stability.contigs.groups empty

make.contigs seems to run OK and lists the groups with the numbers of sequences in each at the end, but stability.contigs.groups is empty.

I would be most grateful for any advice.

Can you post the command you are running and the contents of the files file?

Pat

Thanks.

Command was:

make.contigs(file=stability.files, processors=8)

Contents of stability.files:
03_01_0324 03_01_0324_S16_L001_R1_001.fastq.gz 03_01_0324_S16_L001_R2_001.fastq.gz
03_01_0325 03_01_0325_S2_L001_R1_001.fastq.gz 03_01_0325_S2_L001_R2_001.fastq.gz
03_01_0326 03_01_0326_S12_L001_R1_001.fastq.gz 03_01_0326_S12_L001_R2_001.fastq.gz
03_01_0327 03_01_0327_S3_L001_R1_001.fastq.gz 03_01_0327_S3_L001_R2_001.fastq.gz
03_01_0329 03_01_0329_S10_L001_R1_001.fastq.gz 03_01_0329_S10_L001_R2_001.fastq.gz
03_01_0331 03_01_0331_S9_L001_R1_001.fastq.gz 03_01_0331_S9_L001_R2_001.fastq.gz
03_01_0333 03_01_0333_S6_L001_R1_001.fastq.gz 03_01_0333_S6_L001_R2_001.fastq.gz
03_01_0338 03_01_0338_S13_L001_R1_001.fastq.gz 03_01_0338_S13_L001_R2_001.fastq.gz
03_01_0341 03_01_0341_S17_L001_R1_001.fastq.gz 03_01_0341_S17_L001_R2_001.fastq.gz
03_01_0342 03_01_0342_S19_L001_R1_001.fastq.gz 03_01_0342_S19_L001_R2_001.fastq.gz
03_01_0343 03_01_0343_S14_L001_R1_001.fastq.gz 03_01_0343_S14_L001_R2_001.fastq.gz
03_01_0344 03_01_0344_S5_L001_R1_001.fastq.gz 03_01_0344_S5_L001_R2_001.fastq.gz
03_01_0345 03_01_0345_S15_L001_R1_001.fastq.gz 03_01_0345_S15_L001_R2_001.fastq.gz
03_01_0346 03_01_0346_S8_L001_R1_001.fastq.gz 03_01_0346_S8_L001_R2_001.fastq.gz
03_01_0492 03_01_0492_S7_L001_R1_001.fastq.gz 03_01_0492_S7_L001_R2_001.fastq.gz
03_01_0494 03_01_0494_S4_L001_R1_001.fastq.gz 03_01_0494_S4_L001_R2_001.fastq.gz
03_01_0496 03_01_0496_S18_L001_R1_001.fastq.gz 03_01_0496_S18_L001_R2_001.fastq.gz
03_08_0137 03_08_0137_S143_L001_R1_001.fastq.gz 03_08_0137_S143_L001_R2_001.fastq.gz
03_08_0138 03_08_0138_S142_L001_R1_001.fastq.gz 03_08_0138_S142_L001_R2_001.fastq.gz
03_08_0139 03_08_0139_S147_L001_R1_001.fastq.gz 03_08_0139_S147_L001_R2_001.fastq.gz
03_08_0140 03_08_0140_S141_L001_R1_001.fastq.gz 03_08_0140_S141_L001_R2_001.fastq.gz
03_08_0141 03_08_0141_S148_L001_R1_001.fastq.gz 03_08_0141_S148_L001_R2_001.fastq.gz
03_08_0144 03_08_0144_S146_L001_R1_001.fastq.gz 03_08_0144_S146_L001_R2_001.fastq.gz
03_08_0518 03_08_0518_S145_L001_R1_001.fastq.gz 03_08_0518_S145_L001_R2_001.fastq.gz
03_08_0519 03_08_0519_S144_L001_R1_001.fastq.gz 03_08_0519_S144_L001_R2_001.fastq.gz
03_12_0079 03_12_0079_S165_L001_R1_001.fastq.gz 03_12_0079_S165_L001_R2_001.fastq.gz
