[2023-03-18 06:37:17,657] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:17,657] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:17,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg5184edf7-40e4-4425-9c73-1634db55bf63/dqc_reference
[2023-03-18 06:37:18,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:18,754] [INFO] Task started: Prodigal
[2023-03-18 06:37:18,754] [INFO] Running command: cat /var/lib/cwl/stg7c5e9d65-dd5f-402a-a19d-e4aa5b07e971/OceanDNA-b26887.fa | prodigal -d OceanDNA-b26887/cds.fna -a OceanDNA-b26887/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:37,466] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:37,466] [INFO] Task started: HMMsearch
[2023-03-18 06:37:37,466] [INFO] Running command: hmmsearch --tblout OceanDNA-b26887/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5184edf7-40e4-4425-9c73-1634db55bf63/dqc_reference/reference_markers.hmm OceanDNA-b26887/protein.faa > /dev/null
[2023-03-18 06:37:37,675] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:37,675] [INFO] Found 6/6 markers.
[2023-03-18 06:37:37,697] [INFO] Query marker FASTA was written to OceanDNA-b26887/markers.fasta
[2023-03-18 06:37:37,697] [INFO] Task started: Blastn
[2023-03-18 06:37:37,697] [INFO] Running command: blastn -query OceanDNA-b26887/markers.fasta -db /var/lib/cwl/stg5184edf7-40e4-4425-9c73-1634db55bf63/dqc_reference/reference_markers.fasta -out OceanDNA-b26887/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:38,517] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:38,518] [INFO] Selected 28 target genomes.
[2023-03-18 06:37:38,518] [INFO] Target genome list was writen to OceanDNA-b26887/target_genomes.txt
[2023-03-18 06:37:38,531] [INFO] Task started: fastANI
[2023-03-18 06:37:38,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5e9d65-dd5f-402a-a19d-e4aa5b07e971/OceanDNA-b26887.fa --refList OceanDNA-b26887/target_genomes.txt --output OceanDNA-b26887/fastani_result.tsv --threads 1
[2023-03-18 06:38:03,208] [INFO] Task succeeded: fastANI
[2023-03-18 06:38:03,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5184edf7-40e4-4425-9c73-1634db55bf63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:38:03,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5184edf7-40e4-4425-9c73-1634db55bf63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:38:03,223] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:38:03,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:38:03,224] [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
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	79.0277	190	977	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.6384	216	977	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	77.5063	166	977	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.413	129	977	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.3838	169	977	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.3223	191	977	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	77.3208	175	977	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	77.3078	178	977	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	77.3053	183	977	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.2586	176	977	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.2238	160	977	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	77.2161	187	977	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	77.2044	182	977	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	77.1899	198	977	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	77.1829	188	977	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	77.1295	178	977	95	below_threshold
Salaquimonas pukyongi	strain=RR3-28	GCA_001953055.1	2712698	2712698	type	True	77.1269	168	977	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	77.1221	177	977	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	77.0745	189	977	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	77.0709	196	977	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.0666	197	977	95	below_threshold
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	77.021	115	977	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.9745	146	977	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.9745	146	977	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	76.9337	159	977	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	76.891	124	977	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	76.7745	111	977	95	below_threshold
Consotaella salsifontis	strain=USBA 369	GCA_900167365.1	1365950	1365950	type	True	76.1769	102	977	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:38:03,224] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26887/tc_result.tsv
[2023-03-18 06:38:03,224] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:38:03,224] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:38:03,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5184edf7-40e4-4425-9c73-1634db55bf63/dqc_reference/checkm_data
[2023-03-18 06:38:03,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:38:03,229] [INFO] Task started: CheckM
[2023-03-18 06:38:03,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26887/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26887/checkm_input OceanDNA-b26887/checkm_result
[2023-03-18 06:38:53,113] [INFO] Task succeeded: CheckM
[2023-03-18 06:38:53,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:38:53,116] [INFO] ===== Completeness check finished =====
[2023-03-18 06:38:53,117] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:38:53,117] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26887/markers.fasta)
[2023-03-18 06:38:53,117] [INFO] Task started: Blastn
[2023-03-18 06:38:53,117] [INFO] Running command: blastn -query OceanDNA-b26887/markers.fasta -db /var/lib/cwl/stg5184edf7-40e4-4425-9c73-1634db55bf63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26887/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:38:54,697] [INFO] Task succeeded: Blastn
[2023-03-18 06:38:54,698] [INFO] Selected 31 target genomes.
[2023-03-18 06:38:54,698] [INFO] Target genome list was writen to OceanDNA-b26887/target_genomes_gtdb.txt
[2023-03-18 06:38:54,835] [INFO] Task started: fastANI
[2023-03-18 06:38:54,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5e9d65-dd5f-402a-a19d-e4aa5b07e971/OceanDNA-b26887.fa --refList OceanDNA-b26887/target_genomes_gtdb.txt --output OceanDNA-b26887/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:39:21,396] [INFO] Task succeeded: fastANI
[2023-03-18 06:39:21,413] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:39:21,413] [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
GCA_002698425.1	s__Oricola sp002698425	78.8471	201	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	78.0457	189	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	77.876	274	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	77.5744	204	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898995.1	s__63-22 sp001898995	77.5643	142	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__63-22	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006442815.1	s__Mesorhizobium sp006442815	77.4839	164	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_016591715.1	s__Mesorhizobium sp016591715	77.4231	179	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	77.3928	130	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300335.1	s__Nitratireductor pacificus	77.3368	190	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	77.3248	206	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176035.2	s__Mesorhizobium opportunistum	77.3208	175	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.26	95.55	0.85	0.80	10	-
GCF_016836705.1	s__Mesorhizobium caraganae	77.2937	179	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	96.20	0.88	0.86	3	-
GCF_003952505.1	s__Mesorhizobium sp003952505	77.2712	183	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_003012705.1	s__Pseudaminobacter soli	77.2621	170	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091085.1	s__Mesorhizobium sp019091085	77.2438	184	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001558695.1	s__Paramesorhizobium deserti	77.2413	166	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439355.1	s__Mesorhizobium sp006439355	77.233	182	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824805.1	s__Mesorhizobium sp000824805	77.2153	176	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045125.1	s__Pseudaminobacter camelthorni	77.2032	188	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	77.1899	198	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356515.1	s__Mesorhizobium loti_C	77.1821	185	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.70	98.70	0.94	0.94	2	-
GCA_017305925.1	s__JAFKJW01 sp017305925	77.1585	160	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JAFKJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	77.1439	190	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953055.1	s__Salaquimonas pukyongi	77.1269	168	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Salaquimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503535.1	s__Mesorhizobium sp005503535	77.0871	197	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196765.1	s__Mycoplana azooxidifex	76.9203	160	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300515.1	s__Nitratireductor indicus	76.891	124	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004827385.1	s__Sinorhizobium sp004827385	76.872	138	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815515.1	s__Aureimonas populi	76.7745	111	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144345.1	s__Devosia_A sp004144345	76.6148	95	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167365.1	s__Consotaella salsifontis	76.1473	104	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Consotaella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:39:21,413] [INFO] GTDB search result was written to OceanDNA-b26887/result_gtdb.tsv
[2023-03-18 06:39:21,413] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:39:21,416] [INFO] DFAST_QC result json was written to OceanDNA-b26887/dqc_result.json
[2023-03-18 06:39:21,416] [INFO] DFAST_QC completed!
[2023-03-18 06:39:21,416] [INFO] Total running time: 0h2m4s