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feather output incomplete #9

Closed qizhijie closed 5 years ago

qizhijie commented 5 years ago

Hi there,

I tried to run the entire MAPS pipeline on one of the PLAC-seq data but encountered the following error: FileNotFoundError: File b'/home/qizhijie/Data/iMARGI_project/enhancer_promoter/MAPS_output/H1_H3K4me3/feather_output/H1_H3K4me3_current/H1_H3K4me3.chr1.shrt.vip.bed' does not exist

I checked the H1_H3K4me4_current directory and found all the *.paired files. But all the *.chr* files are missing. Do you have any idea what was going wrong here? Thanks, I appreciate it.

Zhijie

armenabnousi commented 5 years ago

Hi Zhijie,

In the feather_output directory there should be a *feather.log file, could you provide the content of that file? Thanks!

qizhijie commented 5 years ago

The content is as followed:

Tue May 28 21:18:43 2019 starting mapping and filtering operation Tue May 28 21:18:43 2019 calling bwa for /home/qizhijie/Data/iMARGI_project/iMARGI_data/Hiseq/PLACSeq_fastq_merged/H1_H3K4me3_R1.fastq Tue May 28 23:54:08 2019 calling bwa for /home/qizhijie/Data/iMARGI_project/iMARGI_data/Hiseq/PLACSeq_fastq_merged/H1_H3K4me3_R2.fastq Wed May 29 03:01:40 2019 calling samtools sort for /home/qizhijie/Data/iMARGI_project/enhancer_promoter/MAPS_output/H1_H3K4me3/feather_output/H1_H3K4me3_20190528_211840/tempfiles/H1_H3K4me3_R1.fastq.bwa.sam storing in /home/qizhijie/Data/iMARGI_project/enhancer_promoter/MAPS_output/H1_H3K4me3/feather_output/H1_H3K4me3_20190528_211840/tempfiles/H1_H3K4me3_R1.fastq.bwa.sam.srtn Wed May 29 03:43:16 2019 calling samtools sort for /home/qizhijie/Data/iMARGI_project/enhancer_promoter/MAPS_output/H1_H3K4me3/feather_output/H1_H3K4me3_20190528_211840/tempfiles/H1_H3K4me3_R2.fastq.bwa.sam storing in /home/qizhijie/Data/iMARGI_project/enhancer_promoter/MAPS_output/H1_H3K4me3/feather_output/H1_H3K4me3_20190528_211840/tempfiles/H1_H3K4me3_R2.fastq.bwa.sam.srtn Wed May 29 04:26:30 2019 merging /home/qizhijie/Data/iMARGI_project/enhancer_promoter/MAPS_output/H1_H3K4me3/feather_output/H1_H3K4me3_20190528_211840/tempfiles/H1_H3K4me3_R1.fastq.bwa.sam.srtn and /home/qizhijie/Data/iMARGI_project/enhancer_promoter/MAPS_output/H1_H3K4me3/feather_output/H1_H3K4me3_20190528_211840/tempfiles/H1_H3K4me3_R2.fastq.bwa.sam.srtn Wed May 29 08:17:26 2019 filtering and pairing reads Wed May 29 12:49:28 2019 paired bam file generated. Sorting by coordinates. Wed May 29 13:25:59 2019 calling samtools rmdup Wed May 29 15:53:20 2019 calling samtools flagstat on mapped file Wed May 29 15:59:45 2019 calling samtools flagstat on mapped and duplicate-removed file Wed May 29 16:05:24 2019 calling samtools sort for sorting by query names Wed May 29 16:57:28 2019 finishing filtering Wed May 29 16:57:28 2019 starting the splitting operation NOTE: Too many chromosomes. Generating bed files only for ones without an underscore in their name Wed May 29 20:04:14 2019 generating long, intra-chromosomal bedpe file(s) Wed May 29 20:04:14 2019 writing to the combined bedpe file Wed May 29 20:39:40 2019 splitting completed

Thanks for the help.

armenabnousi commented 5 years ago

It looks like the feather has completed without any errors. My guess is there is a problem with the chromosome names. Are there any .shrt.vip.bed or .long.bedpe files in the feather_output directory? Can you also post the output from running: samtools view -H <feather_output/H1_H3K4me3_20190528_211840/*.paired.rmdup.bam> Thanks!