03_12_0081 03_12_0081_S169_L001_R1_001.fastq.gz 03_12_0081_S169_L001_R2_001.fastq.gz
03_12_0083 03_12_0083_S168_L001_R1_001.fastq.gz 03_12_0083_S168_L001_R2_001.fastq.gz
03_12_0084 03_12_0084_S164_L001_R1_001.fastq.gz 03_12_0084_S164_L001_R2_001.fastq.gz
03_12_0088 03_12_0088_S150_L001_R1_001.fastq.gz 03_12_0088_S150_L001_R2_001.fastq.gz
03_12_0461 03_12_0461_S166_L001_R1_001.fastq.gz 03_12_0461_S166_L001_R2_001.fastq.gz
03_12_0462 03_12_0462_S151_L001_R1_001.fastq.gz 03_12_0462_S151_L001_R2_001.fastq.gz
03_12_0464 03_12_0464_S167_L001_R1_001.fastq.gz 03_12_0464_S167_L001_R2_001.fastq.gz
03_12_0465 03_12_0465_S162_L001_R1_001.fastq.gz 03_12_0465_S162_L001_R2_001.fastq.gz
03_12_0467 03_12_0467_S163_L001_R1_001.fastq.gz 03_12_0467_S163_L001_R2_001.fastq.gz
03_16_0201 03_16_0201_S115_L001_R1_001.fastq.gz 03_16_0201_S115_L001_R2_001.fastq.gz
03_16_0202 03_16_0202_S114_L001_R1_001.fastq.gz 03_16_0202_S114_L001_R2_001.fastq.gz
03_16_0203 03_16_0203_S116_L001_R1_001.fastq.gz 03_16_0203_S116_L001_R2_001.fastq.gz
03_16_0206 03_16_0206_S113_L001_R1_001.fastq.gz 03_16_0206_S113_L001_R2_001.fastq.gz
03_16_0437 03_16_0437_S112_L001_R1_001.fastq.gz 03_16_0437_S112_L001_R2_001.fastq.gz
03_16_0438 03_16_0438_S119_L001_R1_001.fastq.gz 03_16_0438_S119_L001_R2_001.fastq.gz
03_16_0440 03_16_0440_S118_L001_R1_001.fastq.gz 03_16_0440_S118_L001_R2_001.fastq.gz
03_16_0442 03_16_0442_S117_L001_R1_001.fastq.gz 03_16_0442_S117_L001_R2_001.fastq.gz
03_16_0443 03_16_0443_S120_L001_R1_001.fastq.gz 03_16_0443_S120_L001_R2_001.fastq.gz
03_17_0207 03_17_0207_S126_L001_R1_001.fastq.gz 03_17_0207_S126_L001_R2_001.fastq.gz
03_17_0208 03_17_0208_S152_L001_R1_001.fastq.gz 03_17_0208_S152_L001_R2_001.fastq.gz
03_17_0209 03_17_0209_S122_L001_R1_001.fastq.gz 03_17_0209_S122_L001_R2_001.fastq.gz
03_17_0211 03_17_0211_S123_L001_R1_001.fastq.gz 03_17_0211_S123_L001_R2_001.fastq.gz
03_17_0212 03_17_0212_S125_L001_R1_001.fastq.gz 03_17_0212_S125_L001_R2_001.fastq.gz
03_17_0220 03_17_0220_S124_L001_R1_001.fastq.gz 03_17_0220_S124_L001_R2_001.fastq.gz
03_17_0222 03_17_0222_S154_L001_R1_001.fastq.gz 03_17_0222_S154_L001_R2_001.fastq.gz
03_17_0223 03_17_0223_S153_L001_R1_001.fastq.gz 03_17_0223_S153_L001_R2_001.fastq.gz
03_17_0229 03_17_0229_S106_L001_R1_001.fastq.gz 03_17_0229_S106_L001_R2_001.fastq.gz
03_17_0230 03_17_0230_S121_L001_R1_001.fastq.gz 03_17_0230_S121_L001_R2_001.fastq.gz
03_17_0231 03_17_0231_S131_L001_R1_001.fastq.gz 03_17_0231_S131_L001_R2_001.fastq.gz
03_17_0232 03_17_0232_S130_L001_R1_001.fastq.gz 03_17_0232_S130_L001_R2_001.fastq.gz
03_17_0280 03_17_0280_S159_L001_R1_001.fastq.gz 03_17_0280_S159_L001_R2_001.fastq.gz
