Cannot decompress

[yuansliu]

Hi Tomasz,

I clone the latest source code (access data Oct 10, 2019).

Run the following cmd: ./PgRC -i test.fastq test.pgrc

All output as following:

Filtered 704 (including 704 containing N) reads (out of 500000) in 750 msec. HQ reads count: 499296 Found 1386 duplicates. Overlapping done in 4620 msec Found 13424 both-side overlapped reads in 4630 msec HQ reads count: 13424 Found 1386 duplicates. Overlapping done in 40 msec LQ reads count: 485872 N reads count: 704 Target pseudogenome length: 337996 readsAlignmentSeedLength (minCharsPerMismatch, matchingMode): 38 (6, c) Feeding pseudogenome sequence... copMEM PARAMETERS: l = 38; K = 28; HASH_SIZE = 16777216; k1 = 5; k2 = 2 Matched 30264 reads (456312 left; 15428 better-matches). False matches reported: 5953141. Feeding rc of pseudogenome sequence... copMEM PARAMETERS: l = 38; K = 28; HASH_SIZE = 16777216; k1 = 5; k2 = 2 Matched 33900 reads (452676 left; 22536 better-matches). False matches reported: 7414429. LQ reads count: 452031 Found 0 duplicates. Overlapping done in 5910 msec N reads count: 645 Found 0 duplicates. Overlapping done in 0 msec Source pseudogenome length: 337996 copMEM PARAMETERS: l = 50; K = 36; HASH_SIZE = 16777216; k1 = 5; k2 = 3 Destination pseudogenome length: 41350429 Final size of Pg: 41174938 (removed: 178332 (0.4%); 17773 chars in overlapped dest symbol) Destination pseudogenome length: 64745 Final size of Pg: 64440 (removed: 310 (0.4%); 0 chars in overlapped dest symbol) Final size of Pg: 172696 (removed: 167060 (49.4%); 61718 chars in overlapped dest symbol)

Created PgRC of size 10153394 bytes in 59.96 s.

Then, I try to decompress it using the following cmd: ./PgRC -i test.pgrc -d decresult

BUT, the output is:

Cannot read pseudogenome properties (decresult/good does not open).

[kowallus]

The correct command for decompression would be: ./PgRC -d test.pgrc Sorry, the usage description is confusing. Thanks for info I will make an update.

[yuansliu]

TKS