[2024-01-24 11:51:37,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,329] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,329] [INFO] DQC Reference Directory: /var/lib/cwl/stgfabd09cb-091b-42bc-9e47-d4155e5a365c/dqc_reference
[2024-01-24 11:51:38,609] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,610] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,610] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c0e06d9-59da-481e-b41a-cf1fc2a74213/GCF_004363725.1_ASM436372v1_genomic.fna.gz | prodigal -d GCF_004363725.1_ASM436372v1_genomic.fna/cds.fna -a GCF_004363725.1_ASM436372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:52,135] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:52,135] [INFO] Task started: HMMsearch
[2024-01-24 11:51:52,135] [INFO] Running command: hmmsearch --tblout GCF_004363725.1_ASM436372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfabd09cb-091b-42bc-9e47-d4155e5a365c/dqc_reference/reference_markers.hmm GCF_004363725.1_ASM436372v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:52,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:52,400] [INFO] Found 6/6 markers.
[2024-01-24 11:51:52,444] [INFO] Query marker FASTA was written to GCF_004363725.1_ASM436372v1_genomic.fna/markers.fasta
[2024-01-24 11:51:52,444] [INFO] Task started: Blastn
[2024-01-24 11:51:52,444] [INFO] Running command: blastn -query GCF_004363725.1_ASM436372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfabd09cb-091b-42bc-9e47-d4155e5a365c/dqc_reference/reference_markers.fasta -out GCF_004363725.1_ASM436372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:53,354] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:53,359] [INFO] Selected 27 target genomes.
[2024-01-24 11:51:53,359] [INFO] Target genome list was writen to GCF_004363725.1_ASM436372v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:53,370] [INFO] Task started: fastANI
[2024-01-24 11:51:53,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0e06d9-59da-481e-b41a-cf1fc2a74213/GCF_004363725.1_ASM436372v1_genomic.fna.gz --refList GCF_004363725.1_ASM436372v1_genomic.fna/target_genomes.txt --output GCF_004363725.1_ASM436372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:24,382] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:24,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfabd09cb-091b-42bc-9e47-d4155e5a365c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:24,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfabd09cb-091b-42bc-9e47-d4155e5a365c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:24,406] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:24,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:24,406] [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
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	100.0	1455	1460	95	conclusive
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	85.7543	929	1460	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	81.0542	702	1460	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	80.2817	667	1460	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	80.2799	615	1460	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	80.22	666	1460	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	80.1884	681	1460	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	80.1726	613	1460	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	80.1616	603	1460	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	80.1605	675	1460	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	80.1244	632	1460	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	80.078	674	1460	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	80.0216	631	1460	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	79.96	698	1460	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	79.8384	606	1460	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	79.505	561	1460	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	79.4207	586	1460	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.9697	464	1460	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9541	464	1460	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.7078	495	1460	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	78.046	365	1460	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	78.0338	364	1460	95	below_threshold
Rhizobium altiplani	strain=BR 10423	GCA_001542405.1	1864509	1864509	type	True	77.3739	276	1460	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	76.9699	156	1460	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	76.1558	116	1460	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.1431	110	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:24,408] [INFO] DFAST Taxonomy check result was written to GCF_004363725.1_ASM436372v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:24,408] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:24,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:24,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfabd09cb-091b-42bc-9e47-d4155e5a365c/dqc_reference/checkm_data
[2024-01-24 11:52:24,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:24,450] [INFO] Task started: CheckM
[2024-01-24 11:52:24,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363725.1_ASM436372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363725.1_ASM436372v1_genomic.fna/checkm_input GCF_004363725.1_ASM436372v1_genomic.fna/checkm_result
[2024-01-24 11:53:06,957] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:06,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:07,000] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:07,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:07,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363725.1_ASM436372v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:07,001] [INFO] Task started: Blastn
[2024-01-24 11:53:07,002] [INFO] Running command: blastn -query GCF_004363725.1_ASM436372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfabd09cb-091b-42bc-9e47-d4155e5a365c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363725.1_ASM436372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:08,659] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:08,664] [INFO] Selected 26 target genomes.
[2024-01-24 11:53:08,664] [INFO] Target genome list was writen to GCF_004363725.1_ASM436372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:08,688] [INFO] Task started: fastANI
[2024-01-24 11:53:08,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0e06d9-59da-481e-b41a-cf1fc2a74213/GCF_004363725.1_ASM436372v1_genomic.fna.gz --refList GCF_004363725.1_ASM436372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363725.1_ASM436372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:43,829] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:43,855] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:43,856] [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_004363725.1	s__Mesorhizobium defluvii	100.0	1455	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.28	99.28	0.87	0.87	2	conclusive
GCF_014201615.1	s__Mesorhizobium lusatiense	85.7459	929	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	81.0292	705	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_001427385.1	s__Mesorhizobium sp001427385	80.7079	669	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427285.1	s__Mesorhizobium sp001427285	80.5909	645	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	80.5274	631	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_016756535.1	s__Mesorhizobium sp016756535	80.4637	680	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	80.4431	713	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003952505.1	s__Mesorhizobium sp003952505	80.4098	666	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_008727715.1	s__Mesorhizobium terrae	80.3394	687	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	-
GCF_006442815.1	s__Mesorhizobium sp006442815	80.3155	656	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017874015.1	s__Pseudaminobacter sp017874015	80.1299	578	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439355.1	s__Mesorhizobium sp006439355	80.1192	659	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002294995.1	s__Mesorhizobium sp002294995	80.1176	651	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472705.1	s__Mesorhizobium erdmanii	80.1134	638	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	97.39	0.90	0.90	3	-
GCF_900099905.1	s__Mesorhizobium muleiense	80.0304	630	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCA_004017275.1	s__Mesorhizobium sp004017275	79.9441	655	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.13	97.50	0.90	0.85	4	-
GCF_018555685.1	s__Aminobacter anthyllidis	79.8948	650	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	79.8585	604	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002075885.1	s__Mesorhizobium manganicum	79.7653	561	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	79.5125	561	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471515.1	s__Rhizobium sp900471515	78.0219	380	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	98.55	0.92	0.91	6	-
GCF_003985145.1	s__Rhizobium anhuiense	78.0077	368	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
GCF_014842915.1	s__Roseibium litorale	76.9549	157	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	75.0226	106	1460	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:43,858] [INFO] GTDB search result was written to GCF_004363725.1_ASM436372v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:43,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:43,863] [INFO] DFAST_QC result json was written to GCF_004363725.1_ASM436372v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:43,864] [INFO] DFAST_QC completed!
[2024-01-24 11:53:43,864] [INFO] Total running time: 0h2m7s