03_17_0282 03_17_0282_S155_L001_R1_001.fastq.gz 03_17_0282_S155_L001_R2_001.fastq.gz
03_17_0283 03_17_0283_S156_L001_R1_001.fastq.gz 03_17_0283_S156_L001_R2_001.fastq.gz
03_17_0284 03_17_0284_S158_L001_R1_001.fastq.gz 03_17_0284_S158_L001_R2_001.fastq.gz
03_17_0304 03_17_0304_S160_L001_R1_001.fastq.gz 03_17_0304_S160_L001_R2_001.fastq.gz
03_17_0307 03_17_0307_S161_L001_R1_001.fastq.gz 03_17_0307_S161_L001_R2_001.fastq.gz
03_17_0362 03_17_0362_S157_L001_R1_001.fastq.gz 03_17_0362_S157_L001_R2_001.fastq.gz
03_17_0364 03_17_0364_S133_L001_R1_001.fastq.gz 03_17_0364_S133_L001_R2_001.fastq.gz
03_17_0370 03_17_0370_S134_L001_R1_001.fastq.gz 03_17_0370_S134_L001_R2_001.fastq.gz
03_17_0456 03_17_0456_S132_L001_R1_001.fastq.gz 03_17_0456_S132_L001_R2_001.fastq.gz
03_21_0297 03_21_0297_S111_L001_R1_001.fastq.gz 03_21_0297_S111_L001_R2_001.fastq.gz
03_21_0300 03_21_0300_S127_L001_R1_001.fastq.gz 03_21_0300_S127_L001_R2_001.fastq.gz
03_21_0302 03_21_0302_S129_L001_R1_001.fastq.gz 03_21_0302_S129_L001_R2_001.fastq.gz
03_21_0539 03_21_0539_S128_L001_R1_001.fastq.gz 03_21_0539_S128_L001_R2_001.fastq.gz
04_25_0319 04_25_0319_S139_L001_R1_001.fastq.gz 04_25_0319_S139_L001_R2_001.fastq.gz
04_25_0320 04_25_0320_S137_L001_R1_001.fastq.gz 04_25_0320_S137_L001_R2_001.fastq.gz
04_25_0321 04_25_0321_S149_L001_R1_001.fastq.gz 04_25_0321_S149_L001_R2_001.fastq.gz
04_25_0322 04_25_0322_S138_L001_R1_001.fastq.gz 04_25_0322_S138_L001_R2_001.fastq.gz
04_25_0363 04_25_0363_S140_L001_R1_001.fastq.gz 04_25_0363_S140_L001_R2_001.fastq.gz
04_27_0317 04_27_0317_S135_L001_R1_001.fastq.gz 04_27_0317_S135_L001_R2_001.fastq.gz
04_27_0477 04_27_0477_S136_L001_R1_001.fastq.gz 04_27_0477_S136_L001_R2_001.fastq.gz
0521_7 0521_7_S108_L001_R1_001.fastq.gz 0521_7_S108_L001_R2_001.fastq.gz
102 102_S193_L001_R1_001.fastq.gz 102_S193_L001_R2_001.fastq.gz
103 103_S199_L001_R1_001.fastq.gz 103_S199_L001_R2_001.fastq.gz
104 104_S190_L001_R1_001.fastq.gz 104_S190_L001_R2_001.fastq.gz
107 107_S200_L001_R1_001.fastq.gz 107_S200_L001_R2_001.fastq.gz
113 113_S175_L001_R1_001.fastq.gz 113_S175_L001_R2_001.fastq.gz
114 114_S177_L001_R1_001.fastq.gz 114_S177_L001_R2_001.fastq.gz
117 117_S174_L001_R1_001.fastq.gz 117_S174_L001_R2_001.fastq.gz
118 118_S176_L001_R1_001.fastq.gz 118_S176_L001_R2_001.fastq.gz
12 12_S25_L001_R1_001.fastq.gz 12_S25_L001_R2_001.fastq.gz
122 122_S178_L001_R1_001.fastq.gz 122_S178_L001_R2_001.fastq.gz
124 124_S173_L001_R1_001.fastq.gz 124_S173_L001_R2_001.fastq.gz
128 128_S44_L001_R1_001.fastq.gz 128_S44_L001_R2_001.fastq.gz
129 129_S41_L001_R1_001.fastq.gz 129_S41_L001_R2_001.fastq.gz
