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caleblareau / mgatk

mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
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Missing .rds output files #99

Open Cesco16 opened 2 months ago

Cesco16 commented 2 months ago

Describe the bug

We run the following command for ATAC sample:

mgatk tenx -i cellranger/ATAC-SC05/possorted_bam.bam -n ATAC-SC05 -o ATAC_mgatk/ATAC-SC05 -c 32 -bt CB -b cellranger/ATAC-SC05/filtered_peak_bc_matrix/barcodes.tsv --keep-temp-files

The problem is that .rds files are missing. How to solve the issue?

totale 20K drwxr-xr-x 2 francesco.casadei20 domain^users 4,0K giu 19 14:34 fasta drwxr-xr-x 2 francesco.casadei20 domain^users 4,0K giu 19 14:40 final drwxr-xr-x 4 francesco.casadei20 domain^users 4,0K giu 19 14:37 logs drwxr-xr-x 4 francesco.casadei20 domain^users 4,0K giu 19 14:37 qc drwxr-xr-x 8 francesco.casadei20 domain^users 4,0K giu 19 14:37 temp

./fasta: totale 24K -rw-r--r-- 1 francesco.casadei20 domain^users 17K giu 19 14:34 chrM.fasta -rw-r--r-- 1 francesco.casadei20 domain^users 19 giu 19 14:34 chrM.fasta.fai

./final: totale 169M -rw-r--r-- 1 francesco.casadei20 domain^users 29M giu 19 14:39 ATAC-SC05.A.txt.gz -rw-r--r-- 1 francesco.casadei20 domain^users 13K giu 19 14:40 ATAC-SC05.cell_heteroplasmic_df.tsv.gz -rw-r--r-- 1 francesco.casadei20 domain^users 74M giu 19 14:39 ATAC-SC05.coverage.txt.gz -rw-r--r-- 1 francesco.casadei20 domain^users 29M giu 19 14:39 ATAC-SC05.C.txt.gz -rw-r--r-- 1 francesco.casadei20 domain^users 48K giu 19 14:38 ATAC-SC05.depthTable.txt -rw-r--r-- 1 francesco.casadei20 domain^users 14M giu 19 14:39 ATAC-SC05.G.txt.gz -rw-r--r-- 1 francesco.casadei20 domain^users 24M giu 19 14:39 ATAC-SC05.T.txt.gz -rw-r--r-- 1 francesco.casadei20 domain^users 1,0M giu 19 14:40 ATAC-SC05.variant_stats.tsv.gz -rw-r--r-- 1 francesco.casadei20 domain^users 27K giu 19 14:40 ATAC-SC05.vmr_strand_plot.png -rw-r--r-- 1 francesco.casadei20 domain^users 119K giu 19 14:34 chrM_refAllele.txt

./logs: totale 16K -rw-r--r-- 1 francesco.casadei20 domain^users 539 giu 19 14:37 ATAC-SC05.parameters.txt -rw-r--r-- 1 francesco.casadei20 domain^users 0 giu 19 14:37 ATAC-SC05.snakemake_tenx.log -rw-r--r-- 1 francesco.casadei20 domain^users 379 giu 19 14:37 base.mgatk.log drwxr-xr-x 2 francesco.casadei20 domain^users 4,0K giu 19 14:37 filterlogs drwxr-xr-x 2 francesco.casadei20 domain^users 4,0K giu 19 14:38 rmdupslogs

Describe the sequencing assay being analyzed

It is a mtscATAC-seq sample. If I run "samtools idxstats possorted_bam.bam" I get:

