[2024-01-24 11:51:09,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:09,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:09,864] [INFO] DQC Reference Directory: /var/lib/cwl/stg61c3a898-0f6f-4629-9273-b92dcb3a1b15/dqc_reference
[2024-01-24 11:51:11,141] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,142] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg8495b595-d1ef-4b2b-921e-4a2924b78cee/GCF_002238045.1_ASM223804v1_genomic.fna.gz | prodigal -d GCF_002238045.1_ASM223804v1_genomic.fna/cds.fna -a GCF_002238045.1_ASM223804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:20,811] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:20,811] [INFO] Task started: HMMsearch
[2024-01-24 11:51:20,811] [INFO] Running command: hmmsearch --tblout GCF_002238045.1_ASM223804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61c3a898-0f6f-4629-9273-b92dcb3a1b15/dqc_reference/reference_markers.hmm GCF_002238045.1_ASM223804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:21,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:21,103] [INFO] Found 6/6 markers.
[2024-01-24 11:51:21,148] [INFO] Query marker FASTA was written to GCF_002238045.1_ASM223804v1_genomic.fna/markers.fasta
[2024-01-24 11:51:21,149] [INFO] Task started: Blastn
[2024-01-24 11:51:21,149] [INFO] Running command: blastn -query GCF_002238045.1_ASM223804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61c3a898-0f6f-4629-9273-b92dcb3a1b15/dqc_reference/reference_markers.fasta -out GCF_002238045.1_ASM223804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:22,201] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:22,205] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:22,205] [INFO] Target genome list was writen to GCF_002238045.1_ASM223804v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:22,230] [INFO] Task started: fastANI
[2024-01-24 11:51:22,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg8495b595-d1ef-4b2b-921e-4a2924b78cee/GCF_002238045.1_ASM223804v1_genomic.fna.gz --refList GCF_002238045.1_ASM223804v1_genomic.fna/target_genomes.txt --output GCF_002238045.1_ASM223804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:44,786] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:44,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61c3a898-0f6f-4629-9273-b92dcb3a1b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:44,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61c3a898-0f6f-4629-9273-b92dcb3a1b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:44,804] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:44,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:44,804] [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
Notoacmeibacter marinus	strain=XMTR2A4	GCA_002238045.1	1876515	1876515	type	True	100.0	1095	1095	95	conclusive
Notoacmeibacter ruber	strain=M2BS9Y-3-1	GCA_003668555.1	2670375	2670375	type	True	79.7389	538	1095	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.9653	272	1095	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	77.9213	282	1095	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	77.8464	242	1095	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.8418	244	1095	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	77.8325	278	1095	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.7458	247	1095	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	77.5826	257	1095	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	77.5568	241	1095	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	77.4467	204	1095	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.4414	273	1095	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.4412	220	1095	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	77.4258	245	1095	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.4165	207	1095	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	77.4014	191	1095	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.3997	258	1095	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	77.384	223	1095	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	77.38	208	1095	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.3453	260	1095	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.3441	234	1095	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	77.2079	244	1095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:44,807] [INFO] DFAST Taxonomy check result was written to GCF_002238045.1_ASM223804v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:44,808] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:44,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:44,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61c3a898-0f6f-4629-9273-b92dcb3a1b15/dqc_reference/checkm_data
[2024-01-24 11:51:44,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:44,844] [INFO] Task started: CheckM
[2024-01-24 11:51:44,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002238045.1_ASM223804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002238045.1_ASM223804v1_genomic.fna/checkm_input GCF_002238045.1_ASM223804v1_genomic.fna/checkm_result
[2024-01-24 11:52:15,894] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:15,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:15,916] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:15,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:15,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002238045.1_ASM223804v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:15,917] [INFO] Task started: Blastn
[2024-01-24 11:52:15,917] [INFO] Running command: blastn -query GCF_002238045.1_ASM223804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61c3a898-0f6f-4629-9273-b92dcb3a1b15/dqc_reference/reference_markers_gtdb.fasta -out GCF_002238045.1_ASM223804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:17,843] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:17,846] [INFO] Selected 23 target genomes.
[2024-01-24 11:52:17,846] [INFO] Target genome list was writen to GCF_002238045.1_ASM223804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:17,872] [INFO] Task started: fastANI
[2024-01-24 11:52:17,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg8495b595-d1ef-4b2b-921e-4a2924b78cee/GCF_002238045.1_ASM223804v1_genomic.fna.gz --refList GCF_002238045.1_ASM223804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002238045.1_ASM223804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:35,638] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:35,655] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:35,656] [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_002238045.1	s__Notoacmeibacter marinus	100.0	1095	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Notoacmeibacter	95.0	97.91	97.88	0.92	0.92	3	conclusive
GCF_003668555.1	s__Notoacmeibacter ruber	79.761	538	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Notoacmeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708825.1	s__Zhengella sp002708825	78.0276	290	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	99.96	99.96	0.93	0.93	2	-
GCF_019091085.1	s__Mesorhizobium sp019091085	78.0187	258	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	77.9572	262	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727065.1	s__Zhengella mangrovi	77.9092	283	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	77.8439	277	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	77.8418	244	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421645.1	s__Aurantimonas coralicida	77.7664	260	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_003289965.1	s__Mesorhizobium atlanticum	77.7363	248	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513935.1	s__Mesorhizobium sp000513935	77.6657	233	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.65	0.86	0.84	7	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	77.617	255	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	77.6117	262	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	77.5815	239	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911015.1	s__Aliihoeflea sp012911015	77.4749	228	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	77.4582	235	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	77.442	271	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300515.1	s__Nitratireductor indicus	77.4014	191	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	77.399	153	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201615.1	s__Mesorhizobium lusatiense	77.38	208	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724355.1	s__Aminobacter sp001724355	77.3511	175	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200175.1	s__Rhizobium lentis_A	77.2294	197	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.97	0.99	0.98	4	-
GCA_001603335.1	s__Alpha-05 sp001603335	76.0118	57	1095	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:35,657] [INFO] GTDB search result was written to GCF_002238045.1_ASM223804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:35,658] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:35,662] [INFO] DFAST_QC result json was written to GCF_002238045.1_ASM223804v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:35,662] [INFO] DFAST_QC completed!
[2024-01-24 11:52:35,662] [INFO] Total running time: 0h1m26s