132 132_S43_L001_R1_001.fastq.gz 132_S43_L001_R2_001.fastq.gz
133 133_S42_L001_R1_001.fastq.gz 133_S42_L001_R2_001.fastq.gz
134 134_S45_L001_R1_001.fastq.gz 134_S45_L001_R2_001.fastq.gz
145 145_S77_L001_R1_001.fastq.gz 145_S77_L001_R2_001.fastq.gz
147 147_S78_L001_R1_001.fastq.gz 147_S78_L001_R2_001.fastq.gz
148 148_S69_L001_R1_001.fastq.gz 148_S69_L001_R2_001.fastq.gz
150 150_S75_L001_R1_001.fastq.gz 150_S75_L001_R2_001.fastq.gz
152 152_S74_L001_R1_001.fastq.gz 152_S74_L001_R2_001.fastq.gz
153 153_S73_L001_R1_001.fastq.gz 153_S73_L001_R2_001.fastq.gz
156 156_S70_L001_R1_001.fastq.gz 156_S70_L001_R2_001.fastq.gz
158 158_S72_L001_R1_001.fastq.gz 158_S72_L001_R2_001.fastq.gz
16 16_S57_L001_R1_001.fastq.gz 16_S57_L001_R2_001.fastq.gz
161 161_S79_L001_R1_001.fastq.gz 161_S79_L001_R2_001.fastq.gz
162 162_S76_L001_R1_001.fastq.gz 162_S76_L001_R2_001.fastq.gz
165 165_S60_L001_R1_001.fastq.gz 165_S60_L001_R2_001.fastq.gz
166 166_S71_L001_R1_001.fastq.gz 166_S71_L001_R2_001.fastq.gz
169 169_S195_L001_R1_001.fastq.gz 169_S195_L001_R2_001.fastq.gz
17 17_S58_L001_R1_001.fastq.gz 17_S58_L001_R2_001.fastq.gz
172 172_S188_L001_R1_001.fastq.gz 172_S188_L001_R2_001.fastq.gz
184 184_S179_L001_R1_001.fastq.gz 184_S179_L001_R2_001.fastq.gz
186 186_S182_L001_R1_001.fastq.gz 186_S182_L001_R2_001.fastq.gz
188 188_S197_L001_R1_001.fastq.gz 188_S197_L001_R2_001.fastq.gz
19 19_S96_L001_R1_001.fastq.gz 19_S96_L001_R2_001.fastq.gz
192 192_S181_L001_R1_001.fastq.gz 192_S181_L001_R2_001.fastq.gz
195 195_S198_L001_R1_001.fastq.gz 195_S198_L001_R2_001.fastq.gz
196 196_S183_L001_R1_001.fastq.gz 196_S183_L001_R2_001.fastq.gz
197 197_S184_L001_R1_001.fastq.gz 197_S184_L001_R2_001.fastq.gz
23 23_S102_L001_R1_001.fastq.gz 23_S102_L001_R2_001.fastq.gz
234 234_S109_L001_R1_001.fastq.gz 234_S109_L001_R2_001.fastq.gz
236 236_S51_L001_R1_001.fastq.gz 236_S51_L001_R2_001.fastq.gz
244 244_S204_L001_R1_001.fastq.gz 244_S204_L001_R2_001.fastq.gz
246 246_S203_L001_R1_001.fastq.gz 246_S203_L001_R2_001.fastq.gz
249 249_S205_L001_R1_001.fastq.gz 249_S205_L001_R2_001.fastq.gz
250 250_S207_L001_R1_001.fastq.gz 250_S207_L001_R2_001.fastq.gz
259 259_S94_L001_R1_001.fastq.gz 259_S94_L001_R2_001.fastq.gz
262 262_S63_L001_R1_001.fastq.gz 262_S63_L001_R2_001.fastq.gz
263 263_S64_L001_R1_001.fastq.gz 263_S64_L001_R2_001.fastq.gz
264 264_S65_L001_R1_001.fastq.gz 264_S65_L001_R2_001.fastq.gz
267 267_S62_L001_R1_001.fastq.gz 267_S62_L001_R2_001.fastq.gz
272 272_S56_L001_R1_001.fastq.gz 272_S56_L001_R2_001.fastq.gz
273 273_S52_L001_R1_001.fastq.gz 273_S52_L001_R2_001.fastq.gz
279 279_S53_L001_R1_001.fastq.gz 279_S53_L001_R2_001.fastq.gz