qizhijie commented 5 years ago

Yes, there is H1_H3K4me3.shrt.vip.bed file and H1_H3K4me3.long.intra.bedpe I realize that I actually mapped to the refseq genome, so there could be a problem with the chromosome names. Maybe you can confirm this by the following output as requested @HD VN:1.5 SO:coordinate @SQ SN:NC_000001.11 LN:248956422 @SQ SN:NT_187361.1 LN:175055 @SQ SN:NT_187362.1 LN:32032 @SQ SN:NT_187363.1 LN:127682 @SQ SN:NT_187364.1 LN:66860 @SQ SN:NT_187365.1 LN:40176 @SQ SN:NT_187366.1 LN:42210 @SQ SN:NT_187367.1 LN:176043 @SQ SN:NT_187368.1 LN:40745 @SQ SN:NT_187369.1 LN:41717 @SQ SN:NC_000002.12 LN:242193529 @SQ SN:NT_187370.1 LN:161471 @SQ SN:NT_187371.1 LN:153799 @SQ SN:NC_000003.12 LN:198295559 @SQ SN:NT_167215.1 LN:155397 @SQ SN:NC_000004.12 LN:190214555 @SQ SN:NT_113793.3 LN:209709 @SQ SN:NC_000005.10 LN:181538259 @SQ SN:NT_113948.1 LN:92689 @SQ SN:NC_000006.12 LN:170805979 @SQ SN:NC_000007.14 LN:159345973 @SQ SN:NC_000008.11 LN:145138636 @SQ SN:NC_000009.12 LN:138394717 @SQ SN:NT_187372.1 LN:40062 @SQ SN:NT_187373.1 LN:38054 @SQ SN:NT_187374.1 LN:176845 @SQ SN:NT_187375.1 LN:39050 @SQ SN:NC_000010.11 LN:133797422 @SQ SN:NC_000011.10 LN:135086622 @SQ SN:NT_187376.1 LN:100316 @SQ SN:NC_000012.12 LN:133275309 @SQ SN:NC_000013.11 LN:114364328 @SQ SN:NC_000014.9 LN:107043718 @SQ SN:NT_113796.3 LN:201709 @SQ SN:NT_167219.1 LN:211173 @SQ SN:NT_187377.1 LN:194050 @SQ SN:NT_113888.1 LN:191469 @SQ SN:NT_187378.1 LN:38115 @SQ SN:NT_187379.1 LN:39555 @SQ SN:NT_187380.1 LN:172810 @SQ SN:NT_187381.1 LN:43739 @SQ SN:NC_000015.10 LN:101991189 @SQ SN:NT_187382.1 LN:448248 @SQ SN:NC_000016.10 LN:90338345 @SQ SN:NT_187383.1 LN:1872759 @SQ SN:NC_000017.11 LN:83257441 @SQ SN:NT_113930.2 LN:185591 @SQ SN:NT_187384.1 LN:280839 @SQ SN:NT_187385.1 LN:112551 @SQ SN:NC_000018.10 LN:80373285 @SQ SN:NC_000019.10 LN:58617616 @SQ SN:NC_000020.11 LN:64444167 @SQ SN:NC_000021.9 LN:46709983 @SQ SN:NC_000022.11 LN:50818468 @SQ SN:NT_187386.1 LN:150754 @SQ SN:NT_187387.1 LN:41543 @SQ SN:NT_187388.1 LN:179772 @SQ SN:NT_187389.1 LN:165050 @SQ SN:NT_187390.1 LN:42811 @SQ SN:NT_187391.1 LN:181920 @SQ SN:NT_187392.1 LN:103838 @SQ SN:NT_187393.1 LN:99375 @SQ SN:NT_187394.1 LN:73985 @SQ SN:NC_000023.11 LN:156040895 @SQ SN:NC_000024.10 LN:57227415 @SQ SN:NT_187395.1 LN:37240 @SQ SN:NT_187396.1 LN:2274 @SQ SN:NT_187397.1 LN:2165 @SQ SN:NT_187398.1 LN:1942 @SQ SN:NT_187399.1 LN:1472 @SQ SN:NT_187400.1 LN:21476 @SQ SN:NT_187401.1 LN:4416 @SQ SN:NT_187402.1 LN:1201 @SQ SN:NT_187403.1 LN:1444 @SQ SN:NT_187404.1 LN:2276 @SQ SN:NT_187405.1 LN:998 @SQ SN:NT_187406.1 LN:12399 @SQ SN:NT_187407.1 LN:37690 @SQ SN:NT_187408.1 LN:1179 @SQ SN:NT_187409.1 LN:2646 @SQ SN:NT_187410.1 LN:2489 @SQ SN:NT_187411.1 LN:1029 @SQ SN:NT_187412.1 LN:2145 @SQ SN:NT_187413.1 