[2023-03-17 07:44:37,002] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:37,005] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:37,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e7d9f4-7725-4319-b883-34e08d659bbe/dqc_reference
[2023-03-17 07:44:38,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,852] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,852] [INFO] Running command: cat /var/lib/cwl/stg7e820dfe-d9d2-47e7-8ad9-b95815dcb32b/OceanDNA-b35935.fa | prodigal -d OceanDNA-b35935/cds.fna -a OceanDNA-b35935/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:58,282] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:58,282] [INFO] Task started: HMMsearch
[2023-03-17 07:44:58,282] [INFO] Running command: hmmsearch --tblout OceanDNA-b35935/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e7d9f4-7725-4319-b883-34e08d659bbe/dqc_reference/reference_markers.hmm OceanDNA-b35935/protein.faa > /dev/null
[2023-03-17 07:44:58,499] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:58,499] [INFO] Found 6/6 markers.
[2023-03-17 07:44:58,519] [INFO] Query marker FASTA was written to OceanDNA-b35935/markers.fasta
[2023-03-17 07:44:58,520] [INFO] Task started: Blastn
[2023-03-17 07:44:58,520] [INFO] Running command: blastn -query OceanDNA-b35935/markers.fasta -db /var/lib/cwl/stg20e7d9f4-7725-4319-b883-34e08d659bbe/dqc_reference/reference_markers.fasta -out OceanDNA-b35935/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:44:59,370] [INFO] Task succeeded: Blastn
[2023-03-17 07:44:59,371] [INFO] Selected 29 target genomes.
[2023-03-17 07:44:59,371] [INFO] Target genome list was writen to OceanDNA-b35935/target_genomes.txt
[2023-03-17 07:44:59,400] [INFO] Task started: fastANI
[2023-03-17 07:44:59,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e820dfe-d9d2-47e7-8ad9-b95815dcb32b/OceanDNA-b35935.fa --refList OceanDNA-b35935/target_genomes.txt --output OceanDNA-b35935/fastani_result.tsv --threads 1
[2023-03-17 07:45:17,181] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:17,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e7d9f4-7725-4319-b883-34e08d659bbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:17,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e7d9f4-7725-4319-b883-34e08d659bbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:17,197] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:17,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:45:17,197] [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
Immundisolibacter cernigliae	strain=TR3.2	GCA_001697225.1	1810504	1810504	type	True	84.1413	727	1021	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.8518	192	1021	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.8419	150	1021	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.7935	282	1021	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	76.7759	165	1021	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.7661	171	1021	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.7333	211	1021	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	76.7138	193	1021	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	76.7093	192	1021	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.6946	122	1021	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	76.6729	196	1021	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.6549	252	1021	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.6134	219	1021	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.5911	189	1021	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	76.5871	185	1021	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.514	156	1021	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.5098	193	1021	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.5092	156	1021	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.4537	159	1021	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.3934	154	1021	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	76.3505	194	1021	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.3485	196	1021	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	76.3366	223	1021	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.3154	184	1021	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	76.3107	173	1021	95	below_threshold
Wenzhouxiangella marina	strain=DSM 103414	GCA_014203035.1	1579979	1579979	type	True	76.2908	74	1021	95	below_threshold
Wenzhouxiangella marina	strain=KCTC 42284	GCA_001187785.1	1579979	1579979	type	True	76.2657	75	1021	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.0551	167	1021	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	75.9284	281	1021	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:45:17,197] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35935/tc_result.tsv
[2023-03-17 07:45:17,198] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:17,198] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:17,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e7d9f4-7725-4319-b883-34e08d659bbe/dqc_reference/checkm_data
[2023-03-17 07:45:17,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:17,203] [INFO] Task started: CheckM
[2023-03-17 07:45:17,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35935/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35935/checkm_input OceanDNA-b35935/checkm_result
[2023-03-17 07:46:09,879] [INFO] Task succeeded: CheckM
[2023-03-17 07:46:09,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:46:09,882] [INFO] ===== Completeness check finished =====
[2023-03-17 07:46:09,883] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:46:09,883] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35935/markers.fasta)
[2023-03-17 07:46:09,883] [INFO] Task started: Blastn
[2023-03-17 07:46:09,883] [INFO] Running command: blastn -query OceanDNA-b35935/markers.fasta -db /var/lib/cwl/stg20e7d9f4-7725-4319-b883-34e08d659bbe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35935/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:46:11,554] [INFO] Task succeeded: Blastn
[2023-03-17 07:46:11,555] [INFO] Selected 20 target genomes.
[2023-03-17 07:46:11,555] [INFO] Target genome list was writen to OceanDNA-b35935/target_genomes_gtdb.txt
[2023-03-17 07:46:11,592] [INFO] Task started: fastANI
[2023-03-17 07:46:11,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e820dfe-d9d2-47e7-8ad9-b95815dcb32b/OceanDNA-b35935.fa --refList OceanDNA-b35935/target_genomes_gtdb.txt --output OceanDNA-b35935/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:46:22,777] [INFO] Task succeeded: fastANI
[2023-03-17 07:46:22,788] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:46:22,788] [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_003526065.1	s__Immundisolibacter sp003526065	84.3588	455	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697225.1	s__Immundisolibacter cernigliae	84.1154	731	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359565.1	s__Immundisolibacter sp014359565	84.0936	705	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937385.1	s__QNFN01 sp009937385	77.1703	152	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__QNFN01;f__QNFN01;g__QNFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712635.1	s__JADJWH01 sp016712635	77.0842	160	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.8126	281	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494165.1	s__S144-34 sp015494165	76.7972	171	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.6985	246	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.6882	175	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002897735.1	s__BMS3Abin12 sp002897735	76.6001	105	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__21-64-14;f__21-64-14;g__BMS3Abin12	95.0	99.84	99.73	0.95	0.93	3	-
GCF_000429065.1	s__Silanimonas lenta	76.5669	166	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	76.5346	212	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378305.1	s__Thioalkalivibrio sp000378305	76.4305	119	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	98.92	98.55	0.95	0.94	12	-
GCA_002995625.1	s__UDEA-SF1 sp002995625	76.2696	171	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UDEA-SF1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	76.2545	111	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCF_018122625.2	s__Coralloluteibacterium stylophorae	76.1407	229	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Coralloluteibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127625.1	s__Aquisalimonas sp007127625	76.1065	81	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	98.40	98.40	0.79	0.79	2	-
GCA_011374975.1	s__Thiogranum sp011374975	75.9894	99	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054615.1	s__FEN-1219 sp011054615	75.9239	98	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__FEN-1219	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938575.1	s__UBA5518 sp903938575	75.7474	74	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	98.92	98.84	0.83	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-17 07:46:22,788] [INFO] GTDB search result was written to OceanDNA-b35935/result_gtdb.tsv
[2023-03-17 07:46:22,788] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:46:22,791] [INFO] DFAST_QC result json was written to OceanDNA-b35935/dqc_result.json
[2023-03-17 07:46:22,791] [INFO] DFAST_QC completed!
[2023-03-17 07:46:22,791] [INFO] Total running time: 0h1m46s