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Using the same version of sratoolkit generates different data sizes #866

Closed yanpinlu closed 6 months ago

yanpinlu commented 8 months ago

@stineaj @kmt @Miserlou different linux accounts, using the same version of sra-tools, the same data, the same command will produce different sizes of fastaq datasets. What causes this? Is it dependent on the existing environment of different accounts? sratoolkit version 3.0.0 command fasterq-dump SRR10984994.1 --include-technical -S -p -e 20 -O /home/scrna_seq/fastq_all / image

klymenko commented 8 months ago

What is the output of srapath SRR10984994.1 for those cases?

yanpinlu commented 8 months ago

What is the output of for those cases?srapath SRR10984994.1

I'm sorry I didn't get it right. I first go to the folder where the SRA data is stored, and when I run fasterq-dump SRR10984982.1 --include-technical -S -p -e 20 -O /home/scrna_seq/fastq_all/, The output is three files SRR10984982.1_1.fastQ, SRR10984982.1_2.FASTQ, SRR10984982.1_2.FASTQ,SRR10984982.1_3.fastq, the figure above shows two different computers using the same command, the same data set, to produce different sizes of fastq results

klymenko commented 8 months ago

Did fasterq-dump succeed in both cases?

yanpinlu commented 8 months ago

Did succeed in both cases?fasterq-dump

Yes, no errors occurred

klymenko commented 8 months ago

Did you have the same messages printed by fasterq-dump in both cases?

yanpinlu commented 8 months ago

在这两种情况下，您是否打印了相同的消息？fasterq-dump

yes , Same command and same prompt output img_v2_3d5af631-29d4-4468-9014-8953157c878g image

klymenko commented 8 months ago

Could you compare fastq-files?

yanpinlu commented 8 months ago

Could you compare fastq-files?

  • Do they have the same number of lines?
  • Is the difference in identifiers?
  • Sequence or quality lines?

They have the same number of lines and the beginning end sequence is somewhat inconsistent img_v2_7a2ecc55-1ed8-461b-ae28-4bec47753e6g

klymenko commented 8 months ago

Could you head a small number of lines from each file, diff them and post the result here? Not screenshots?

yanpinlu commented 8 months ago

Could you head a small number of lines from each file, diff them and post the result here? Not screenshots?

head -n 10 SRR10984982.1_1.fastq（ first environment）（34528.11MB） @SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8 NCAGCCGT +SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8

AAFFJFJ

@SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8 NCAGCCGT +SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8

<AFFJJJ

@SRR10984982.1.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=8 NCAGCCGT

head -n 10 SRR10984982.1_1.fastq（ second environment）（33761.33MB） @SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8 NCAGCCGT +SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8

AAFFJFJ

@SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8 NCAGCCGT +SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8

<AFFJJJ

@SRR10984982.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=8 NCAGCCGT

head -n 10 SRR10984982.1_2.fastq（ first environment）（89736.30MB） @SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150 NCTATTGGTCCAGTGCTCCCGCGTGGTTTCTTATATGGGGTTATCTCCAGAAGGAGAAGATAAAAGGAGAAGCCGAAGGGAAAGGAATAAGATGGCTGCAGCCAAATGCCGCAATCGGAGGAGGGAGCTGACTGATACACTCCAAGCGGA +SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150

AAAFJJJJJJJJ7JJJ-J<JJJFJJJJJF-FFJFJJJJAJFAFJ<F<JJ<<JA<-<-FJ-7FJFJJJJ-<-<7AJJJFJ7-FAJJJJJJJJJJJJ7JJJ7FA--77FFJJAJJ---7FJF<-7AAA7AJFJJJ-A--FJJFJJF-<JF7

@SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150 NACACTCCAATGGATACCCAGCACACTTTCTTATATGGGGGGGGGCTTGGGCTGGTTCGGCCGCTTGGCGCCCCCGCGGAGGGTACCCGGCGGCGGCCTTTGGCCTTTAGCGGGGCTTCGGCAGTTGTCTGGGATAGTCAGGATGTGGGG +SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150

AA<AJJJFJJJF-FJF7A7JJJJJAJJJJJJJJFJJJJJAJ7J<-F<-AF--7----A<7<FA-7--7-----7--A--7----7J--7-7<--7-7-7-777-7<A7----7--7------7F-A777-A--77-AAF-7--7--7--