chr1 248956422 15169030 120518 chr10 133797422 6109312 51427 chr11 135086622 6573119 55059 chr12 133275309 6065148 50724 chr13 114364328 3422146 27614 chr14 107043718 3812776 32500 chr15 101991189 4290596 35377 chr16 90338345 4042610 35407 chr17 83257441 5008634 44966 chr18 80373285 2677759 22073 chr19 58617616 3850496 35527 chr2 242193529 10381404 109487 chr20 64444167 2979968 25482 chr21 46709983 3052626 23087 chr22 50818468 2141629 19279 chr3 198295559 8364029 68875 chr4 190214555 6094151 49191 chr5 181538259 7554870 70809 chr6 170805979 7187941 58871 chr7 159345973 6247819 52414 chr8 145138636 5718600 46950 chr9 138394717 4888133 40679 chrM 16569 24045264 245084 chrX 156040895 2583619 22925 chrY 57227415 378639 3580 KI270728.1 1872759 12697 203 KI270727.1 448248 1995 9 KI270442.1 392061 15617 171 KI270729.1 280839 15814 159 GL000225.1 211173 49745 827 KI270743.1 210658 4772 39 GL000008.2 209709 5652 62 GL000009.2 201709 4557 56 KI270747.1 198735 2673 18 KI270722.1 194050 2991 26 GL000194.1 191469 7537 87 KI270742.1 186739 6654 36 GL000205.2 185591 50572 396 GL000195.1 182896 34878 278 KI270736.1 181920 11226 93 KI270733.1 179772 306428 1584 GL000224.1 179693 8140 91 GL000219.1 179198 8063 84 KI270719.1 176845 1999 23 GL000216.2 176608 26519 250 KI270712.1 176043 2236 45 KI270706.1 175055 3005 22 KI270725.1 172810 2344 20 KI270744.1 168472 10500 60 KI270734.1 165050 4029 73 GL000213.1 164239 581 23 GL000220.1 161802 264612 9070 KI270715.1 161471 2262 17 GL000218.1 161147 9810 58 KI270749.1 158759 2101 16 KI270741.1 157432 1235 16 GL000221.1 155397 4412 40 KI270716.1 153799 2302 42 KI270731.1 150754 1641 23 KI270751.1 150742 4176 23 KI270750.1 148850 1620 19 KI270519.1 138126 2733 25 GL000214.1 137718 9779 47 KI270708.1 127682 1341 8 KI270730.1 112551 4410 45 KI270438.1 112505 50176 343 KI270737.1 103838 2293 36 KI270721.1 100316 1268 13 KI270738.1 99375 1290 15 KI270748.1 93321 1211 16 KI270435.1 92983 1850 15 GL000208.1 92689 1092 3 KI270538.1 91309 2417 10 KI270756.1 79590 2171 25 KI270739.1 73985 519 3 KI270757.1 71251 1735 17 KI270709.1 66860 10435 70 KI270746.1 66486 1226 15 KI270753.1 62944 577 9 KI270589.1 44474 1067 3 KI270726.1 43739 160 0 KI270735.1 42811 2013 22 KI270711.1 42210 1517 4 KI270745.1 41891 2152 8 KI270714.1 41717 1474 21 KI270732.1 41543 1405 12 KI270713.1 40745 7040 124 KI270754.1 40191 592 8 KI270710.1 40176 334 6 KI270717.1 40062 2863 17 KI270724.1 39555 932 19 KI270720.1 39050 668 10 KI270723.1 38115 1678 14 KI270718.1 38054 543 10 KI270317.1 37690 29 1 KI270740.1 37240 467 6 KI270755.1 36723 273 3 KI270707.1 32032 943 5 KI270579.1 31033 237 2 KI270752.1 27745 1500 82 KI270512.1 22689 459 5 KI270322.1 21476 119 1 GL000226.1 15008 656 0 KI270311.1 12399 152 0 KI270366.1 8320 69 1 KI270511.1 8127 98 0 KI270448.1 7992 131 0 KI270521.1 7642 94 0 KI270581.1 7046 89 2 KI270582.1 6504 52 0 KI270515.1 6361 312 2 KI270588.1 6158 153 1 KI270591.1 5796 408 1 KI270522.1 5674 34 0 KI270507.1 5353 190 0 KI270590.1 4685 346 2 KI270584.1 4513 197 0 KI270320.1 4416 195 3 KI270382.1 4215 14 0 KI270468.1 4055 85 2 KI270467.1 3920 2758 8 KI270362.1 3530 14 0 KI270517.1 3253 161 0 KI270593.1 3041 63 1 KI270528.1 2983 72 0 KI270587.1 2969 20 0 KI270364.1 2855 10 0 KI270371.1 2805 34 0 KI270333.1 2699 683 9 KI270374.1 2656 2 0 KI270411.1 2646 73 1 KI270414.1 2489 64 0 KI270510.1 2415 80 1 KI270390.1 2387 14 0 KI270375.1 2378 25 1 KI270420.1 2321 20 0 KI270509.1 2318 80 1 KI270315.1 2276 56 0 KI270302.1 2274 50 0 KI270518.1 2186 67 0 KI270530.1 2168 0 0 KI270304.1 2165 36 0 KI270418.1 2145 24 0 KI270424.1 2140 18 0 KI270417.1 2043 0 0 KI270508.1 1951 108 1 KI270303.1 1942 60 0 KI270381.1 1930 3 1 KI270529.1 1899 24 0 KI270425.1 1884 20 0 KI270396.1 1880 56 0 KI270363.1 1803 20 0 KI270386.1 1788 14 0 KI270465.1 1774 72 0 KI270383.1 1750 8 0 KI270384.1 1658 8 0 KI270330.1 1652 328 2 KI270372.1 1650 2 0 KI270548.1 1599 38 0 KI270580.1 1553 78 0 KI270387.1 1537 38 24 KI270391.1 1484 8 0 KI270305.1 1472 38 0 KI270373.1 1451 12 0 KI270422.1 1445 46 0 KI270316.1 1444 15 1 KI270340.1 1428 10 0 KI270338.1 1428 0 0 KI270583.1 1400 36 1 KI270334.1 1368 14 0 KI270429.1 1361 21 0 KI270393.1 1308 33 1 KI270516.1 1300 12 0 KI270389.1 1298 32 0 KI270466.1 1233 636 6 KI270388.1 1216 4 0 KI270544.1 1202 22 0 KI270310.1 1201 86 0 KI270412.1 1179 22 0 KI270395.1 1143 42 0 KI270376.1 1136 0 0 KI270337.1 1121 477 4 KI270335.1 1048 14 0 KI270378.1 1048 0 0 KI270379.1 1045 2 0 KI270329.1 1040 22 0 KI270419.1 1029 0 0 KI270336.1 1026 200 2 KI270312.1 998 8 0 KI270539.1 993 0 0 KI270385.1 990 10 0 KI270423.1 981 14 0 KI270392.1 971 2 0 KI270394.1 970 18 0

caleblareau commented 2 months ago

Everything else is there, so its an issue with the R installation.

Can you verify your R executable version has these packages:

Cesco16 commented 2 months ago

Hi,

yes it seems something like that. However, we solved the issue by running the to_rds.R script separately on the previous output files. We got the .rds files. Thank you for the support!