[2023-03-17 02:31:12,847] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg07e6f936-1070-4d3b-8fb8-0f87a0c1d085/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stgf9b51f98-9308-4039-844d-8d5de969bfde/OceanDNA-b26822.fa | prodigal -d OceanDNA-b26822/cds.fna -a OceanDNA-b26822/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:37,200] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:37,201] [INFO] Task started: HMMsearch
[2023-03-17 02:31:37,201] [INFO] Running command: hmmsearch --tblout OceanDNA-b26822/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07e6f936-1070-4d3b-8fb8-0f87a0c1d085/dqc_reference/reference_markers.hmm OceanDNA-b26822/protein.faa > /dev/null
[2023-03-17 02:31:37,427] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:37,428] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9b51f98-9308-4039-844d-8d5de969bfde/OceanDNA-b26822.fa]
[2023-03-17 02:31:37,461] [INFO] Query marker FASTA was written to OceanDNA-b26822/markers.fasta
[2023-03-17 02:31:37,462] [INFO] Task started: Blastn
[2023-03-17 02:31:37,462] [INFO] Running command: blastn -query OceanDNA-b26822/markers.fasta -db /var/lib/cwl/stg07e6f936-1070-4d3b-8fb8-0f87a0c1d085/dqc_reference/reference_markers.fasta -out OceanDNA-b26822/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:38,328] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:38,329] [INFO] Selected 18 target genomes.
[2023-03-17 02:31:38,329] [INFO] Target genome list was writen to OceanDNA-b26822/target_genomes.txt
[2023-03-17 02:31:38,340] [INFO] Task started: fastANI
[2023-03-17 02:31:38,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b51f98-9308-4039-844d-8d5de969bfde/OceanDNA-b26822.fa --refList OceanDNA-b26822/target_genomes.txt --output OceanDNA-b26822/fastani_result.tsv --threads 1
[2023-03-17 02:31:56,920] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:56,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07e6f936-1070-4d3b-8fb8-0f87a0c1d085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:56,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07e6f936-1070-4d3b-8fb8-0f87a0c1d085/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:56,931] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:56,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:31:56,931] [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
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	88.8246	903	1214	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	81.4679	693	1214	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	80.8106	610	1214	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.575	444	1214	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	79.0747	423	1214	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.9275	463	1214	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	78.8	426	1214	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.7834	415	1214	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	78.7522	421	1214	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.7358	386	1214	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	78.7154	454	1214	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	78.6543	442	1214	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	78.6285	396	1214	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	78.5428	465	1214	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	78.4308	396	1214	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.3215	371	1214	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.311	372	1214	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	78.1101	342	1214	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:31:56,931] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26822/tc_result.tsv
[2023-03-17 02:31:56,932] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:56,932] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:56,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07e6f936-1070-4d3b-8fb8-0f87a0c1d085/dqc_reference/checkm_data
[2023-03-17 02:31:56,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:56,990] [INFO] Task started: CheckM
[2023-03-17 02:31:56,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26822/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26822/checkm_input OceanDNA-b26822/checkm_result
[2023-03-17 02:32:53,256] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:53,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.10%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:53,261] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:53,261] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:53,261] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26822/markers.fasta)
[2023-03-17 02:32:53,262] [INFO] Task started: Blastn
[2023-03-17 02:32:53,263] [INFO] Running command: blastn -query OceanDNA-b26822/markers.fasta -db /var/lib/cwl/stg07e6f936-1070-4d3b-8fb8-0f87a0c1d085/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26822/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:54,989] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:54,990] [INFO] Selected 18 target genomes.
[2023-03-17 02:32:54,990] [INFO] Target genome list was writen to OceanDNA-b26822/target_genomes_gtdb.txt
[2023-03-17 02:32:55,432] [INFO] Task started: fastANI
[2023-03-17 02:32:55,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b51f98-9308-4039-844d-8d5de969bfde/OceanDNA-b26822.fa --refList OceanDNA-b26822/target_genomes_gtdb.txt --output OceanDNA-b26822/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:33:13,402] [INFO] Task succeeded: fastANI
[2023-03-17 02:33:13,413] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:33:13,413] [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_001889605.1	s__Mesorhizobium_E oceanicum	88.8504	901	1214	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_014495845.1	s__Mesorhizobium_E sp014495845	81.445	697	1214	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_003970795.1	s__Mesorhizobium_E carbonis	80.8308	608	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	79.5926	502	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	79.5521	446	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	79.4995	530	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	79.469	542	1214	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	79.3396	476	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	79.3361	398	1214	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_008180155.1	s__Aquamicrobium_A microcysteis	79.1235	443	1214	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_004791025.1	s__Mesorhizobium sp004791025	78.9059	480	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_011045125.1	s__Pseudaminobacter camelthorni	78.8965	462	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952505.1	s__Mesorhizobium sp003952505	78.88	435	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_014206975.1	s__Aminobacter aganoensis	78.8042	425	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCA_001510895.1	s__Mesorhizobium loti_A	78.7254	459	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002295115.1	s__Mesorhizobium sp002295115	78.6641	434	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	78.5242	452	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727065.1	s__Zhengella mangrovi	78.1206	341	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Zhengella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:33:13,413] [INFO] GTDB search result was written to OceanDNA-b26822/result_gtdb.tsv
[2023-03-17 02:33:13,414] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:33:13,415] [INFO] DFAST_QC result json was written to OceanDNA-b26822/dqc_result.json
[2023-03-17 02:33:13,416] [INFO] DFAST_QC completed!
[2023-03-17 02:33:13,416] [INFO] Total running time: 0h2m1s