@SRR10984982.1.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=150 NGTTACGTCTAGTCACCGTTGAATGTTTATATAGAGGTTGTCTTGACAAGAGCGGCTTCATCGGGCGGGAGCCCGGCTCCGGCAGCTCCTTCCTCCTCTTCCTCCGCGTCCTCCGCCTCCGGATTTTGGGGGCTAGATGTCCTCTCTCGG

head -n 10 SRR10984982.1_2.fastq（ second environment）（88969.52MB） @SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150 NCTATTGGTCCAGTGCTCCCGCGTGGTTTCTTATATGGGGTTATCTCCAGAAGGAGAAGATAAAAGGAGAAGCCGAAGGGAAAGGAATAAGATGGCTGCAGCCAAATGCCGCAATCGGAGGAGGGAGCTGACTGATACACTCCAAGCGGA +SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150

AAAFJJJJJJJJ7JJJ-J<JJJFJJJJJF-FFJFJJJJAJFAFJ<F<JJ<<JA<-<-FJ-7FJFJJJJ-<-<7AJJJFJ7-FAJJJJJJJJJJJJ7JJJ7FA--77FFJJAJJ---7FJF<-7AAA7AJFJJJ-A--FJJFJJF-<JF7

@SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150 NACACTCCAATGGATACCCAGCACACTTTCTTATATGGGGGGGGGCTTGGGCTGGTTCGGCCGCTTGGCGCCCCCGCGGAGGGTACCCGGCGGCGGCCTTTGGCCTTTAGCGGGGCTTCGGCAGTTGTCTGGGATAGTCAGGATGTGGGG +SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150

AA<AJJJFJJJF-FJF7A7JJJJJAJJJJJJJJFJJJJJAJ7J<-F<-AF--7----A<7<FA-7--7-----7--A--7----7J--7-7<--7-7-7-777-7<A7----7--7------7F-A777-A--77-AAF-7--7--7--

@SRR10984982.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=150 NGTTACGTCTAGTCACCGTTGAATGTTTATATAGAGGTTGTCTTGACAAGAGCGGCTTCATCGGGCGGGAGCCCGGCTCCGGCAGCTCCTTCCTCCTCTTCCTCCGCGTCCTCCGCCTCCGGATTTTGGGGGCTAGATGTCCTCTCTCGG

head -n 10 SRR10984982.1_3.fastq（ first environment）（89736.30MB） +SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJFFJJJJFJJJJJJJJJJJJFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFFJFJ @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 ATGATGGAGTACATGATAGGGAGGAACCAGGCTTTAAAGTTCCGCACGTCCTTCTTGGAGCACAAAGACTCGAACAAAGTGTAGTCCACTGTGGTGTTGTCTCCGATGTAATCGTCCGTGACCTCATCTTGACACAGGCATACCTGGAAA +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AAFFFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJFFJ7-<FFFJJJJJJJAJA<FJJJ7FJFJJA @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCAGAAGGTATAGGGGTTAGTCCTTGCTATATTATGCTTGGCTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCCAGGTTTCAATT +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJFJJFJJJJFJJJJJJJ

head -n 10 SRR10984982.1_3.fastq（ second environment）（88969.52MB） @SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150 NGCAGGTCGGTGAGCTGCCAGGATGAACTCTAGGTTTTCCTTCTCCTTCAGCAGGTGGGCAATCTCGGTCTGCAAAGCAGACTTGTCATCTTCTGGTTGGTCTGGCTCCGCTTGGGGTGTATCAGTCAGCCGCCTCCTCCGGTTGCGGCA +SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150

A<AFFFJJJ<FAJJJJJJ<AJAJJFJFFJJJJ-AJJJAAJ-<-FJFJJJJFFJJF-F<7F<JF7FFJA7JF<FJAFJ-J-F-F-<FFJ7JJJJFJJFAA7AFF-7<F<<FJ<FJ-F-----JJJ-<AJ7))A<J7)F<FJJJ)A<AJJ)

@SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150 NCCGCTGTTCTCCAGCGTCTGCACCAGCAGGTCTCGCAGCTCGGTGTCCTCCTCGGCCACCACTGCGGCCGCCGTCGCCGCCATCTTTCGTCTCCAAGACAACCGCCGAAGCCGCGCTAACGGCCAACGGCCGCAGCATGGTACACTCCG +SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150

