Error while running the Rscript of HAWK

[Asutu]

Hi,

while running runHAWK I'm finding the following error message:

Loading required package: iterators
Loading required package: parallel
      [,1]
 [1,]    1
 [2,]    1
 [3,]    1
 [4,]    1
 [5,]    1
 [6,]    1
 [7,]    1
 [8,]    1
 [9,]    1
[10,]    1
[11,]    0
[12,]    0
[13,]    0
[14,]    0
[15,]    0
[16,]    0
[17,]    0
[18,]    0
[19,]    0
[20,]    0
Error in read.table(con, nrow = CHUNK_SIZE) : no lines available in input
Execution halted

The origin of this error seems to be related with this line

Rscript $hawkDir/log_reg_case.R

And looking at log_reg_case.R the con variable is read from file case_out_w_bonf_top.kmerDiff, however this file seems to be OK with the expected number of lines:

$ wc -l case_out_w_bonf_top.kmerDiff
200000 case_out_w_bonf_top.kmerDiff
$ head case_out_w_bonf_top.kmerDiff
AAAAAAAAAAAAAATAATAAACATTCGAAAA	8244	3442	0.000000e+00	560	430	553	1224	1295	795	742	1006	762	877	206	814	308	200	231	127	306	147	202	168
AAAAAAAAAAAAATAATAAACATTCGAAAAA	8946	3615	0.000000e+00	610	470	619	1311	1397	870	803	1123	806	937	215	890	326	200	233	127	309	167	203	175
AAAAAAAAAAAATAATAAACATTCGAAAAAC	9153	3691	0.000000e+00	649	468	639	1319	1398	883	816	1148	818	1015	218	900	352	202	231	129	305	198	200	170
AAAAAAAAAAAGTCTGCCTTTTCTCTGGAGA	14081	5252	0.000000e+00	2894	1042	748	2000	1252	1179	1022	1232	999	1713	1473	976	919	164	160	55	217	58	70	42
AAAAAAAAAAATAATAAACATTCGAAAAACA	11324	4550	0.000000e+00	855	536	784	1553	1489	1071	944	1453	1111	1528	284	1111	455	257	270	154	352	277	219	202
AAAAAAAAAAATTTTTTTAATGATACGGCGA	25637	14508	0.000000e+00	3813	1093	1501	5835	2198	1966	1683	1328	3183	3037	3704	2160	3139	611	620	88	359	332	239	166
AAAAAAAAAATAATAAACATTCGAAAAACAA	11531	4580	0.000000e+00	884	565	808	1586	1489	1073	924	1505	1126	1571	277	1134	479	253	268	152	339	281	218	204
AAAAAAAAAATTAAAGCTCCGCGGAGCATCG	4874	1644	0.000000e+00	206	277	486	465	660	502	184	659	731	704	229	559	117	124	36	51	83	27	14	54
AAAAAAAAAATTTTTTTAATGATACGGCGAC	41213	22332	0.000000e+00	6029	1621	2347	9495	3585	3250	2457	1962	5330	5137	5413	3433	4948	932	963	140	564	526	383	273
AAAAAAAAAATTTTTTTCAAGCAGAAGACGG	13056	6739	0.000000e+00	2036	556	780	2873	1111	1059	755	575	1732	1579	1713	1071	1654	211	252	24	115	108	75	81

Any ideas/workarounds about this issue?

Many thanks,
Pedro

Edit:

I think this is the same as #6, which suggests that is actually OK to continue as long as files pvals_*_top.txt have the same number of lines as the respective *_out_w_bonf_top.kmerDiff.

[atifrahman]

Yes, if they have the same number of lines, it should be fine.