28 28_S101_L001_R1_001.fastq.gz 28_S101_L001_R2_001.fastq.gz
285 285_S28_L001_R1_001.fastq.gz 285_S28_L001_R2_001.fastq.gz
289 289_S27_L001_R1_001.fastq.gz 289_S27_L001_R2_001.fastq.gz
291 291_S29_L001_R1_001.fastq.gz 291_S29_L001_R2_001.fastq.gz
292 292_S30_L001_R1_001.fastq.gz 292_S30_L001_R2_001.fastq.gz
30 30_S99_L001_R1_001.fastq.gz 30_S99_L001_R2_001.fastq.gz
31 31_S103_L001_R1_001.fastq.gz 31_S103_L001_R2_001.fastq.gz
332 332_S1_L001_R1_001.fastq.gz 332_S1_L001_R2_001.fastq.gz
351 351_S61_L001_R1_001.fastq.gz 351_S61_L001_R2_001.fastq.gz
37 37_S170_L001_R1_001.fastq.gz 37_S170_L001_R2_001.fastq.gz
371 371_S59_L001_R1_001.fastq.gz 371_S59_L001_R2_001.fastq.gz
378 378_S90_L001_R1_001.fastq.gz 378_S90_L001_R2_001.fastq.gz
38 38_S171_L001_R1_001.fastq.gz 38_S171_L001_R2_001.fastq.gz
380 380_S194_L001_R1_001.fastq.gz 380_S194_L001_R2_001.fastq.gz
381 381_S186_L001_R1_001.fastq.gz 381_S186_L001_R2_001.fastq.gz
382 382_S196_L001_R1_001.fastq.gz 382_S196_L001_R2_001.fastq.gz
386 386_S185_L001_R1_001.fastq.gz 386_S185_L001_R2_001.fastq.gz
39 39_S172_L001_R1_001.fastq.gz 39_S172_L001_R2_001.fastq.gz
390 390_S180_L001_R1_001.fastq.gz 390_S180_L001_R2_001.fastq.gz
396 396_S208_L001_R1_001.fastq.gz 396_S208_L001_R2_001.fastq.gz
397 397_S93_L001_R1_001.fastq.gz 397_S93_L001_R2_001.fastq.gz
402 402_S54_L001_R1_001.fastq.gz 402_S54_L001_R2_001.fastq.gz
403 403_S55_L001_R1_001.fastq.gz 403_S55_L001_R2_001.fastq.gz
406 406_S187_L001_R1_001.fastq.gz 406_S187_L001_R2_001.fastq.gz
408 408_S97_L001_R1_001.fastq.gz 408_S97_L001_R2_001.fastq.gz
413 413_S98_L001_R1_001.fastq.gz 413_S98_L001_R2_001.fastq.gz
418 418_S110_L001_R1_001.fastq.gz 418_S110_L001_R2_001.fastq.gz
420 420_S206_L001_R1_001.fastq.gz 420_S206_L001_R2_001.fastq.gz
424 424_S23_L001_R1_001.fastq.gz 424_S23_L001_R2_001.fastq.gz
426 426_S24_L001_R1_001.fastq.gz 426_S24_L001_R2_001.fastq.gz
427 427_S20_L001_R1_001.fastq.gz 427_S20_L001_R2_001.fastq.gz
434 434_S21_L001_R1_001.fastq.gz 434_S21_L001_R2_001.fastq.gz
435 435_S104_L001_R1_001.fastq.gz 435_S104_L001_R2_001.fastq.gz
446 446_S201_L001_R1_001.fastq.gz 446_S201_L001_R2_001.fastq.gz
45 45_S49_L001_R1_001.fastq.gz 45_S49_L001_R2_001.fastq.gz
453 453_S192_L001_R1_001.fastq.gz 453_S192_L001_R2_001.fastq.gz
46 46_S40_L001_R1_001.fastq.gz 46_S40_L001_R2_001.fastq.gz
473 473_S46_L001_R1_001.fastq.gz 473_S46_L001_R2_001.fastq.gz
48 48_S50_L001_R1_001.fastq.gz 48_S50_L001_R2_001.fastq.gz
482 482_S105_L001_R1_001.fastq.gz 482_S105_L001_R2_001.fastq.gz
49 49_S36_L001_R1_001.fastq.gz 49_S36_L001_R2_001.fastq.gz
497 497_S11_L001_R1_001.fastq.gz 497_S11_L001_R2_001.fastq.gz