A-<AFJJJ-<J-FJJJJJJFJJFJFJAFJJFJ-7JJJJJJJ-A<FJJJJJF<JJJ<JJ<AAJJ<FJJFJJAJJJ-AJ7J-F-JJJF-7<<JA--<AF<F7AJJ7FF--AFAF<JAAF7AF-F<AF<JJJJ)AA)F)<-7AJ7<--<FA-

@SRR10984982.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=150 NCCAGGAAGGTCTCTCCCCCGCTGGCCTCACAGTTCAGGGCGTCAAACTTAGGGTTGACAGCACAGAAGCCACTGACCCAGGTGGACTGTGGGAGCCGAACATCGTGATAGCACTTGTCGTCCTTGGCCGTCTGTCGAAACACGTGGCGG

tail -n 10 SRR10984982.1_1.fastq（ first environment） +SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=8 AAFFFJJJ @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=8 CAGAGGCC +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=8 AAFFFJJJ @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=8 CAGAGGCC +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=8 AAFFFJJJ

tail -n 10 SRR10984982.1_1.fastq（ second environment） +SRR10984982.201006875 GWNJ-0842:539:GW1908022346th:1:2224:18954:72965 length=8 AAFF#JJJ @SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=8 ATCTNTAG +SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=8 AAFF#JJJ @SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=8 ATCTNTAG +SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=8 AAFF#JJJ

tail -n 10 SRR10984982.1_2.fastq （ first environment） +SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJFJJJJJFJJJJJJF @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AGCATACTCCGCAAGCTCCTCAGAGGTTTCTTATATGGGAGACAGGGGTAGTGCGAGGCCGGGCACAGCCTTCCTGTGTGGTTTTACCGCCCAGAGAGCGTCATGGACCTGGGGAAACCAATGAAAAGCGTGCTGGTGGTGGCTCTCCTT +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJ @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 GTTTCTAGTGCACTTATGCCGCTGTGTTTCTTATATGGGGCTAAACCTAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATA +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

tail -n 10 SRR10984982.1_2.fastq （ second environment）

+SRR10984982.201006875 GWNJ-0842:539:GW1908022346th:1:2224:18954:72965 length=150 AAFFFJJJJFJJJJJJJJJJJJJJJJJJJAFFJJFJJJJJJJJJ#JJJJJJJJJ##JJJJJJ#JJJJJJJJ#J#JJJJFJ#J#J#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJ##F###JJ#JJ#J#J#JJ#JJ#JJ @SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 CACACCTCACGTTGGCTTTATCTCCTTTTCTTATATGGGGATTCNTGAAGCTGANNGCATTCNGGCCGAGANGNCTCGCTNCNTNGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGGCNTGGANNCNNNCCNGCNTNCNCCNAANAT +SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJ##JJJJJJ#JJJJJJJJ#J#FJJJJJ#J#J#JJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJ#JJJJ##J###JJ#JJ#J#J#JJ#JJ#JF @SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 AACACGTTCCTCTAGCCCCACTCATTTTTCTTATATGGGGTCAGNGTCTCCTCANNCGCCGANATGCTGGTNANGGCGCCNCNANCCGTCCTCCTGCTGCTCTCGGCGGCCCTGGCCCTGANCGAGNNCNNNGCNGGNTNCNACNCCNTG +SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJ##JJJJJJ#JJJJJJJJ#F#JJJJJJ#J#J#JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJA#JJJJ##J###JJ#JJ#J#J#FJ#JJ#FJ

tail -n 10 SRR10984982.1_3.fastq（ first environment） +SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJFFJJJJFJJJJJJJJJJJJFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFFJFJ @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 ATGATGGAGTACATGATAGGGAGGAACCAGGCTTTAAAGTTCCGCACGTCCTTCTTGGAGCACAAAGACTCGAACAAAGTGTAGTCCACTGTGGTGTTGTCTCCGATGTAATCGTCCGTGACCTCATCTTGACACAGGCATACCTGGAAA +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AAFFFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJFFJ7-<FFFJJJJJJJAJA<FJJJ7FJFJJA @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCAGAAGGTATAGGGGTTAGTCCTTGCTATATTATGCTTGGCTATAATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCCAGGTTTCAATT +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJFJJFJJJJFJJJJJJJ

tail -n 10 SRR10984982.1_3.fastq （ second environment） +SRR10984982.201006875 GWNJ-0842:539:GW1908022346th:1:2224:18954:72965 length=150 A#A#FAJJF#JJJ#JF#JJJ#JJ#JJ#J##J#JJ##JJJJJJJJJJJJ7FAFJF#JJJFJJF#JJJJJJJJJJ#JJ#JJJJAJJJ#J#JJJJJJJJJJJJJJFFF##7FAJFJJJFJF<FJJ#JJAJJJJJJ#JJJFJJJJ7JJFJAJJF @SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 GNGNTGAATNCAGNGTNGTANAANAGNTNNANAGNNCAGTCCTTGCTGAAAGACNAGTCTGANTGCTCCACTTNTTNAATTCTCTNTNCATTCTTCAGTAAGTCANNTTCAATGTCGGATGGNTGAAACCCANACACATAGCAATTCAGG +SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 A#A#AFJJJ#JJJ#JJ#JJJ#JJ#JJ#J##J#JJ##JJJJJJJJJJJJJJJJAJ#JJJJJFJ#JJJJFJJJJJ#JJ#JJJJJJJJ#J#JJJJJJJJJJJJJJJJJ##JAFJJJFJJJJJJJJ#JJJJFJJFF#JJJJJJJJJJJJJJJJJ @SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 ANTNAGATGNAGCNGGNCTCNCCNCGNCNNGNCCNNGNCATGGCGGTGTCGAAANACCTCATNGAGTGGGAGCNGGNCCAGGTCTNGNTCAGGGCCAGGGCCGCCNNGAGCAGCAGGAGGACNGTNCGGGGCNCCATGACCAGCATCTCG +SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 A#A#FJJJJ#JJJ#JJ#JJJ#JJ#JJ#J##J#JJ##J#JJJJJJJJJJJJJJJJ#JJJJJJJ#JFFAAJJJJJ#JJ#FJJJJJJJ#J#FJJJJJJJJJJJFJJJJ##JJJJJJJFJJJJJFJ#J7#FJJJJJ#FJJA<FJJJJJJJJFJJ

klymenko commented 8 months ago

Great job!

Next step, for each pair of files:

  1. Create files with results of head from your previous comments in the same directory, e.g.,SRR10984982.1_2.fastq.1 and SRR10984982.1_2.fastq.2.
  2. Run diff SRR10984982.1_2.fastq.1 SRR10984982.1_2.fastq.2.
  3. Post results here.
yanpinlu commented 8 months ago

Great job!

Next step, for each pair of files:

  1. Create files with results of head from your previous comments in the same directory, e.g.,SRR10984982.1_2.fastq.1 and SRR10984982.1_2.fastq.2.
  2. Run diff SRR10984982.1_2.fastq.1 SRR10984982.1_2.fastq.2.
  3. Post results here.

[luyanping@gpu01 sra]$ diff "/home/luyanping/data/sra/ SRR10984982.1_2.fastq.2" "/home/luyanping/dat a/sra/ SRR10984982.1_2.fastq.1" 2c2 < @SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8

@SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8 4c4 < +SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8

+SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=8 6c6 < @SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8

@SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8 8c8 < +SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8

+SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=8 10c10 < @SRR10984982.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=8

@SRR10984982.1.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=8 14c14 < @SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150

@SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150 16c16 < +SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150

+SRR10984982.1.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150 18c18 < @SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150

@SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150 20c20 < +SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150

+SRR10984982.1.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150 22c22 < @SRR10984982.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=150

