[2023-03-16 17:17:45,191] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:17:45,191] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:17:45,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg889a5ea0-348a-46d8-a8c5-2eeee1a9f0f9/dqc_reference
[2023-03-16 17:17:46,319] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:17:46,320] [INFO] Task started: Prodigal
[2023-03-16 17:17:46,320] [INFO] Running command: cat /var/lib/cwl/stg3017e163-3d28-4346-b706-2ed5d2b2cbef/OceanDNA-b44662.fa | prodigal -d OceanDNA-b44662/cds.fna -a OceanDNA-b44662/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:18:00,360] [INFO] Task succeeded: Prodigal
[2023-03-16 17:18:00,361] [INFO] Task started: HMMsearch
[2023-03-16 17:18:00,361] [INFO] Running command: hmmsearch --tblout OceanDNA-b44662/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg889a5ea0-348a-46d8-a8c5-2eeee1a9f0f9/dqc_reference/reference_markers.hmm OceanDNA-b44662/protein.faa > /dev/null
[2023-03-16 17:18:00,552] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:18:00,553] [INFO] Found 6/6 markers.
[2023-03-16 17:18:00,575] [INFO] Query marker FASTA was written to OceanDNA-b44662/markers.fasta
[2023-03-16 17:18:00,576] [INFO] Task started: Blastn
[2023-03-16 17:18:00,576] [INFO] Running command: blastn -query OceanDNA-b44662/markers.fasta -db /var/lib/cwl/stg889a5ea0-348a-46d8-a8c5-2eeee1a9f0f9/dqc_reference/reference_markers.fasta -out OceanDNA-b44662/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:18:01,290] [INFO] Task succeeded: Blastn
[2023-03-16 17:18:01,291] [INFO] Selected 30 target genomes.
[2023-03-16 17:18:01,291] [INFO] Target genome list was writen to OceanDNA-b44662/target_genomes.txt
[2023-03-16 17:18:01,308] [INFO] Task started: fastANI
[2023-03-16 17:18:01,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg3017e163-3d28-4346-b706-2ed5d2b2cbef/OceanDNA-b44662.fa --refList OceanDNA-b44662/target_genomes.txt --output OceanDNA-b44662/fastani_result.tsv --threads 1
[2023-03-16 17:18:17,520] [INFO] Task succeeded: fastANI
[2023-03-16 17:18:17,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg889a5ea0-348a-46d8-a8c5-2eeee1a9f0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:18:17,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg889a5ea0-348a-46d8-a8c5-2eeee1a9f0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:18:17,535] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:18:17,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:18:17,536] [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	79.4687	310	588	95	below_threshold
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	76.7062	68	588	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	76.5906	71	588	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	76.5736	73	588	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	76.5607	88	588	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	76.514	68	588	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	76.4878	65	588	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.4872	76	588	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	76.4785	71	588	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	76.4622	64	588	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	76.4555	82	588	95	below_threshold
Stenotrophomonas maltophilia	strain=ATCC 13637	GCA_001997185.1	40324	40324	type	True	76.445	68	588	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	76.4213	73	588	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	76.4181	86	588	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	76.4109	65	588	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.4022	79	588	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	76.3763	89	588	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	76.3693	80	588	95	below_threshold
Xanthomonas campestris	strain=NCPPB 347	GCA_020731405.1	339	339	pathovar	True	76.3646	67	588	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	76.2974	69	588	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	76.248	77	588	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	76.2473	77	588	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	76.1438	68	588	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	76.0476	88	588	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	75.9722	57	588	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	75.9445	64	588	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	75.9165	51	588	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	75.5457	64	588	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:18:17,536] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44662/tc_result.tsv
[2023-03-16 17:18:17,537] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:18:17,537] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:18:17,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg889a5ea0-348a-46d8-a8c5-2eeee1a9f0f9/dqc_reference/checkm_data
[2023-03-16 17:18:17,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:18:17,543] [INFO] Task started: CheckM
[2023-03-16 17:18:17,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44662/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44662/checkm_input OceanDNA-b44662/checkm_result
[2023-03-16 17:18:59,501] [INFO] Task succeeded: CheckM
[2023-03-16 17:18:59,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.63%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:18:59,505] [INFO] ===== Completeness check finished =====
[2023-03-16 17:18:59,506] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:18:59,506] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44662/markers.fasta)
[2023-03-16 17:18:59,507] [INFO] Task started: Blastn
[2023-03-16 17:18:59,507] [INFO] Running command: blastn -query OceanDNA-b44662/markers.fasta -db /var/lib/cwl/stg889a5ea0-348a-46d8-a8c5-2eeee1a9f0f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44662/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:19:00,934] [INFO] Task succeeded: Blastn
[2023-03-16 17:19:00,936] [INFO] Selected 29 target genomes.
