[2023-03-16 03:23:47,642] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:47,642] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:47,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg3481f131-7d71-4060-9cae-a297ed0b4d80/dqc_reference
[2023-03-16 03:23:49,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:49,415] [INFO] Task started: Prodigal
[2023-03-16 03:23:49,415] [INFO] Running command: cat /var/lib/cwl/stgae3191b9-65ac-4385-bfb4-0ec04ca10b7b/OceanDNA-b44638.fa | prodigal -d OceanDNA-b44638/cds.fna -a OceanDNA-b44638/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:27,999] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:28,000] [INFO] Task started: HMMsearch
[2023-03-16 03:24:28,000] [INFO] Running command: hmmsearch --tblout OceanDNA-b44638/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3481f131-7d71-4060-9cae-a297ed0b4d80/dqc_reference/reference_markers.hmm OceanDNA-b44638/protein.faa > /dev/null
[2023-03-16 03:24:28,237] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:28,238] [INFO] Found 6/6 markers.
[2023-03-16 03:24:28,267] [INFO] Query marker FASTA was written to OceanDNA-b44638/markers.fasta
[2023-03-16 03:24:28,267] [INFO] Task started: Blastn
[2023-03-16 03:24:28,267] [INFO] Running command: blastn -query OceanDNA-b44638/markers.fasta -db /var/lib/cwl/stg3481f131-7d71-4060-9cae-a297ed0b4d80/dqc_reference/reference_markers.fasta -out OceanDNA-b44638/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:29,080] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:29,081] [INFO] Selected 26 target genomes.
[2023-03-16 03:24:29,081] [INFO] Target genome list was writen to OceanDNA-b44638/target_genomes.txt
[2023-03-16 03:24:29,094] [INFO] Task started: fastANI
[2023-03-16 03:24:29,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3191b9-65ac-4385-bfb4-0ec04ca10b7b/OceanDNA-b44638.fa --refList OceanDNA-b44638/target_genomes.txt --output OceanDNA-b44638/fastani_result.tsv --threads 1
[2023-03-16 03:24:46,400] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:46,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3481f131-7d71-4060-9cae-a297ed0b4d80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:46,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3481f131-7d71-4060-9cae-a297ed0b4d80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:46,414] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:46,414] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:46,414] [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
Pseudomarimonas arenosa	strain=CAU 1598	GCA_014841215.1	2774145	2774145	type	True	81.2273	950	1647	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	77.2172	295	1647	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	77.1874	281	1647	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	77.1699	240	1647	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	77.1476	231	1647	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	77.147	251	1647	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	77.1458	234	1647	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	77.1446	259	1647	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	77.1345	290	1647	95	below_threshold
Stenotrophomonas maltophilia	strain=NCTC10257	GCA_900186865.1	40324	40324	type	True	77.1241	239	1647	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	77.0893	284	1647	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	77.0795	234	1647	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	77.0755	235	1647	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	77.0583	238	1647	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	77.0074	260	1647	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	76.9931	224	1647	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	76.9682	244	1647	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	76.9672	209	1647	95	below_threshold
Stenotrophomonas terrae	strain=DSM 18941	GCA_001431465.1	405446	405446	type	True	76.9658	223	1647	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	76.9351	233	1647	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	76.8831	253	1647	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.7807	231	1647	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	76.7281	204	1647	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.7122	211	1647	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.6784	227	1647	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.6355	198	1647	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:46,414] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44638/tc_result.tsv
[2023-03-16 03:24:46,414] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:46,414] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:46,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3481f131-7d71-4060-9cae-a297ed0b4d80/dqc_reference/checkm_data
[2023-03-16 03:24:46,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:46,433] [INFO] Task started: CheckM
[2023-03-16 03:24:46,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44638/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44638/checkm_input OceanDNA-b44638/checkm_result
[2023-03-16 03:26:18,164] [INFO] Task succeeded: CheckM
[2023-03-16 03:26:18,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:26:18,518] [INFO] ===== Completeness check finished =====
[2023-03-16 03:26:18,518] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:26:18,518] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44638/markers.fasta)
[2023-03-16 03:26:18,519] [INFO] Task started: Blastn
[2023-03-16 03:26:18,520] [INFO] Running command: blastn -query OceanDNA-b44638/markers.fasta -db /var/lib/cwl/stg3481f131-7d71-4060-9cae-a297ed0b4d80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44638/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:26:20,060] [INFO] Task succeeded: Blastn
[2023-03-16 03:26:20,061] [INFO] Selected 28 target genomes.
[2023-03-16 03:26:20,061] [INFO] Target genome list was writen to OceanDNA-b44638/target_genomes_gtdb.txt
[2023-03-16 03:26:20,482] [INFO] Task started: fastANI
[2023-03-16 03:26:20,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3191b9-65ac-4385-bfb4-0ec04ca10b7b/OceanDNA-b44638.fa --refList OceanDNA-b44638/target_genomes_gtdb.txt --output OceanDNA-b44638/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:26:38,774] [INFO] Task succeeded: fastANI
[2023-03-16 03:26:38,789] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:26:38,789] [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_014841215.1	s__CAU-1598 sp014841215	81.2288	949	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__CAU-1598	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202935.1	s__Rehaibacterium terrae	77.4523	305	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643775.1	s__Arenimonas soli	77.4122	277	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970865.1	s__Stenotrophomonas maltophilia_AR	77.3259	239	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428685.1	s__Lysobacter sp001428685	77.3079	282	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCA_014946745.1	s__Aquimonas sp014946745	77.2699	307	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Aquimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	77.2697	221	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_002138415.1	s__Stenotrophomonas maltophilia_G	77.2538	237	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.93	95.59	0.89	0.87	14	-
GCF_000743535.1	s__Arenimonas donghaensis	77.2496	260	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199795.1	s__Xanthomonas_A sp014199795	77.2432	267	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
GCF_008017755.1	s__VRTS01 sp008017755	77.2357	217	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__VRTS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	77.1945	300	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	77.1874	281	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	77.1538	258	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192255.1	s__Stenotrophomonas sp002192255	77.1448	243	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.64	95.45	0.89	0.84	9	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	77.1407	246	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_000185965.1	s__Pseudoxanthomonas suwonensis_A	77.1397	251	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001431625.1	s__Stenotrophomonas geniculata	77.1345	235	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.51	96.26	0.87	0.77	45	-
GCA_017302035.1	s__Pseudoxanthomonas sp017302035	77.0923	205	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.26	99.26	0.94	0.94	2	-
GCF_014202825.1	s__Chiayiivirga flava	76.9907	282	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Chiayiivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	76.9837	219	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
GCF_018847975.1	s__Lysobacter sp018847975	76.9577	303	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	76.9326	234	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	76.7441	216	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	76.717	223	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017837635.1	s__Frateuria_A sp017837635	76.6468	197	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427505.1	s__Rhodanobacter sp000427505	76.5475	202	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.93	99.93	0.96	0.96	2	-
GCA_013362045.1	s__Frateuria_A sp013362045	76.5065	163	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:26:38,789] [INFO] GTDB search result was written to OceanDNA-b44638/result_gtdb.tsv
[2023-03-16 03:26:38,790] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:26:38,792] [INFO] DFAST_QC result json was written to OceanDNA-b44638/dqc_result.json
[2023-03-16 03:26:38,792] [INFO] DFAST_QC completed!
[2023-03-16 03:26:38,792] [INFO] Total running time: 0h2m51s