Inconsistent alignments depending on whether reference file is gzipped or not

[AaronRuben]

Hi,

I am using mashmap v3.1.3 and I noticed that the same alignment was reported multiple times in the output file. For example, here is the output for reference chromosome 21:

ptg000091l	861542	0	861542	+	chr21	45090682	152523	1014065	13	861542	20	id:f:0.990785	kc:f:0.283563
ptg000217l	527266	0	527266	+	chr21	45090682	178973	706239	12	527266	20	id:f:0.990089	kc:f:0.331461
ptg000217l	527266	0	527266	+	chr21	45090682	178973	706239	12	527266	20	id:f:0.990089	kc:f:0.331461
ptg000203l	686331	0	686331	+	chr21	45090682	179063	865394	15	686331	25	id:f:0.996609	kc:f:0.235299
ptg000268l	916773	0	916773	+	chr21	45090682	582998	1499771	3	916773	12	id:f:0.93172	kc:f:0.0635271
ptg000268l	916773	0	916773	+	chr21	45090682	582998	1499771	3	916773	12	id:f:0.93172	kc:f:0.0635271
ptg000268l	916773	0	916773	+	chr21	45090682	582998	1499771	3	916773	12	id:f:0.93172	kc:f:0.0635271
ptg000145l	2623179	0	2623179	+	chr21	45090682	1133648	3756827	12	2623179	19	id:f:0.98662	kc:f:0.255438
ptg000158l	1222257	0	1222257	+	chr21	45090682	1565548	2787805	3	1222257	12	id:f:0.936192	kc:f:0.214653
ptg000158l	1222257	0	1222257	+	chr21	45090682	1565548	2787805	3	1222257	12	id:f:0.936192	kc:f:0.214653
ptg000158l	1222257	0	1222257	+	chr21	45090682	1565548	2787805	3	1222257	12	id:f:0.936192	kc:f:0.214653
ptg000158l	1222257	0	1222257	+	chr21	45090682	1565548	2787805	3	1222257	12	id:f:0.936192	kc:f:0.214653
ptg000158l	1222257	0	1222257	+	chr21	45090682	1565548	2787805	3	1222257	12	id:f:0.936192	kc:f:0.214653
ptg000158l	1222257	0	1222257	+	chr21	45090682	1565548	2787805	3	1222257	12	id:f:0.936192	kc:f:0.214653
ptg000160l	848270	0	848270	+	chr21	45090682	2308763	3157033	8	848270	16	id:f:0.972836	kc:f:0.583853
ptg000160l	848270	0	848270	+	chr21	45090682	2308763	3157033	8	848270	16	id:f:0.972836	kc:f:0.583853
ptg000151l	555938	0	555938	+	chr21	45090682	2459556	3015494	15	555938	22	id:f:0.993434	kc:f:1.23635
ptg000172l	1014256	0	1014256	+	chr21	45090682	2577878	3592134	10	1014256	17	id:f:0.980634	kc:f:0.597447
ptg000215l	318592	0	318592	+	chr21	45090682	5433633	5752225	19	318592	29	id:f:0.998634	kc:f:0.130072
ptg000025l	2865536	0	2865536	+	chr21	45090682	5830375	8695911	10	2865536	17	id:f:0.978886	kc:f:0.474346
ptg000176l	584981	0	584981	-	chr21	45090682	8297841	8882822	9	584981	16	id:f:0.977014	kc:f:0.599697
ptg000176l	584981	0	584981	+	chr21	45090682	8297841	8882822	9	584981	16	id:f:0.977014	kc:f:0.599697
ptg000176l	584981	0	584981	+	chr21	45090682	8297841	8882822	9	584981	16	id:f:0.977014	kc:f:0.599697
ptg000176l	584981	0	584981	+	chr21	45090682	8297841	8882822	9	584981	16	id:f:0.977014	kc:f:0.599697
ptg000093l	3796125	0	3796125	+	chr21	45090682	8542762	12338887	19	3796125	29	id:f:0.998634	kc:f:0.41517
ptg000125l	2794119	0	2794119	+	chr21	45090682	9318318	12112437	18	2794119	25	id:f:0.997158	kc:f:0.524907
ptg000290l	812527	0	812527	+	chr21	45090682	10614047	11426574	4	812527	13	id:f:0.945935	kc:f:0.117817
ptg000293l	206332	0	206332	+	chr21	45090682	10988834	11195166	10	206332	17	id:f:0.978886	kc:f:0.0164015
ptg000292l	229265	0	229265	+	chr21	45090682	11199120	11428385	11	229265	17	id:f:0.982112	kc:f:0.0476858
ptg000033l	27686851	0	27686851	+	chr21	45090682	24117979	45090681	20	27686851	255	id:f:1	kc:f:0.872569
ptg000115l	3037875	0	3037875	+	chr21	45090682	38473000	41510875	18	3037875	25	id:f:0.997158	kc:f:0.865375
ptg000147l	1146249	0	1146249	+	chr21	45090682	42104328	43250577	19	1146249	29	id:f:0.998634	kc:f:1.36605
ptg000047l	2315813	0	2315813	+	chr21	45090682	43904919	45090681	19	2315813	29	id:f:0.998634	kc:f:1.30252