5 5_S22_L001_R1_001.fastq.gz 5_S22_L001_R2_001.fastq.gz
507 507_S39_L001_R1_001.fastq.gz 507_S39_L001_R2_001.fastq.gz
508 508_S35_L001_R1_001.fastq.gz 508_S35_L001_R2_001.fastq.gz
51 51_S37_L001_R1_001.fastq.gz 51_S37_L001_R2_001.fastq.gz
510 510_S33_L001_R1_001.fastq.gz 510_S33_L001_R2_001.fastq.gz
512 512_S32_L001_R1_001.fastq.gz 512_S32_L001_R2_001.fastq.gz
52 52_S47_L001_R1_001.fastq.gz 52_S47_L001_R2_001.fastq.gz
522 522_S68_L001_R1_001.fastq.gz 522_S68_L001_R2_001.fastq.gz
523 523_S66_L001_R1_001.fastq.gz 523_S66_L001_R2_001.fastq.gz
524 524_S67_L001_R1_001.fastq.gz 524_S67_L001_R2_001.fastq.gz
529 529_S107_L001_R1_001.fastq.gz 529_S107_L001_R2_001.fastq.gz
54 54_S48_L001_R1_001.fastq.gz 54_S48_L001_R2_001.fastq.gz
541 541_S100_L001_R1_001.fastq.gz 541_S100_L001_R2_001.fastq.gz
55 55_S34_L001_R1_001.fastq.gz 55_S34_L001_R2_001.fastq.gz
57 57_S31_L001_R1_001.fastq.gz 57_S31_L001_R2_001.fastq.gz
58 58_S38_L001_R1_001.fastq.gz 58_S38_L001_R2_001.fastq.gz
59 59_S85_L001_R1_001.fastq.gz 59_S85_L001_R2_001.fastq.gz
61 61_S89_L001_R1_001.fastq.gz 61_S89_L001_R2_001.fastq.gz
65 65_S87_L001_R1_001.fastq.gz 65_S87_L001_R2_001.fastq.gz
66 66_S86_L001_R1_001.fastq.gz 66_S86_L001_R2_001.fastq.gz
67 67_S88_L001_R1_001.fastq.gz 67_S88_L001_R2_001.fastq.gz
69 69_S92_L001_R1_001.fastq.gz 69_S92_L001_R2_001.fastq.gz
70 70_S84_L001_R1_001.fastq.gz 70_S84_L001_R2_001.fastq.gz
72 72_S91_L001_R1_001.fastq.gz 72_S91_L001_R2_001.fastq.gz
73 73_S81_L001_R1_001.fastq.gz 73_S81_L001_R2_001.fastq.gz
74 74_S80_L001_R1_001.fastq.gz 74_S80_L001_R2_001.fastq.gz
76 76_S82_L001_R1_001.fastq.gz 76_S82_L001_R2_001.fastq.gz
77 77_S83_L001_R1_001.fastq.gz 77_S83_L001_R2_001.fastq.gz
8 8_S26_L001_R1_001.fastq.gz 8_S26_L001_R2_001.fastq.gz
91 91_S202_L001_R1_001.fastq.gz 91_S202_L001_R2_001.fastq.gz
92 92_S189_L001_R1_001.fastq.gz 92_S189_L001_R2_001.fastq.gz
96 96_S191_L001_R1_001.fastq.gz 96_S191_L001_R2_001.fastq.gz
Mock Mock_S95_L001_R1_001.fastq.gz Mock_S95_L001_R2_001.fastq.gz

Thanks for reporting this bug. The 3 column file format using compressed files in the make.contigs command is producing a blank group file in version 1.36. This will be fixed in version 1.37 coming soon. As a workaround you can decompress your fastq files.

Thanks. Worked fine with decompressed files.

I just reproduced the bug and confirmed than decompressing solves the issue–thanks for working on a fix. Another (minor) issue is that file reporting in interactive mode is unordered (e.g. “files 44 of 369”, next file outputs “files 112 of 369”), making it difficult to monitor progress.