[2024-01-24 13:46:00,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:00,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:00,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cbea8eb-66f9-4645-8d52-5eea544afac4/dqc_reference
[2024-01-24 13:46:02,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,151] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,152] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd77ab64-a78e-4c56-b6a4-a542dcf727bb/GCF_030028905.1_ASM3002890v1_genomic.fna.gz | prodigal -d GCF_030028905.1_ASM3002890v1_genomic.fna/cds.fna -a GCF_030028905.1_ASM3002890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:18,938] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:18,939] [INFO] Task started: HMMsearch
[2024-01-24 13:46:18,939] [INFO] Running command: hmmsearch --tblout GCF_030028905.1_ASM3002890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cbea8eb-66f9-4645-8d52-5eea544afac4/dqc_reference/reference_markers.hmm GCF_030028905.1_ASM3002890v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:19,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:19,256] [INFO] Found 6/6 markers.
[2024-01-24 13:46:19,321] [INFO] Query marker FASTA was written to GCF_030028905.1_ASM3002890v1_genomic.fna/markers.fasta
[2024-01-24 13:46:19,322] [INFO] Task started: Blastn
[2024-01-24 13:46:19,322] [INFO] Running command: blastn -query GCF_030028905.1_ASM3002890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cbea8eb-66f9-4645-8d52-5eea544afac4/dqc_reference/reference_markers.fasta -out GCF_030028905.1_ASM3002890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:20,423] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:20,427] [INFO] Selected 30 target genomes.
[2024-01-24 13:46:20,427] [INFO] Target genome list was writen to GCF_030028905.1_ASM3002890v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:20,441] [INFO] Task started: fastANI
[2024-01-24 13:46:20,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd77ab64-a78e-4c56-b6a4-a542dcf727bb/GCF_030028905.1_ASM3002890v1_genomic.fna.gz --refList GCF_030028905.1_ASM3002890v1_genomic.fna/target_genomes.txt --output GCF_030028905.1_ASM3002890v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:56,433] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:56,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cbea8eb-66f9-4645-8d52-5eea544afac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:56,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cbea8eb-66f9-4645-8d52-5eea544afac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:56,456] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:56,457] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:56,457] [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
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.255	698	1730	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	79.9453	680	1730	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	79.9025	733	1730	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	79.7765	738	1730	95	below_threshold
Rhizobium metallidurans	strain=DSM 26575	GCA_014196505.1	1265931	1265931	type	True	79.7691	679	1730	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	79.7286	751	1730	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.7241	723	1730	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	79.6167	724	1730	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.5929	630	1730	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	79.5525	620	1730	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	79.5383	755	1730	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	79.5203	752	1730	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	79.4621	714	1730	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	79.451	666	1730	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	79.4078	747	1730	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	79.4063	689	1730	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	79.3925	742	1730	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	79.3745	692	1730	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	79.3477	636	1730	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	79.3391	714	1730	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	79.2722	640	1730	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	79.1798	676	1730	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	78.9305	521	1730	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	78.8328	509	1730	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	78.8264	620	1730	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	78.7967	542	1730	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.7919	599	1730	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	78.4503	512	1730	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.7511	342	1730	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.7132	346	1730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:56,459] [INFO] DFAST Taxonomy check result was written to GCF_030028905.1_ASM3002890v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:56,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:56,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:56,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cbea8eb-66f9-4645-8d52-5eea544afac4/dqc_reference/checkm_data
[2024-01-24 13:46:56,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:56,511] [INFO] Task started: CheckM
[2024-01-24 13:46:56,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030028905.1_ASM3002890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030028905.1_ASM3002890v1_genomic.fna/checkm_input GCF_030028905.1_ASM3002890v1_genomic.fna/checkm_result
[2024-01-24 13:47:43,880] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:43,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:43,901] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:43,902] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:43,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030028905.1_ASM3002890v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:43,903] [INFO] Task started: Blastn
[2024-01-24 13:47:43,903] [INFO] Running command: blastn -query GCF_030028905.1_ASM3002890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cbea8eb-66f9-4645-8d52-5eea544afac4/dqc_reference/reference_markers_gtdb.fasta -out GCF_030028905.1_ASM3002890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:45,934] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:45,938] [INFO] Selected 29 target genomes.
[2024-01-24 13:47:45,938] [INFO] Target genome list was writen to GCF_030028905.1_ASM3002890v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:45,973] [INFO] Task started: fastANI
[2024-01-24 13:47:45,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd77ab64-a78e-4c56-b6a4-a542dcf727bb/GCF_030028905.1_ASM3002890v1_genomic.fna.gz --refList GCF_030028905.1_ASM3002890v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030028905.1_ASM3002890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:19,167] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:19,203] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:48:19,204] [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_003122325.1	s__Rhizobium album	80.2484	773	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940685.1	s__Ensifer adhaerens_E	79.9523	772	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007205.1	s__Ensifer adhaerens_D	79.8907	761	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195095.1	s__Rhizobium sp014195095	79.8425	731	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919405.1	s__Ensifer sp000799055	79.7922	777	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.37	96.05	0.91	0.88	3	-
GCF_002531725.1	s__Rhizobium sp002531725	79.7818	744	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471515.1	s__Rhizobium sp900471515	79.7479	719	1730	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	79.7214	752	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
GCF_001424985.1	s__Pararhizobium sp001424985	79.7151	683	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000018545.1	s__Sinorhizobium fredii_A	79.6935	694	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305935.1	s__Rhizobium sp017305935	79.6455	737	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177415.1	s__Neorhizobium oryzae_A	79.6096	686	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651865.1	s__Sinorhizobium glycinis	79.4967	666	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282095.2	s__Neorhizobium sp000282095	79.4966	652	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985895.1	s__Neorhizobium galegae_B	79.4921	667	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.06	98.00	0.96	0.95	4	-
GCF_000732195.1	s__Neorhizobium vignae	79.4434	667	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	79.4354	685	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471605.1	s__Neorhizobium sp900471605	79.4305	676	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCF_001461695.1	s__Sinorhizobium fredii	79.3629	711	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	96.82	0.88	0.82	17	-
GCA_000985875.1	s__Neorhizobium galegae_C	79.3174	675	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCF_000513895.1	s__Sinorhizobium sp000513895	79.1858	655	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466605.1	s__Rhizobium sp900466605	79.1348	556	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282035.1	s__Rhizobium sp000282035	79.0925	614	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.50	0.88	0.87	4	-
GCA_900468805.1	s__Rhizobium sp900468805	79.0643	676	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.10	98.22	0.94	0.90	7	-
GCF_014197145.1	s__Gellertiella hungarica	79.008	570	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Gellertiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195325.1	s__Rhizobium sp014195325	78.8991	605	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196535.1	s__Rhizobium_B borbori	78.7627	454	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_B	95.0	98.16	98.16	0.88	0.88	2	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	78.7098	581	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_014196515.1	s__Agrobacterium skierniewicense	77.7132	346	1730	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.07	98.07	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:19,206] [INFO] GTDB search result was written to GCF_030028905.1_ASM3002890v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:19,206] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:19,212] [INFO] DFAST_QC result json was written to GCF_030028905.1_ASM3002890v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:19,213] [INFO] DFAST_QC completed!
[2024-01-24 13:48:19,213] [INFO] Total running time: 0h2m18s