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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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psmc: cli.c:72: psmc_parse_pattern: Assertion `isdigit(*p) || *p == '*' || *p == '+' || *p == '\0'' failed. #40

Open kuangzhuoran opened 2 years ago

kuangzhuoran commented 2 years ago

Hi ! when i running PSMC , I met this error in step "psmc -N25 -t15 -r5 -p "4+252+4+6" -o diploid.psmc diploid.psmcfa seq 100 | xargs -i echo psmc -N25 -t15 -r5 -b -p "4+252+4+6" \ -o round-{}.psmc split.fa | sh"

Well, most of my average depth is very low(0.48~0.8)，The average depth of only two samples is 16 and 1.18 (Let me call them both B and C). And in step "fq2psmcfa -q20 1.fq.gz > 1.psmcfa", Only the output file size of B and C is not 0, So I use the output file of B/C in next step

In step :"psmc -N25 -t15 -r5 -p "4+252+4+6" -o diploid.psmc diploid.psmcfa seq 100 | xargs -i echo psmc -N25 -t15 -r5 -b -p "4+252+4+6" \ -o round-{}.psmc split.fa | sh"

I got an error as shown in the title， of course the output file size (round-{}.psmc) is 0.

Furthermore, The size of my reference genome is 3M（a bacteria ）, Metagenome sequencing data were used for mapping And the abundance of this bacteria is not high. If I use the most abundant bacteria，From the reads on the mapping, The lowest average depth is 3 to 4

kuangzhuoran commented 2 years ago

psmc: cli.c:72: psmc_parse_pattern: Assertion isdigit(*p) || *p == '*' || *p == '+' || *p == '\0'' failed. sh: line 17: 55228 Aborted (core dumped) /data/01/user164/software/psmc/psmc -N25 -t15 -r5 -b -p “4+25*2+4+6” -o 3.round-17.psmc C3.psmcfa.split psmc: cli.c:72: psmc_parse_pattern: Assertionisdigit(p) || p == '' || p == '+' || *p == '\0'' failed.