LN:2321 @SQ SN:NT_187414.1 LN:2140 @SQ SN:NT_187415.1 LN:2043 @SQ SN:NT_187416.1 LN:1445 @SQ SN:NT_187417.1 LN:981 @SQ SN:NT_187418.1 LN:1884 @SQ SN:NT_187419.1 LN:1361 @SQ SN:NT_187420.1 LN:392061 @SQ SN:NT_187421.1 LN:1233 @SQ SN:NT_187422.1 LN:1774 @SQ SN:NT_187423.1 LN:3920 @SQ SN:NT_187424.1 LN:92983 @SQ SN:NT_187425.1 LN:112505 @SQ SN:NT_187426.1 LN:4055 @SQ SN:NT_187427.1 LN:2415 @SQ SN:NT_187428.1 LN:2318 @SQ SN:NT_187429.1 LN:2186 @SQ SN:NT_187430.1 LN:1951 @SQ SN:NT_187431.1 LN:1300 @SQ SN:NT_187432.1 LN:22689 @SQ SN:NT_187433.1 LN:138126 @SQ SN:NT_187434.1 LN:5674 @SQ SN:NT_187435.1 LN:8127 @SQ SN:NT_187436.1 LN:6361 @SQ SN:NT_187437.1 LN:5353 @SQ SN:NT_187438.1 LN:3253 @SQ SN:NT_187439.1 LN:1899 @SQ SN:NT_187440.1 LN:2983 @SQ SN:NT_187441.1 LN:2168 @SQ SN:NT_187442.1 LN:993 @SQ SN:NT_187443.1 LN:91309 @SQ SN:NT_187444.1 LN:1202 @SQ SN:NT_187445.1 LN:1599 @SQ SN:NT_187446.1 LN:1400 @SQ SN:NT_187447.1 LN:2969 @SQ SN:NT_187448.1 LN:1553 @SQ SN:NT_187449.1 LN:7046 @SQ SN:NT_187450.1 LN:31033 @SQ SN:NT_187451.1 LN:44474 @SQ SN:NT_187452.1 LN:4685 @SQ SN:NT_187453.1 LN:4513 @SQ SN:NT_187454.1 LN:6504 @SQ SN:NT_187455.1 LN:6158 @SQ SN:NT_187456.1 LN:3041 @SQ SN:NT_187457.1 LN:5796 @SQ SN:NT_187458.1 LN:1652 @SQ SN:NT_187459.1 LN:1040 @SQ SN:NT_187460.1 LN:1368 @SQ SN:NT_187461.1 LN:2699 @SQ SN:NT_187462.1 LN:1048 @SQ SN:NT_187463.1 LN:1428 @SQ SN:NT_187464.1 LN:1428 @SQ SN:NT_187465.1 LN:1026 @SQ SN:NT_187466.1 LN:1121 @SQ SN:NT_187467.1 LN:1803 @SQ SN:NT_187468.1 LN:2855 @SQ SN:NT_187469.1 LN:3530 @SQ SN:NT_187470.1 LN:8320 @SQ SN:NT_187471.1 LN:1048 @SQ SN:NT_187472.1 LN:1045 @SQ SN:NT_187473.1 LN:1298 @SQ SN:NT_187474.1 LN:2387 @SQ SN:NT_187475.1 LN:1537 @SQ SN:NT_187476.1 LN:1143 @SQ SN:NT_187477.1 LN:1880 @SQ SN:NT_187478.1 LN:1216 @SQ SN:NT_187479.1 LN:970 @SQ SN:NT_187480.1 LN:1788 @SQ SN:NT_187481.1 LN:1484 @SQ SN:NT_187482.1 LN:1750 @SQ SN:NT_187483.1 LN:1308 @SQ SN:NT_187484.1 LN:1658 @SQ SN:NT_187485.1 LN:971 @SQ SN:NT_187486.1 LN:1930 @SQ SN:NT_187487.1 LN:990 @SQ SN:NT_187488.1 LN:4215 @SQ SN:NT_187489.1 LN:1136 @SQ SN:NT_187490.1 LN:2656 @SQ SN:NT_187491.1 LN:1650 @SQ SN:NT_187492.1 LN:1451 @SQ SN:NT_187493.1 LN:2378 @SQ SN:NT_187494.1 LN:2805 @SQ SN:NT_187495.1 LN:7992 @SQ SN:NT_187496.1 LN:7642 @SQ SN:NT_113901.1 LN:182896 @SQ SN:NT_167213.1 LN:179198 @SQ SN:NT_167214.1 LN:161802 @SQ SN:NT_167218.1 LN:179693 @SQ SN:NT_187497.1 LN:157432 @SQ SN:NT_167220.1 LN:15008 @SQ SN:NT_167208.1 LN:164239 @SQ SN:NT_187498.1 LN:210658 @SQ SN:NT_187499.1 LN:168472 @SQ SN:NT_187500.1 LN:41891 @SQ SN:NT_187501.1 LN:66486 @SQ SN:NT_187502.1 LN:198735 @SQ SN:NT_187503.1 LN:93321 @SQ SN:NT_187504.1 LN:158759 @SQ SN:NT_187505.1 LN:148850 @SQ SN:NT_187506.1 LN:150742 @SQ SN:NT_187508.1 LN:62944 @SQ SN:NT_187509.1 LN:40191 @SQ SN:NT_187510.1 LN:36723 @SQ SN:NT_187511.1 LN:79590 @SQ SN:NT_187512.1 LN:71251 @SQ SN:NT_167209.1 LN:137718 @SQ SN:NT_187513.1 LN:186739 @SQ SN:NT_167211.2 LN:176608 @SQ SN:NT_113889.1 LN:161147 @SQ SN:NW_012132914.1 LN:467143 @SQ SN:NW_015495298.1 LN:278659 @SQ SN:NW_011332688.1 LN:305542 @SQ SN:NW_014040926.1 LN:349938 @SQ SN:NW_009646195.1 LN:166200 @SQ SN:NW_018654706.1 LN:166136 @SQ SN:NW_019805487.1 LN:44955 @SQ SN:NW_009646194.1 LN:186494 @SQ SN:NW_018654707.1 LN:140355 @SQ SN:NW_014040925.1 LN:141019 @SQ SN:NW_017852928.1 LN:551020 @SQ SN:NW_009646196.1 LN:122022 @SQ SN:NW_011332687.1 LN:460100 @SQ SN:NW_018654708.1 LN:330031 @SQ SN:NW_014040927.1 LN:212205 @SQ SN:NW_012132915.1 LN:481245 @SQ SN:NW_018654709.1 LN:181658 @SQ SN:NW_015495299.1 LN:535088 @SQ SN:NW_018654710.1 LN:140361 @SQ SN:NW_011332690.1 LN:365499 @SQ SN:NW_011332689.1 LN:208149 @SQ SN:NW_017363813.1 LN:411654 @SQ SN:NW_009646197.1 LN:451168 @SQ SN:NW_012132916.1 LN:373699 @SQ SN:NW_011332691.1 LN:415308 @SQ SN:NW_018654711.1 LN:175849 @SQ SN:NW_012132917.1 LN:165718 @SQ SN:NW_009646198.1 LN:305979 @SQ SN:NW_019805491.1 LN:105527 @SQ SN:NW_019805492.1 LN:195063 @SQ SN:NW_019805490.1 LN:302885 @SQ SN:NW_019805489.1 LN:197752 @SQ SN:NW_019805488.1 LN:164041 @SQ SN:NW_013171799.1 LN:90922 @SQ SN:NW_013171800.1 LN:163749 @SQ SN:NW_013171801.1 LN:236512 @SQ SN:NW_017363814.1 LN:420675 @SQ SN:NW_015495300.1 LN:230434 @SQ SN:NW_015495301.1 LN:205407 @SQ SN:NW_018654712.1 LN:135987 @SQ SN:NW_009646199.1 LN:139087 @SQ SN:NW_016107297.1 LN:362221 @SQ SN:NW_016107298.1 LN:673059 @SQ SN:NW_018654713.1 LN:242796 @SQ SN:NW_013171803.1 LN:82315 @SQ SN:NW_012132918.1 LN:320750 @SQ SN:NW_009646200.1 LN:268330 @SQ SN:NW_013171802.1 LN:245716 @SQ SN:NW_017363815.1 LN:139427 @SQ SN:NW_019805493.1 LN:172555 @SQ SN:NW_017852929.1 LN:142129 @SQ SN:NW_017852930.1 LN:468267 @SQ SN:NW_018654714.1 LN:589656 @SQ SN:NW_018654715.1 LN:680662 @SQ SN:NW_012132919.1 LN:179932 @SQ SN:NW_018654717.1 LN:6367528 @SQ SN:NW_017852932.1 LN:265876 @SQ SN:NW_017852931.1 LN:156998 @SQ SN:NW_019805494.1 LN:103072 @SQ SN:NW_018654716.1 LN:165120 @SQ SN:NW_013171804.1 LN:163882 @SQ SN:NW_013171805.1 LN:134099 @SQ SN:NW_009646201.1 LN:330164 @SQ SN:NW_011332694.1 LN:420164 @SQ SN:NW_013171806.1 LN:185507 @SQ SN:NW_009646202.1 LN:277797 @SQ SN:NW_013171807.1 LN:264545 @SQ SN:NW_011332693.1 LN:85284 @SQ SN:NW_011332692.1 LN:14347 @SQ SN:NW_015148966.1 LN:196940 @SQ SN:NW_011332695.1 LN:203552 @SQ SN:NW_019805496.1 LN:279644 @SQ SN:NW_019805495.1 LN:305244 @SQ SN:NW_017363816.1 LN:140877 @SQ SN:NW_019805498.1 LN:181167 @SQ SN:NW_019805497.1 LN:301637 @SQ SN:NW_013171808.1 LN:181958 @SQ SN:NW_009646203.1 LN:108875 @SQ SN:NW_013171809.1 LN:109323 @SQ SN:NW_018654718.1 LN:1046838 @SQ SN:NW_011332696.1 LN:541038 @SQ SN:NW_009646204.1 LN:211377 @SQ SN:NW_018654720.1 LN:174808 @SQ SN:NW_015148967.1 LN:315610 @SQ SN:NW_018654719.1 LN:64689 @SQ SN:NW_011332697.1 LN:86533 @SQ SN:NW_019805499.1 LN:154139 @SQ SN:NW_011332699.1 LN:356766 @SQ SN:NW_013171810.1 LN:168146 @SQ SN:NW_009646205.1 LN:35455 @SQ SN:NW_011332700.1 LN:148762 @SQ SN:NW_013171811.1 LN:123480 @SQ SN:NW_011332698.1 LN:206320 @SQ SN:NW_018654722.1 LN:690932 @SQ SN:NW_018654721.1 LN:171798 @SQ SN:NW_011332701.1 LN:4998962 @SQ SN:NW_012132920.1 LN:2365364 @SQ SN:NW_013171812.1 LN:59016 @SQ SN:NW_019805500.1 LN:480415 @SQ SN:NW_017852933.1 LN:1927115 @SQ SN:NW_013171813.1 LN:267463 @SQ SN:NW_018654723.1 LN:78609 @SQ SN:NW_012132921.1 LN:169136 @SQ SN:NW_017363817.1 LN:281919 @SQ SN:NW_016107299.1 LN:154723 @SQ SN:NW_017363819.1 LN:276292 @SQ SN:NW_017363818.1 LN:246895 @SQ SN:NW_019805501.1 LN:116753 @SQ SN:NW_019805503.1 LN:163186 @SQ SN:NW_014040928.1 LN:205101 @SQ SN:NW_019805502.1 LN:230843 @SQ SN:NW_013171814.1 LN:407387 @SQ SN:NW_018654724.1 LN:93070 @SQ SN:NW_014040929.1 LN:405389 @SQ SN:NW_009646206.1 LN:370917 @SQ SN:NW_016107300.1 LN:163926 @SQ SN:NW_016107301.1 LN:170206 @SQ SN:NW_016107302.1 LN:168131 @SQ SN:NW_016107303.1 LN:293522 @SQ SN:NW_016107304.1 LN:241058 @SQ SN:NW_016107305.1 LN:159285 @SQ SN:NW_016107306.1 LN:178197 @SQ SN:NW_016107307.1 LN:166713 @SQ SN:NW_016107308.1 LN:99845 @SQ SN:NW_016107309.1 LN:161095 @SQ SN:NW_016107310.1 LN:223118 @SQ SN:NW_016107311.1 LN:100553 @SQ SN:NW_016107313.1 LN:171263 @SQ SN:NW_016107314.1 LN:145691 @SQ SN:NW_016107312.1 LN:156965 @SQ SN:NW_009646207.1 LN:156562 @SQ SN:NW_014040930.1 LN:155930 @SQ SN:NW_014040931.1 LN:174749 @SQ SN:NW_009646208.1 LN:153027 @SQ SN:NW_015148968.1 LN:145162 @SQ SN:NW_015148969.1 LN:101037 @SQ SN:NW_017363820.1 LN:188004 @SQ SN:NW_018654725.1 LN:48370 @SQ SN:NW_018654726.1 LN:209722 @SQ SN:NW_009646209.1 LN:101150 @SQ SN:NT_187515.1 LN:354444 @SQ SN:NT_187517.1 LN:256271 @SQ SN:NT_187514.1 LN:109528 @SQ SN:NT_187520.1 LN:185285 @SQ SN:NW_003315905.1 LN:182439 @SQ SN:NW_003315906.1 LN:110268 @SQ SN:NW_003315907.2 LN:366580 @SQ SN:NT_187521.1 LN:50258 @SQ SN:NT_187519.1 LN:911658 @SQ SN:NT_187516.1 LN:425601 @SQ SN:NT_187518.1 LN:165834 @SQ SN:NT_187525.1 LN:136240 @SQ SN:NT_187526.1 LN:70887 @SQ SN:NT_187529.1 LN:223625 @SQ SN:NT_187522.1 LN:120616 @SQ SN:NW_003315908.1 LN:143390 @SQ SN:NT_187524.1 LN:133041 @SQ SN:NT_187531.1 LN:138019 @SQ SN:NT_187530.1 LN:110395 @SQ SN:NT_187528.1 LN:110099 @SQ SN:NW_003571033.2 LN:96131 @SQ SN:NW_003315909.1 LN:123821 @SQ SN:NT_187527.1 LN:174166 @SQ SN:NT_187523.1 LN:161578 @SQ SN:NW_003871060.2 LN:173151 @SQ SN:NT_187535.1 LN:109187 @SQ SN:NT_187537.1 LN:224108 @SQ SN:NW_003315913.1 LN:180671 @SQ SN:NT_187533.1 LN:173649 @SQ SN:NT_187536.1 LN:248252 @SQ SN:NT_187538.1 LN:113034 @SQ SN:NT_187532.1 LN:205312 @SQ SN:NT_187534.1 LN:162429 @SQ SN:NT_187539.1 LN:184404 @SQ SN:NT_187540.1 LN:220246 @SQ SN:NW_003315915.1 LN:376187 @SQ SN:NT_187541.1 LN:111943 @SQ SN:NT_167250.2 LN:586476 @SQ SN:NT_187544.1 LN:158965 @SQ SN:NW_003315914.1 LN:164536 @SQ SN:NT_187542.1 LN:119912 @SQ SN:NT_187545.1 LN:205944 @SQ SN:NT_187543.1 LN:244096 @SQ SN:NT_187550.1 LN:126136 @SQ SN:NT_187548.1 LN:179043 @SQ SN:NT_187547.1 LN:195710 @SQ SN:NW_003315920.1 LN:82728 @SQ SN:NW_003571036.1 LN:226852 @SQ SN:NT_187551.1 LN:164558 @SQ SN:NW_003315917.2 LN:1612928 @SQ SN:NW_003315918.1 LN:101241 @SQ SN:NT_187549.1 LN:172708 @SQ SN:NW_003315919.1 LN:173459 @SQ SN:NT_187546.1 LN:131892 @SQ SN:NT_167244.2 LN:4672374 @SQ SN:NT_187555.1 LN:175808 @SQ SN:NT_187554.1 LN:152148 @SQ SN:NW_003315921.1 LN:124736 @SQ SN:NT_187556.1 LN:870480 @SQ SN:NT_187557.1 LN:75005 @SQ SN:NW_004166862.2 LN:185823 @SQ SN:NT_187552.1 LN:197536 @SQ SN:NT_187553.1 LN:271782 @SQ SN:NT_187558.1 LN:157952 @SQ SN:NT_187561.1 LN:209586 @SQ SN:NT_187559.1 LN:158166 @SQ SN:NW_003315922.2 LN:119183 @SQ SN:NT_187562.1 LN:1111570 @SQ SN:NT_187564.1 LN:271455 @SQ SN:NT_187563.1 LN:126434 @SQ SN:NT_187560.1 LN:209988 @SQ SN:NT_187572.1 LN:145606 @SQ SN:NT_187568.1 LN:282736 @SQ SN:NT_187565.1 LN:292436 @SQ SN:NT_187576.1 LN:985506 @SQ SN:NT_187570.1 LN:300230 @SQ SN:NT_187577.1 LN:624492 @SQ SN:NT_187566.1 LN:141812 @SQ SN:NT_187567.1 LN:374415 @SQ SN:NT_187574.1 LN:133535 @SQ SN:NT_187575.1 LN:36640 @SQ SN:NT_187573.1 LN:158983 @SQ SN:NT_187571.1 LN:305841 @SQ SN:NT_187569.1 LN:132244 @SQ SN:NW_003315928.1 LN:162988 @SQ SN:NW_003315929.1 LN:71551 @SQ SN:NW_003315930.1 LN:171286 @SQ SN:NW_003315931.1 LN:60032 @SQ SN:NT_187578.1 LN:439082 @SQ SN:NW_003315934.1 LN:179254 @SQ SN:NT_187579.1 LN:181496 @SQ SN:NW_003315935.1 LN:309802 @SQ SN:NT_187580.1 LN:188315 @SQ SN:NT_187586.1 LN:210133 @SQ SN:NT_187584.1 LN:177092 @SQ SN:NT_187585.1 LN:296895 @SQ SN:NT_187583.1 LN:204059 @SQ SN:NW_003315936.1 LN:154407 @SQ SN:NW_003871073.1 LN:200998 @SQ SN:NW_003871074.1 LN:191409 @SQ SN:NT_187582.1 LN:67707 @SQ SN:NT_187581.1 LN:186169 @SQ SN:NW_003571049.1 LN:167313 @SQ SN:NW_003571050.1 LN:408271 @SQ SN:NT_187588.1 LN:40090 @SQ SN:NW_003315938.1 LN:120804 @SQ SN:NT_187587.1 LN:238139 @SQ SN:NW_003315939.2 LN:169178 @SQ SN:NW_003315941.1 LN:138655 @SQ SN:NW_003315942.2 LN:152874 @SQ SN:NT_187590.1 LN:119498 @SQ SN:NW_003315940.1 LN:184319 @SQ SN:NT_187589.1 LN:76061 @SQ SN:NT_187591.1 LN:56134 @SQ SN:NT_187594.1 LN:191684 @SQ SN:NT_187593.1 LN:180306 @SQ SN:NT_187597.1 LN:103832 @SQ SN:NT_187595.1 LN:169134 @SQ SN:NT_187592.1 LN:306913 @SQ SN:NT_187596.1 LN:37287 @SQ SN:NT_187598.1 LN:322166 @SQ SN:NT_187601.1 LN:1511111 @SQ SN:NT_187599.1 LN:180703 @SQ SN:NT_187600.1 LN:1351393 @SQ SN:NT_187602.1 LN:478999 @SQ SN:NT_187604.1 LN:263054 @SQ SN:NT_187603.1 LN:327382 @SQ SN:NW_003315943.1 LN:296527 @SQ SN:NT_187605.1 LN:244917 @SQ SN:NW_003315944.2 LN:388773 @SQ SN:NT_187606.1 LN:430880 @SQ SN:NT_187610.1 LN:134193 @SQ SN:NT_187609.1 LN:63982 @SQ SN:NT_187608.1 LN:232857 @SQ SN:NT_187607.1 LN:2659700 @SQ SN:NW_003315945.1 LN:192462 @SQ SN:NW_003315946.1 LN:89672 @SQ SN:NW_003315952.3 LN:375691 @SQ SN:NT_187613.1 LN:391357 @SQ SN:NT_187611.1 LN:196688 @SQ SN:NT_187614.1 LN:2877074 @SQ SN:NW_003871091.1 LN:278131 @SQ SN:NW_003871092.1 LN:70345 @SQ SN:NW_003315953.2 LN:133151 @SQ SN:NT_167251.2 LN:1821992 @SQ SN:NW_003315954.1 LN:223995 @SQ SN:NT_187615.1 LN:235827 @SQ SN:NT_187616.1 LN:108763 @SQ SN:NW_003315955.1 LN:90219 @SQ SN:NT_187612.1 LN:178921 @SQ SN:NT_187618.1 LN:111737 @SQ SN:NW_003315956.1 LN:289831 @SQ SN:NW_003315959.1 LN:164789 @SQ SN:NW_003315960.1 LN:198278 @SQ SN:NW_003315957.1 LN:104552 @SQ SN:NW_003315958.1 LN:167950 @SQ SN:NW_003315961.1 LN:159547 @SQ SN:NT_187617.1 LN:167999 @SQ SN:NT_187622.1 LN:61734 @SQ SN:NT_187621.1 LN:52969 @SQ SN:NW_003315962.1 LN:385657 @SQ SN:NW_003315964.2 LN:170222 @SQ SN:NW_003315965.1 LN:188024 @SQ SN:NW_003315963.1 LN:155864 @SQ SN:NT_187619.1 LN:43156 @SQ SN:NT_187620.1 LN:233762 @SQ SN:NW_003571054.1 LN:987716 @SQ SN:NW_003315966.2 LN:128386 @SQ SN:NT_187623.1 LN:118774 @SQ SN:NT_187625.1 LN:58661 @SQ SN:NT_187624.1 LN:183433 @SQ SN:NW_003315967.2 LN:63917 @SQ SN:NT_187628.1 LN:166743 @SQ SN:NT_187627.1 LN:143900 @SQ SN:NW_003315968.2 LN:201197 @SQ SN:NW_003315969.2 LN:74653 @SQ SN:NW_003315970.2 LN:116689 @SQ SN:NT_187626.1 LN:82692 @SQ SN:NT_187629.1 LN:259914 @SQ SN:NT_187632.1 LN:186262 @SQ SN:NT_187633.1 LN:304135 @SQ SN:NT_187630.1 LN:263666 @SQ SN:NT_187631.1 LN:101331 @SQ SN:NW_003315972.2 LN:96924 @SQ SN:NW_003315971.2 LN:162811 @SQ SN:NT_187634.1 LN:284869 @SQ SN:NT_187635.1 LN:144206 @SQ SN:NT_187646.1 LN:162212 @SQ SN:NT_187648.1 LN:214158 @SQ SN:NT_187647.1 LN:161218 @SQ SN:NT_187649.1 LN:162896 @SQ SN:NT_187650.1 LN:378547 @SQ SN:NT_187651.1 LN:1144418 @SQ SN:NT_187652.1 LN:130957 @SQ SN:NT_113891.3 LN:4795265 @SQ SN:NT_187653.1 LN:190869 @SQ SN:NT_187655.1 LN:136959 @SQ SN:NT_187654.1 LN:318687 @SQ SN:NT_187656.1 LN:106711 @SQ SN:NT_187657.1 LN:214625 @SQ SN:NT_187658.1 LN:572349 @SQ SN:NT_187659.1 LN:196384 @SQ SN:NT_187660.1 LN:5161414 @SQ SN:NT_187662.1 LN:137721 @SQ SN:NT_187664.1 LN:157099 @SQ SN:NT_187661.1 LN:325800 @SQ SN:NW_003871093.1 LN:88070 @SQ SN:NT_187663.1 LN:1423190 @SQ SN:NT_187665.1 LN:174061 @SQ SN:NT_187666.1 LN:157710 @SQ SN:NW_003571055.2 LN:729520 @SQ SN:NW_004504305.1 LN:74013 @SQ SN:NT_187667.1 LN:274009 @SQ SN:NT_187678.1 LN:166540 @SQ SN:NT_187679.1 