@SRR10984982.1.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=150 24a25

26,35c27,36 < @SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150 < NGCAGGTCGGTGAGCTGCCAGGATGAACTCTAGGTTTTCCTTCTCCTTCAGCAGGTGGGCAATCTCGGTCTGCAAAGCAGACTTGTCATCTTCTGGTTG GTCTGGCTCCGCTTGGGGTGTATCAGTCAGCCGCCTCCTCCGGTTGCGGCA < +SRR10984982.1 GWNJ-0842:539:GW1908022346th:1:1101:14336:1538 length=150 < #A<AFFFJJJ<FAJJJJJJ<AJAJJFJFFJJJJ-AJJJAAJ-<-FJFJJJJFFJJF-F<7F<JF7FFJA7JF<FJAFJ-J-F-F-<FFJ7JJJJFJJFA A7AFF-7<F<<FJ<FJ-F-----JJJ-<AJ7))A<J7)F<FJJJ)A<AJJ) < @SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150 < NCCGCTGTTCTCCAGCGTCTGCACCAGCAGGTCTCGCAGCTCGGTGTCCTCCTCGGCCACCACTGCGGCCGCCGTCGCCGCCATCTTTCGTCTCCAAGA CAACCGCCGAAGCCGCGCTAACGGCCAACGGCCGCAGCATGGTACACTCCG < +SRR10984982.2 GWNJ-0842:539:GW1908022346th:1:1101:14763:1538 length=150 < #A-<AFJJJ-<J-FJJJJJJFJJFJFJAFJJFJ-7JJJJJJJ-A<FJJJJJF<JJJ<JJ<AAJJ<FJJFJJAJJJ-AJ7J-F-JJJF-7<<JA--<AF< F7AJJ7FF--AFAF<JAAF7AF-F<AF<JJJJ)AA)F)<-7AJ7<--<FA- < @SRR10984982.3 GWNJ-0842:539:GW1908022346th:1:1101:22171:1538 length=150 < NCCAGGAAGGTCTCTCCCCCGCTGGCCTCACAGTTCAGGGCGTCAAACTTAGGGTTGACAGCACAGAAGCCACTGACCCAGGTGGACTGTGGGAGCCGA ACATCGTGATAGCACTTGTCGTCCTTGGCCGTCTGTCGAAACACGTGGCGG

+SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJFFJJJJFJJJJJJJJJJJJFJJJJF JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFFJFJ @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 ATGATGGAGTACATGATAGGGAGGAACCAGGCTTTAAAGTTCCGCACGTCCTTCTTGGAGCACAAAGACTCGAACAAAGTGTAGTCCACTGTGGTGTTG TCTCCGATGTAATCGTCCGTGACCTCATCTTGACACAGGCATACCTGGAAA +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AAFFFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJ JJJJJJJJJJJJJJJJJFJJFFJ7-<FFFJJJJJJJAJA<FJJJ7FJFJJA @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCAGAAGGTATAGGGGTTAGTCCTTGCTATATTATGCTTGGCTATA ATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCCAGGTTTCAATT +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJ JJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJFJJFJJJJFJJJJJJJ 38,47c39,49 < +SRR10984982.201006875 GWNJ-0842:539:GW1908022346th:1:2224:18954:72965 length=8 < AAFF#JJJ < @SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=8 < ATCTNTAG < +SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=8 < AAFF#JJJ < @SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=8 < ATCTNTAG < +SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=8 < AAFF#JJJ

+SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=8 AAFFFJJJ @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=8 CAGAGGCC +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=8 AAFFFJJJ @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=8 CAGAGGCC +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=8 AAFFFJJJ