[2023-03-16 17:19:00,936] [INFO] Target genome list was writen to OceanDNA-b44662/target_genomes_gtdb.txt
[2023-03-16 17:19:01,020] [INFO] Task started: fastANI
[2023-03-16 17:19:01,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg3017e163-3d28-4346-b706-2ed5d2b2cbef/OceanDNA-b44662.fa --refList OceanDNA-b44662/target_genomes_gtdb.txt --output OceanDNA-b44662/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:19:26,261] [INFO] Task succeeded: fastANI
[2023-03-16 17:19:26,275] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:19:26,275] [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	79.4687	310	588	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	76.8364	94	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970865.1	s__Stenotrophomonas maltophilia_AR	76.8237	75	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720345.1	s__Thermomonas sp016720345	76.7809	75	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_008119715.1	s__Xanthomonas_A sontii	76.7048	83	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.63	96.72	0.89	0.85	12	-
GCF_016735495.2	s__Lysobacter sp016735495	76.6357	70	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197275.1	s__Xanthomonas campestris_B	76.5743	66	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.71	98.71	0.92	0.92	2	-
GCA_019115725.1	s__Luteimonas excrementigallinarum	76.5713	54	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101175.1	s__Stenotrophomonas pavanii	76.5607	88	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.59	98.08	0.91	0.84	20	-
GCF_007667275.1	s__Stenotrophomonas maltophilia_AE	76.5375	75	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.01	98.01	0.93	0.93	2	-
GCA_004322005.1	s__Rhodanobacter sp004322005	76.52	54	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346925.1	s__Stenotrophomonas maltophilia_A	76.5111	79	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.29	95.44	0.89	0.84	41	-
GCF_009765165.1	s__Lysobacter panacisoli	76.4622	64	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199795.1	s__Xanthomonas_A sp014199795	76.4422	83	588	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_002940085.1	s__Xanthomonas_A sacchari	76.4181	86	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.45	95.41	0.95	0.91	6	-
GCF_014206815.1	s__Xanthomonas_A sacchari_B	76.4147	85	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000426365.1	s__Arenimonas composti	76.4022	79	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014202825.1	s__Chiayiivirga flava	76.3941	77	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Chiayiivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014946745.1	s__Aquimonas sp014946745	76.3859	102	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Aquimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	76.3196	60	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900113425.1	s__Stenotrophomonas maltophilia_P	76.3175	63	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.08	97.00	0.92	0.88	10	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	76.2473	77	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	76.1321	68	588	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_016586165.1	s__Dyella sp016586165	76.0797	60	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	76.0135	90	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230695.2	s__Rhodanobacter denitrificans	75.9445	64	588	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.49	98.47	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-16 17:19:26,276] [INFO] GTDB search result was written to OceanDNA-b44662/result_gtdb.tsv
[2023-03-16 17:19:26,276] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:19:26,279] [INFO] DFAST_QC result json was written to OceanDNA-b44662/dqc_result.json
[2023-03-16 17:19:26,279] [INFO] DFAST_QC completed!
[2023-03-16 17:19:26,279] [INFO] Total running time: 0h1m41s