I found this odd so I re-ran it. This time I happened to use an uncompressed version of my reference sequence file and I didn't get duplicated alignments, but I got some new alignments and the positions of previously found alignments changed. Here is again the output for reference chr21:

ptg000091l	861542	0	861542	+	chr21	45090682	173803	1035345	29	861542	22	id:f:0.993222	kc:f:0.33354
ptg000203l	686331	0	686331	+	chr21	45090682	179063	865394	30	686331	22	id:f:0.994209	kc:f:0.315678
ptg000145l	2623179	0	2623179	+	chr21	45090682	1170940	3794119	24	2623179	19	id:f:0.98662	kc:f:0.182862
ptg000151l	555938	0	555938	+	chr21	45090682	2499197	3055135	24	555938	19	id:f:0.98662	kc:f:0.900919
ptg000172l	1014256	0	1014256	+	chr21	45090682	2682656	3696912	27	1014256	20	id:f:0.990289	kc:f:0.642754
ptg000215l	318592	0	318592	+	chr21	45090682	5420070	5738662	38	318592	29	id:f:0.998634	kc:f:0.145981
ptg000025l	2865536	0	2865536	+	chr21	45090682	7220950	10086486	21	2865536	17	id:f:0.981403	kc:f:0.455276
ptg000176l	584981	0	584981	-	chr21	45090682	8381941	8966922	16	584981	16	id:f:0.971897	kc:f:0.557647
ptg000176l	584981	0	584981	+	chr21	45090682	8381941	8966922	16	584981	16	id:f:0.971897	kc:f:0.557647
ptg000176l	584981	0	584981	+	chr21	45090682	8381941	8966922	16	584981	16	id:f:0.971897	kc:f:0.557647
ptg000176l	584981	0	584981	+	chr21	45090682	8381941	8966922	16	584981	16	id:f:0.971897	kc:f:0.557647
ptg000125l	2794119	0	2794119	+	chr21	45090682	9374562	12168681	33	2794119	23	id:f:0.995431	kc:f:0.500231
ptg000293l	206332	0	206332	+	chr21	45090682	11091705	11298037	21	206332	17	id:f:0.980549	kc:f:0.0194184
ptg000292l	229265	0	229265	+	chr21	45090682	11199120	11428385	25	229265	19	id:f:0.986286	kc:f:0.0644872
ptg000033l	27686851	0	27686851	+	chr21	45090682	24229362	45090681	40	27686851	255	id:f:1	kc:f:1.00259
ptg000115l	3037875	0	3037875	+	chr21	45090682	39989460	43027335	37	3037875	27	id:f:0.997911	kc:f:0.951376
ptg000147l	1146249	0	1146249	+	chr21	45090682	42183625	43329874	38	1146249	29	id:f:0.998634	kc:f:1.11024
ptg000047l	2315813	0	2315813	+	chr21	45090682	43904919	45090681	38	2315813	29	id:f:0.998634	kc:f:1.22872

I used these commands:

mashmap --perc_identity 95 --noSplit -r hs1.fa.gz -q hifiasm.bp.unified.fa --threads 32 -o test1.mashmap
gunzip hs1.fa.gz
mashmap --perc_identity 95 --noSplit -r hs1.fa -q hifiasm.bp.unified.fa --threads 32 -o test.mashmap

Any ideas what could trigger such a behavior?

Thanks, Aaron