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Kingsford-Group / squid

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
BSD 3-Clause "New" or "Revised" License
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Segmentation fault: 11 #4

Open ghost opened 6 years ago

ghost commented 6 years ago

Trying to run squid with star-fusion output but it terminates with segmentation fault: 11

Any suggestions on how to fix this issue?

Congm12 commented 6 years ago

Can you provide the full output of squid and your input file size? Is it run on the latest version 1.1?

ghost commented 6 years ago

squid -b ATRT13Aligned.sortedByCoord.out.bam -c ATRT13Chimeric.out.sam.bam -o ATRT13 Reference name GL000191.1 --> 50 Reference name GL000192.1 --> 25 Reference name GL000193.1 --> 28 Reference name GL000194.1 --> 27 Reference name GL000195.1 --> 32 Reference name GL000196.1 --> 69 Reference name GL000197.1 --> 73 Reference name GL000198.1 --> 52 Reference name GL000199.1 --> 40 Reference name GL000200.1 --> 29 Reference name GL000201.1 --> 76 Reference name GL000202.1 --> 65 Reference name GL000203.1 --> 72 Reference name GL000204.1 --> 53 Reference name GL000205.1 --> 36 Reference name GL000206.1 --> 62 Reference name GL000207.1 --> 83 Reference name GL000208.1 --> 51 Reference name GL000209.1 --> 45 Reference name GL000210.1 --> 79 Reference name GL000211.1 --> 41 Reference name GL000212.1 --> 31 Reference name GL000213.1 --> 42 Reference name GL000214.1 --> 47 Reference name GL000215.1 --> 37 Reference name GL000216.1 --> 38 Reference name GL000217.1 --> 39 Reference name GL000218.1 --> 44 Reference name GL000219.1 --> 35 Reference name GL000220.1 --> 43 Reference name GL000221.1 --> 46 Reference name GL000222.1 --> 30 Reference name GL000223.1 --> 33 Reference name GL000224.1 --> 34 Reference name GL000225.1 --> 26 Reference name GL000226.1 --> 82 Reference name GL000227.1 --> 49 Reference name GL000228.1 --> 48 Reference name GL000229.1 --> 81 Reference name GL000230.1 --> 56 Reference name GL000231.1 --> 80 Reference name GL000232.1 --> 63 Reference name GL000233.1 --> 54 Reference name GL000234.1 --> 64 Reference name GL000235.1 --> 77 Reference name GL000236.1 --> 60 Reference name GL000237.1 --> 55 Reference name GL000238.1 --> 66 Reference name GL000239.1 --> 78 Reference name GL000240.1 --> 61 Reference name GL000241.1 --> 59 Reference name GL000242.1 --> 57 Reference name GL000243.1 --> 58 Reference name GL000244.1 --> 67 Reference name GL000245.1 --> 74 Reference name GL000246.1 --> 71 Reference name GL000247.1 --> 75 Reference name GL000248.1 --> 68 Reference name GL000249.1 --> 70 Reference name chr1 --> 0 Reference name chr10 --> 1 Reference name chr11 --> 2 Reference name chr12 --> 3 Reference name chr13 --> 4 Reference name chr14 --> 5 Reference name chr15 --> 6 Reference name chr16 --> 7 Reference name chr17 --> 8 Reference name chr18 --> 9 Reference name chr19 --> 10 Reference name chr2 --> 11 Reference name chr20 --> 12 Reference name chr21 --> 13 Reference name chr22 --> 14 Reference name chr3 --> 15 Reference name chr4 --> 16 Reference name chr5 --> 17 Reference name chr6 --> 18 Reference name chr7 --> 19 Reference name chr8 --> 20 Reference name chr9 --> 21 Reference name chrM --> 22 Reference name chrX --> 23 Reference name chrY --> 24 [Mon Oct 30 11:56:26 2017] Start reading bam file. [Mon Oct 30 11:56:42 2017] Finish sorting Chimeric bam reads. Segmentation fault: 11

