[2023-03-15 03:25:37,042] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:25:37,042] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:25:37,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg51c0f813-7ae4-4a2d-b585-13dd16b269d1/dqc_reference
[2023-03-15 03:25:38,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:25:38,117] [INFO] Task started: Prodigal
[2023-03-15 03:25:38,117] [INFO] Running command: cat /var/lib/cwl/stg483806f2-5814-46d4-af8a-27705c7bc742/OceanDNA-b26905.fa | prodigal -d OceanDNA-b26905/cds.fna -a OceanDNA-b26905/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:26:04,096] [INFO] Task succeeded: Prodigal
[2023-03-15 03:26:04,096] [INFO] Task started: HMMsearch
[2023-03-15 03:26:04,096] [INFO] Running command: hmmsearch --tblout OceanDNA-b26905/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51c0f813-7ae4-4a2d-b585-13dd16b269d1/dqc_reference/reference_markers.hmm OceanDNA-b26905/protein.faa > /dev/null
[2023-03-15 03:26:04,321] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:26:04,322] [INFO] Found 6/6 markers.
[2023-03-15 03:26:04,348] [INFO] Query marker FASTA was written to OceanDNA-b26905/markers.fasta
[2023-03-15 03:26:04,349] [INFO] Task started: Blastn
[2023-03-15 03:26:04,349] [INFO] Running command: blastn -query OceanDNA-b26905/markers.fasta -db /var/lib/cwl/stg51c0f813-7ae4-4a2d-b585-13dd16b269d1/dqc_reference/reference_markers.fasta -out OceanDNA-b26905/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:26:05,288] [INFO] Task succeeded: Blastn
[2023-03-15 03:26:05,288] [INFO] Selected 21 target genomes.
[2023-03-15 03:26:05,289] [INFO] Target genome list was writen to OceanDNA-b26905/target_genomes.txt
[2023-03-15 03:26:05,298] [INFO] Task started: fastANI
[2023-03-15 03:26:05,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg483806f2-5814-46d4-af8a-27705c7bc742/OceanDNA-b26905.fa --refList OceanDNA-b26905/target_genomes.txt --output OceanDNA-b26905/fastani_result.tsv --threads 1
[2023-03-15 03:26:26,446] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:26,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51c0f813-7ae4-4a2d-b585-13dd16b269d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:26:26,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51c0f813-7ae4-4a2d-b585-13dd16b269d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:26:26,459] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:26:26,459] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:26:26,459] [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	81.8107	849	1397	95	below_threshold
Pseudorhizobium halotolerans	strain=AB21	GCA_902153235.3	1233081	1233081	type	True	81.4868	849	1397	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_902502825.2	1335061	1335061	type	True	81.4048	829	1397	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	81.3605	839	1397	95	below_threshold
Pseudorhizobium flavum	strain=DSM 102134	GCA_014201495.1	1335061	1335061	type	True	81.3452	830	1397	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	81.18	809	1397	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.8428	790	1397	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	80.6113	772	1397	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	80.2876	661	1397	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.1199	618	1397	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	80.0883	711	1397	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.9959	567	1397	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.9431	691	1397	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.9404	677	1397	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	79.9031	573	1397	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	79.7404	660	1397	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	79.6414	581	1397	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.6201	596	1397	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.6044	599	1397	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	79.5925	608	1397	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	79.4939	606	1397	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:26:26,459] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26905/tc_result.tsv
[2023-03-15 03:26:26,460] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:26:26,460] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:26:26,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51c0f813-7ae4-4a2d-b585-13dd16b269d1/dqc_reference/checkm_data
[2023-03-15 03:26:26,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:26:26,466] [INFO] Task started: CheckM
[2023-03-15 03:26:26,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26905/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26905/checkm_input OceanDNA-b26905/checkm_result
[2023-03-15 03:27:30,191] [INFO] Task succeeded: CheckM
[2023-03-15 03:27:30,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:27:30,194] [INFO] ===== Completeness check finished =====
[2023-03-15 03:27:30,194] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:27:30,194] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26905/markers.fasta)
[2023-03-15 03:27:30,195] [INFO] Task started: Blastn
[2023-03-15 03:27:30,195] [INFO] Running command: blastn -query OceanDNA-b26905/markers.fasta -db /var/lib/cwl/stg51c0f813-7ae4-4a2d-b585-13dd16b269d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26905/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:27:31,991] [INFO] Task succeeded: Blastn
[2023-03-15 03:27:31,992] [INFO] Selected 23 target genomes.
[2023-03-15 03:27:31,992] [INFO] Target genome list was writen to OceanDNA-b26905/target_genomes_gtdb.txt
[2023-03-15 03:27:32,071] [INFO] Task started: fastANI
[2023-03-15 03:27:32,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg483806f2-5814-46d4-af8a-27705c7bc742/OceanDNA-b26905.fa --refList OceanDNA-b26905/target_genomes_gtdb.txt --output OceanDNA-b26905/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:27:56,504] [INFO] Task succeeded: fastANI
[2023-03-15 03:27:56,517] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:27:56,517] [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	97.6027	1191	1397	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_902502825.2	s__Pseudorhizobium flavum	81.3991	830	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium	95.0	96.75	95.31	0.86	0.77	9	-
GCF_900177415.1	s__Neorhizobium oryzae_A	81.0751	809	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985875.1	s__Neorhizobium galegae_C	80.8937	789	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCF_000282095.2	s__Neorhizobium sp000282095	80.8707	782	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732195.1	s__Neorhizobium vignae	80.8654	788	1397	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	80.8051	793	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCF_017877055.1	s__Neorhizobium galegae_D	80.7803	771	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002968845.1	s__Neorhizobium tomejilense	80.7216	780	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.02	95.22	0.90	0.84	9	-
GCF_000731315.1	s__Neorhizobium galegae	80.6345	769	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.31	95.05	0.87	0.81	4	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	80.261	660	1397	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_018760785.1	s__Rhizobium_A sp018760785	80.237	728	1397	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	80.1898	692	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046245.1	s__Rhizobium_A pseudoryzae	80.0887	711	1397	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_017877135.1	s__Rhizobium_A galegae_A	80.0551	676	1397	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	79.9433	691	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469955.1	s__Neorhizobium sp900469955	79.649	684	1397	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	79.5633	587	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806065.1	s__Allorhizobium sp001724035	79.5611	580	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
GCA_900471515.1	s__Rhizobium sp900471515	79.5217	630	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	98.55	0.92	0.91	6	-
GCF_004358025.1	s__Neorhizobium deserti	79.4258	637	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466945.1	s__Allorhizobium sp900466945	79.3289	576	1397	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	79.0149	596	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.60	98.60	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-15 03:27:56,518] [INFO] GTDB search result was written to OceanDNA-b26905/result_gtdb.tsv
[2023-03-15 03:27:56,518] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:27:56,521] [INFO] DFAST_QC result json was written to OceanDNA-b26905/dqc_result.json
[2023-03-15 03:27:56,521] [INFO] DFAST_QC completed!
[2023-03-15 03:27:56,521] [INFO] Total running time: 0h2m19s