[2024-01-24 12:47:13,758] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:13,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:13,761] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcf24138-ada1-4cc3-b800-b8b91f934641/dqc_reference
[2024-01-24 12:47:15,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:15,243] [INFO] Task started: Prodigal
[2024-01-24 12:47:15,243] [INFO] Running command: gunzip -c /var/lib/cwl/stgef9a167a-9dba-4000-aefd-488ff02123b0/GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna.gz | prodigal -d GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/cds.fna -a GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:30,278] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:30,279] [INFO] Task started: HMMsearch
[2024-01-24 12:47:30,279] [INFO] Running command: hmmsearch --tblout GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcf24138-ada1-4cc3-b800-b8b91f934641/dqc_reference/reference_markers.hmm GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:30,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:30,683] [INFO] Found 6/6 markers.
[2024-01-24 12:47:30,727] [INFO] Query marker FASTA was written to GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/markers.fasta
[2024-01-24 12:47:30,728] [INFO] Task started: Blastn
[2024-01-24 12:47:30,728] [INFO] Running command: blastn -query GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf24138-ada1-4cc3-b800-b8b91f934641/dqc_reference/reference_markers.fasta -out GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:31,813] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:31,817] [INFO] Selected 19 target genomes.
[2024-01-24 12:47:31,817] [INFO] Target genome list was writen to GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/target_genomes.txt
[2024-01-24 12:47:31,825] [INFO] Task started: fastANI
[2024-01-24 12:47:31,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9a167a-9dba-4000-aefd-488ff02123b0/GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna.gz --refList GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/target_genomes.txt --output GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:56,858] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:56,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcf24138-ada1-4cc3-b800-b8b91f934641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:56,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcf24138-ada1-4cc3-b800-b8b91f934641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:56,877] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:56,878] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:56,878] [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
Pseudorhizobium endolithicum	strain=JC140	GCA_902153245.3	1191678	1191678	type	True	81.7622	920	1650	95	below_threshold
Pseudorhizobium flavum	strain=DSM 102134	GCA_014201495.1	1335061	1335061	type	True	81.3171	858	1650	95	below_threshold
Pseudorhizobium halotolerans	strain=AB21	GCA_902153235.3	1233081	1233081	type	True	81.3082	887	1650	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	81.2873	846	1650	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	81.2758	874	1650	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	81.222	883	1650	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.7249	854	1650	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	80.5159	831	1650	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.3181	652	1650	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	80.0491	759	1650	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.9573	753	1650	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	79.9354	715	1650	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.9091	705	1650	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	79.8185	641	1650	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.7443	618	1650	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	79.6466	641	1650	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	79.6464	719	1650	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.6396	620	1650	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.0625	575	1650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:56,885] [INFO] DFAST Taxonomy check result was written to GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/tc_result.tsv
[2024-01-24 12:47:56,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:56,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:56,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcf24138-ada1-4cc3-b800-b8b91f934641/dqc_reference/checkm_data
[2024-01-24 12:47:56,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:56,942] [INFO] Task started: CheckM
[2024-01-24 12:47:56,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/checkm_input GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/checkm_result
[2024-01-24 12:48:41,811] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:41,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:41,841] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:41,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:41,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/markers.fasta)
[2024-01-24 12:48:41,843] [INFO] Task started: Blastn
[2024-01-24 12:48:41,843] [INFO] Running command: blastn -query GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf24138-ada1-4cc3-b800-b8b91f934641/dqc_reference/reference_markers_gtdb.fasta -out GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:44,070] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:44,075] [INFO] Selected 24 target genomes.
[2024-01-24 12:48:44,075] [INFO] Target genome list was writen to GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:44,094] [INFO] Task started: fastANI
[2024-01-24 12:48:44,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9a167a-9dba-4000-aefd-488ff02123b0/GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna.gz --refList GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/target_genomes_gtdb.txt --output GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:10,089] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:10,112] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:10,113] [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
GCA_000722615.1	s__Pseudorhizobium pelagicum	97.1408	1417	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	97.63	97.12	0.87	0.82	8	conclusive
GCF_902153245.2	s__Pseudorhizobium endolithicum	81.7699	919	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	98.09	98.09	0.93	0.93	2	-
GCF_902502825.2	s__Pseudorhizobium flavum	81.2327	882	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	96.75	95.31	0.86	0.77	9	-
GCF_000282095.2	s__Neorhizobium sp000282095	80.7899	831	1650	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	80.7675	831	1650	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	80.735	853	1650	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	80.6999	828	1650	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	80.6876	851	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCA_002968845.1	s__Neorhizobium tomejilense	80.648	840	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.02	95.22	0.90	0.84	9	-
GCF_018760785.1	s__Rhizobium_A sp018760785	80.4173	744	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472675.1	s__Neorhizobium sp900472675	80.2989	745	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	80.1816	704	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
GCF_011046245.1	s__Rhizobium_A pseudoryzae	80.0566	758	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968635.1	s__Neorhizobium alkalisoli	79.9864	749	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	79.8971	642	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864575.1	s__Rhizobium sp900468685	79.852	670	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.95	0.90	0.89	5	-
GCA_900469955.1	s__Neorhizobium sp900469955	79.7626	746	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156055.1	s__Allorhizobium sp900156055	79.6617	610	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968575.1	s__Neorhizobium huautlense	79.6426	720	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCA_900471515.1	s__Rhizobium sp900471515	79.5753	659	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	98.55	0.92	0.91	6	-
GCF_016806065.1	s__Allorhizobium sp001724035	79.4732	622	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
GCA_900466945.1	s__Allorhizobium sp900466945	79.325	618	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001695855.1	s__Ensifer sp001695855	79.1841	625	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.60	98.60	0.94	0.94	3	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	78.955	601	1650	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:10,115] [INFO] GTDB search result was written to GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:10,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:10,120] [INFO] DFAST_QC result json was written to GCF_000705355.1_SOAPdenovo_for_version_1.05_of_Rhizobium_marinus_MGL06_genomic.fna/dqc_result.json
[2024-01-24 12:49:10,121] [INFO] DFAST_QC completed!
[2024-01-24 12:49:10,121] [INFO] Total running time: 0h1m56s