-rw-r--r-- 1 chris staff 6.9G 28 Oct 17:38 ATRT13Aligned.sortedByCoord.out.bam -rw-r--r-- 1 chris staff 4.8G 28 Oct 17:42 ATRT13Aligned.toTranscriptome.out.bam -rw-r--r-- 1 chris staff 102M 28 Oct 17:38 ATRT13Chimeric.out.junction -rw-r--r-- 1 chris staff 583M 28 Oct 17:33 ATRT13Chimeric.out.sam -rw-r--r-- 1 chris staff 145M 29 Oct 19:05 ATRT13Chimeric.out.sam.bam -rw-r--r-- 1 chris staff 1.8K 28 Oct 17:33 ATRT13Log.final.out -rw-r--r-- 1 chris staff 26K 28 Oct 17:33 ATRT13Log.out -rw-r--r-- 1 chris staff 1.2K 28 Oct 17:33 ATRT13Log.progress.out -rw-r--r-- 1 chris staff 1.6M 28 Oct 17:42 ATRT13ReadsPerGene.out.tab -rw-r--r-- 1 chris staff 11M 28 Oct 17:38 ATRT13SJ.out.tab -rw-r--r-- 1 chris staff 1.3G 28 Oct 17:39 ATRT13Signal.Unique.str1.out.bg -rw-r--r-- 1 chris staff 1.5G 28 Oct 17:43 ATRT13Signal.Unique.str2.out.bg -rw-r--r-- 1 chris staff 1.4G 28 Oct 17:34 ATRT13Signal.UniqueMultiple.str1.out.bg -rw-r--r-- 1 chris staff 1.5G 28 Oct 17:39 ATRT13Signal.UniqueMultiple.str2.out.bg drwx--S--- 3 chris staff 102B 28 Oct 17:38 ATRT13_STARtmp

ghost commented 6 years ago

Yes, it is on squid v1.1

Congm12 commented 6 years ago

My current guess is that in your chimeric bam file, there are some reads with only first read or second read aligned. But could you run the following command to help me verify my guess? diff <(samtools view -f64 -F4 ATRT13Chimeric.out.sam.bam | cut -f1 | sort | uniq) <(samtools view -f128 -F4 ATRT13Chimeric.out.sam.bam | cut -f1 | sort | uniq)

ghost commented 6 years ago

I ran the command and the output is below

cl:ATRT13 chris$ diff <(samtools view -f64 -F4 ATRT13Chimeric.out.sam.bam | cut -f1 | sort | uniq) <(samtools view -f128 -F4 ATRT13Chimeric.out.sam.bam | cut -f1 | sort | uniq) 13471d13470 < HWI-ST521:352:C72EDACXX:2:1102:20290:56048 24872d24870 < HWI-ST521:352:C72EDACXX:2:1103:7172:73079 25903d25900 < HWI-ST521:352:C72EDACXX:2:1103:9361:75521 71897a71895

