	1461	95	below_threshold
Nitrobacter hamburgensis	strain=X14	GCA_000013885.1	912	912	type	True	78.8542	367	1461	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:03:17,389] [INFO] DFAST Taxonomy check result was written to GCA_027430935.1_ASM2743093v1_genomic.fna/tc_result.tsv
[2023-06-28 12:03:17,390] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:03:17,390] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:03:17,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42837769-d247-417c-b0c6-7441490f56bb/dqc_reference/checkm_data
[2023-06-28 12:03:17,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:03:17,445] [INFO] Task started: CheckM
[2023-06-28 12:03:17,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027430935.1_ASM2743093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027430935.1_ASM2743093v1_genomic.fna/checkm_input GCA_027430935.1_ASM2743093v1_genomic.fna/checkm_result
[2023-06-28 12:04:01,833] [INFO] Task succeeded: CheckM
[2023-06-28 12:04:01,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 1.66%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:04:01,863] [INFO] ===== Completeness check finished =====
[2023-06-28 12:04:01,864] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:04:01,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027430935.1_ASM2743093v1_genomic.fna/markers.fasta)
[2023-06-28 12:04:01,866] [INFO] Task started: Blastn
[2023-06-28 12:04:01,866] [INFO] Running command: blastn -query GCA_027430935.1_ASM2743093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42837769-d247-417c-b0c6-7441490f56bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_027430935.1_ASM2743093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:03,247] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:03,252] [INFO] Selected 22 target genomes.
[2023-06-28 12:04:03,252] [INFO] Target genome list was writen to GCA_027430935.1_ASM2743093v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:04:03,270] [INFO] Task started: fastANI
[2023-06-28 12:04:03,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg548ad7f4-6157-4ed5-8210-70b9eb718a34/GCA_027430935.1_ASM2743093v1_genomic.fna.gz --refList GCA_027430935.1_ASM2743093v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027430935.1_ASM2743093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:04:34,197] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:34,219] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:04:34,220] [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_900142985.1	s__Bradyrhizobium erythrophlei_B	82.3777	907	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799445.1	s__Bradyrhizobium sp004799445	80.5104	753	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129505.1	s__Bradyrhizobium erythrophlei_D	80.2589	743	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736105.1	s__Bradyrhizobium sp018736105	80.2522	681	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	95.26	95.12	0.88	0.88	3	-
GCA_017881085.1	s__Bradyrhizobium sp017881085	80.0802	621	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129425.1	s__Bradyrhizobium erythrophlei_C	80.0495	710	1461	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	79.9698	718	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.80	95.80	0.83	0.78	5	-
GCF_018130695.1	s__Bradyrhizobium jicamae_B	79.9114	694	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799405.1	s__Bradyrhizobium sp004799405	79.852	617	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000617845.2	s__Bradyrhizobium sp000617845	79.8322	666	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105125.1	s__Bradyrhizobium canariense_A	79.8212	679	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.90	97.90	0.94	0.94	2	-
GCF_000426245.1	s__Bradyrhizobium sp000426245	79.7077	689	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884765.1	s__Bradyrhizobium sp005884765	79.6963	606	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472865.1	s__Bradyrhizobium elkanii_A	79.6795	682	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.78	96.35	0.83	0.83	3	-
GCF_018398875.1	s__Bradyrhizobium sp018398875	79.6434	641	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472965.1	s__Bradyrhizobium murdochi	79.6391	660	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114915.1	s__Bradyrhizobium guangxiense	79.5922	672	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266465.2	s__Bradyrhizobium symbiodeficiens	79.5565	672	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.63	98.60	0.94	0.93	4	-
GCF_015291645.1	s__Bradyrhizobium sp015291645	79.4641	684	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242285.1	s__Bradyrhizobium sp019242285	79.3502	601	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472385.1	s__Bradyrhizobium sp000472385	79.1919	653	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243075.1	s__Bradyrhizobium sp019243075	78.9965	417	1461	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:04:34,222] [INFO] GTDB search result was written to GCA_027430935.1_ASM2743093v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:04:34,222] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:04:34,228] [INFO] DFAST_QC result json was written to GCA_027430935.1_ASM2743093v1_genomic.fna/dqc_result.json
[2023-06-28 12:04:34,229] [INFO] DFAST_QC completed!
[2023-06-28 12:04:34,229] [INFO] Total running time: 0h2m3s