LN:555799 @SQ SN:NT_167245.2 LN:4604811 @SQ SN:NT_187680.1 LN:229282 @SQ SN:NT_187681.1 LN:218612 @SQ SN:NW_003571056.2 LN:1064304 @SQ SN:NT_187682.1 LN:176103 @SQ SN:NT_187688.1 LN:163458 @SQ SN:NT_167246.2 LN:4677643 @SQ SN:NW_003571057.2 LN:1091841 @SQ SN:NT_187689.1 LN:197351 @SQ SN:NT_167247.2 LN:4827813 @SQ SN:NW_003571058.2 LN:1066390 @SQ SN:NT_187690.1 LN:164170 @SQ SN:NT_167248.2 LN:4606388 @SQ SN:NW_003571059.2 LN:1002683 @SQ SN:NT_187691.1 LN:165607 @SQ SN:NT_167249.2 LN:4929269 @SQ SN:NW_003571060.1 LN:987100 @SQ SN:NT_187692.1 LN:76752 @SQ SN:NW_003571061.2 LN:796479 @SQ SN:NT_187693.1 LN:1066800 @SQ SN:NT_187636.1 LN:248807 @SQ SN:NT_187637.1 LN:170399 @SQ SN:NT_187638.1 LN:157053 @SQ SN:NT_187639.1 LN:171027 @SQ SN:NT_187640.1 LN:204239 @SQ SN:NT_187641.1 LN:209512 @SQ SN:NT_187642.1 LN:155532 @SQ SN:NT_187643.1 LN:170698 @SQ SN:NT_187644.1 LN:184499 @SQ SN:NT_187645.1 LN:170680 @SQ SN:NT_187668.1 LN:205194 @SQ SN:NT_187669.1 LN:170665 @SQ SN:NT_187670.1 LN:184516 @SQ SN:NT_187671.1 LN:190932 @SQ SN:NT_187672.1 LN:123111 @SQ SN:NT_187673.1 LN:170701 @SQ SN:NT_187674.1 LN:198005 @SQ SN:NT_187675.1 LN:282224 @SQ SN:NT_187676.1 LN:187935 @SQ SN:NT_187677.1 LN:189352 @SQ SN:NT_187683.1 LN:186203 @SQ SN:NT_187684.1 LN:200773 @SQ SN:NT_187685.1 LN:170148 @SQ SN:NT_187686.1 LN:215732 @SQ SN:NT_187687.1 LN:170537 @SQ SN:NT_113949.2 LN:177381 @SQ SN:NC_012920.1 LN:16569 @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem -t 20 /home/qizhijie/Data/genome/bwa_index_refSeq_genome/refSeq_grch38.fa /home/qizhijie/Data/iMARGI_project/iMARGI_data/Hiseq/PLACSeq_fastq_merged/H1_H3K4me3_R1.fastq @PG ID:bwa-2A559725 PN:bwa VN:0.7.12-r1039 CL:bwa mem -t 20 /home/qizhijie/Data/genome/bwa_index_refSeq_genome/refSeq_grch38.fa /home/qizhijie/Data/iMARGI_project/iMARGI_data/Hiseq/PLACSeq_fastq_merged/H1_H3K4me3_R2.fastq

Thanks

armenabnousi commented 5 years ago

Hi Zhijie,

I'm sorry about the problem you're having. Unfortunately current version of MAPS requires chromosome names to start with "chr" or just the chromosome number (and to only work with autosomal chromosomes, in most cases discards chromosome names that contain a "" character. As you mentioned since you are using the refseq genome your chromosome names are "NT/NC/NW*". Is it possible for you to change the chromosome names? I could possibly upload a different version of the script that will work for your case but might need a little bit of time for that. Hopefully by the end of day today.

qizhijie commented 5 years ago

Hi, As I guess I need to rerun the pipeline anyway, I can just map the reads to UCSC genome where the chromosome names start with chr. Hopefully it will work this time. No need for you to work out a different version. Thanks for the help!