HWI-ST521:352:C72EDACXX:2:1108:8207:98070 90492d90489 < HWI-ST521:352:C72EDACXX:2:1110:6727:17293 94616d94612 < HWI-ST521:352:C72EDACXX:2:1111:14563:72914 96809d96804 < HWI-ST521:352:C72EDACXX:2:1111:18676:48923 132212d132206 < HWI-ST521:352:C72EDACXX:2:1115:11511:46219 133803d133796 < HWI-ST521:352:C72EDACXX:2:1115:14346:32938 147102d147094 < HWI-ST521:352:C72EDACXX:2:1116:21193:73334 147537d147528 < HWI-ST521:352:C72EDACXX:2:1116:3287:11200 151214d151204 < HWI-ST521:352:C72EDACXX:2:1201:10745:18959 164821d164810 < HWI-ST521:352:C72EDACXX:2:1202:2807:96430 195703d195691 < HWI-ST521:352:C72EDACXX:2:1206:11374:82439 226072d226059 < HWI-ST521:352:C72EDACXX:2:1209:14698:100187 250880d250866 < HWI-ST521:352:C72EDACXX:2:1211:5240:59689 269887d269872 < HWI-ST521:352:C72EDACXX:2:1213:2484:26203 291738d291722 < HWI-ST521:352:C72EDACXX:2:1215:4870:53717 303574d303557 < HWI-ST521:352:C72EDACXX:2:1216:8351:65761 332587d332569 < HWI-ST521:352:C72EDACXX:2:1304:11162:8896 342605d342586 < HWI-ST521:352:C72EDACXX:2:1305:12062:53845 342970d342950 < HWI-ST521:352:C72EDACXX:2:1305:12860:83529 343542d343521 < HWI-ST521:352:C72EDACXX:2:1305:13923:39446 354448d354426 < HWI-ST521:352:C72EDACXX:2:1306:16320:25789 356687d356664 < HWI-ST521:352:C72EDACXX:2:1306:20529:28064 357488d357464 < HWI-ST521:352:C72EDACXX:2:1306:2922:95857 397626d397601 < HWI-ST521:352:C72EDACXX:2:1310:3428:43031 446639a446615 HWI-ST521:352:C72EDACXX:2:1315:17839:63325 457626d457601 < HWI-ST521:352:C72EDACXX:2:1316:18765:31926 498127d498101 < HWI-ST521:352:C72EDACXX:2:2104:5809:28840 499951a499926 HWI-ST521:352:C72EDACXX:2:2104:9672:51655 503136d503110 < HWI-ST521:352:C72EDACXX:2:2105:15756:11850 504355d504328 < HWI-ST521:352:C72EDACXX:2:2105:18095:20124 509853d509825 < HWI-ST521:352:C72EDACXX:2:2106:10372:69591 521655d521626 < HWI-ST521:352:C72EDACXX:2:2107:14150:55806 567537d567507 < HWI-ST521:352:C72EDACXX:2:2111:4943:41339 572666d572635 < HWI-ST521:352:C72EDACXX:2:2112:14350:57670 572710d572678 < HWI-ST521:352:C72EDACXX:2:2112:14407:75165 582269d582236 < HWI-ST521:352:C72EDACXX:2:2113:12861:25842 585217d585183 < HWI-ST521:352:C72EDACXX:2:2113:17944:11893 630061d630026 < HWI-ST521:352:C72EDACXX:2:2201:7719:61070 637246d637210 < HWI-ST521:352:C72EDACXX:2:2202:4144:32646 645572d645535 < HWI-ST521:352:C72EDACXX:2:2203:21355:32196 673858d673820 < HWI-ST521:352:C72EDACXX:2:2206:21352:88401 680817d680778 < HWI-ST521:352:C72EDACXX:2:2207:15860:25886 697304d697264 < HWI-ST521:352:C72EDACXX:2:2208:9759:39659 705612d705571 < HWI-ST521:352:C72EDACXX:2:2209:6350:9052 729339d729297 < HWI-ST521:352:C72EDACXX:2:2212:1205:20330 734707d734664 < HWI-ST521:352:C72EDACXX:2:2212:21342:86076 735408a735366 HWI-ST521:352:C72EDACXX:2:2212:3577:78694 755983d755940 < HWI-ST521:352:C72EDACXX:2:2214:21341:10507 761355d761311 < HWI-ST521:352:C72EDACXX:2:2215:12628:78496 762479d762434 < HWI-ST521:352:C72EDACXX:2:2215:14476:54137 769277d769231 < HWI-ST521:352:C72EDACXX:2:2215:7692:56456 773973d773926 < HWI-ST521:352:C72EDACXX:2:2216:16139:25650 777451d777403 < HWI-ST521:352:C72EDACXX:2:2216:4178:21729 785258d785209 < HWI-ST521:352:C72EDACXX:2:2301:19905:77667 785685d785635 < HWI-ST521:352:C72EDACXX:2:2301:2280:8039 822230d822179 < HWI-ST521:352:C72EDACXX:2:2305:3375:17541 828174a828124 HWI-ST521:352:C72EDACXX:2:2306:1502:67066 830846d830795 < HWI-ST521:352:C72EDACXX:2:2306:1990:78599 836703a836653 HWI-ST521:352:C72EDACXX:2:2307:13048:82682 847798a847749 HWI-ST521:352:C72EDACXX:2:2308:15295:72389 855766d855716 < HWI-ST521:352:C72EDACXX:2:2309:11722:19172 885874d885823 < HWI-ST521:352:C72EDACXX:2:2312:10314:35449 887761d887709 < HWI-ST521:352:C72EDACXX:2:2312:13676:52128 894296d894243 < HWI-ST521:352:C72EDACXX:2:2312:6728:33450 908408d908354 < HWI-ST521:352:C72EDACXX:2:2314:13318:33915 912552d912497 < HWI-ST521:352:C72EDACXX:2:2314:2064:68807 924800d924744 < HWI-ST521:352:C72EDACXX:2:2315:5180:96425 930373d930316 < HWI-ST521:352:C72EDACXX:2:2316:15236:75465 cl:ATRT13 chris$

Congm12 commented 6 years ago

Thanks for confirming my guess and for reporting this bug. I will update a new release today or tomorrow.

rdocking commented 6 years ago

Hi there - I'm seeing a similar issue using the Squid 1.4 linux binary downloaded from here.

I ran:

> diff <(samtools view -f64 -F4 A93119Chimeric.out.bam | cut -f1 | sort | uniq) <(samtools view -f128 -F4 A93119Chimeric.out.bam | cut -f1 | sort | uniq)

... and saw no output.

Congm12 commented 6 years ago

Could you provide the detailed output of SQUID?