50,71c52,76 < +SRR10984982.201006875 GWNJ-0842:539:GW1908022346th:1:2224:18954:72965 length=150 < AAFFFJJJJFJJJJJJJJJJJJJJJJJJJAFFJJFJJJJJJJJJ#JJJJJJJJJ##JJJJJJ#JJJJJJJJ#J#JJJJFJ#J#J#JJJJJJJJJJJJJJ JJJJJJJJJJJJJJJJJJJJJJ#JJJJ##F###JJ#JJ#J#J#JJ#JJ#JJ < @SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 < CACACCTCACGTTGGCTTTATCTCCTTTTCTTATATGGGGATTCNTGAAGCTGANNGCATTCNGGCCGAGANGNCTCGCTNCNTNGCCTTAGCTGTGCT CGCGCTACTCTCTCTTTCTGGCNTGGANNCNNNCCNGCNTNCNCCNAANAT < +SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 < AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJ##JJJJJJ#JJJJJJJJ#J#FJJJJJ#J#J#JJJJJJJJJJJJJJ JJJJJJFJJJJJJJJJJJJJJJ#JJJJ##J###JJ#JJ#J#J#JJ#JJ#JF < @SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 < AACACGTTCCTCTAGCCCCACTCATTTTTCTTATATGGGGTCAGNGTCTCCTCANNCGCCGANATGCTGGTNANGGCGCCNCNANCCGTCCTCCTGCTG CTCTCGGCGGCCCTGGCCCTGANCGAGNNCNNNGCNGGNTNCNACNCCNTG < +SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 < AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJ##JJJJJJ#JJJJJJJJ#F#JJJJJJ#J#J#JJJJJJJJJJJJJJ JJJJJJJJJJJJJJJJJJJJJA#JJJJ##J###JJ#JJ#J#J#FJ#JJ#FJ < < tail -n 10 SRR10984982.1_3.fastq < +SRR10984982.201006875 GWNJ-0842:539:GW1908022346th:1:2224:18954:72965 length=150 < A#A#FAJJF#JJJ#JF#JJJ#JJ#JJ#J##J#JJ##JJJJJJJJJJJJ7FAFJF#JJJFJJF#JJJJJJJJJJ#JJ#JJJJAJJJ#J#JJJJJJJJJJJ JJJFFF##7FAJFJJJFJF<FJJ#JJAJJJJJJ#JJJFJJJJ7JJFJAJJF < @SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 < GNGNTGAATNCAGNGTNGTANAANAGNTNNANAGNNCAGTCCTTGCTGAAAGACNAGTCTGANTGCTCCACTTNTTNAATTCTCTNTNCATTCTTCAGT AAGTCANNTTCAATGTCGGATGGNTGAAACCCANACACATAGCAATTCAGG < +SRR10984982.201006876 GWNJ-0842:539:GW1908022346th:1:2224:19197:72965 length=150 < A#A#AFJJJ#JJJ#JJ#JJJ#JJ#JJ#J##J#JJ##JJJJJJJJJJJJJJJJAJ#JJJJJFJ#JJJJFJJJJJ#JJ#JJJJJJJJ#J#JJJJJJJJJJJ JJJJJJ##JAFJJJFJJJJJJJJ#JJJJFJJFF#JJJJJJJJJJJJJJJJJ < @SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 < ANTNAGATGNAGCNGGNCTCNCCNCGNCNNGNCCNNGNCATGGCGGTGTCGAAANACCTCATNGAGTGGGAGCNGGNCCAGGTCTNGNTCAGGGCCAGG GCCGCCNNGAGCAGCAGGAGGACNGTNCGGGGCNCCATGACCAGCATCTCG < +SRR10984982.201006877 GWNJ-0842:539:GW1908022346th:1:2224:19867:72965 length=150 < A#A#FJJJJ#JJJ#JJ#JJJ#JJ#JJ#J##J#JJ##J#JJJJJJJJJJJJJJJJ#JJJJJJJ#JFFAAJJJJJ#JJ#FJJJJJJJ#J#FJJJJJJJJJJ JFJJJJ##JJJJJJJFJJJJJFJ#J7#FJJJJJ#FJJA<FJJJJJJJJFJJ

+SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJ JJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJFJJJJJFJJJJJJF @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AGCATACTCCGCAAGCTCCTCAGAGGTTTCTTATATGGGAGACAGGGGTAGTGCGAGGCCGGGCACAGCCTTCCTGTGTGGTTTTACCGCCCAGAGAGC GTCATGGACCTGGGGAAACCAATGAAAAGCGTGCTGGTGGTGGCTCTCCTT +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFJJJJJJJJJJJJJJJJJ JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJ @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 GTTTCTAGTGCACTTATGCCGCTGTGTTTCTTATATGGGGCTAAACCTAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTT ACCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATA +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJ JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ

tail -n 10 SRR10984982.1_3.fastq +SRR10984982.1.100503438 GWNJ-0842:539:GW1908022346th:1:2208:25540:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJFFJJJJFJJJJJJJJJJJJFJJJJF JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFFJFJ @SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 ATGATGGAGTACATGATAGGGAGGAACCAGGCTTTAAAGTTCCGCACGTCCTTCTTGGAGCACAAAGACTCGAACAAAGTGTAGTCCACTGTGGTGTTG TCTCCGATGTAATCGTCCGTGACCTCATCTTGACACAGGCATACCTGGAAA +SRR10984982.1.100503439 GWNJ-0842:539:GW1908022346th:1:2208:25621:14195 length=150 AAFFFJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJFJJJJJ JJJJJJJJJJJJJJJJJFJJFFJ7-<FFFJJJJJJJAJA<FJJJ7FJFJJA @SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 GGGGGTCTTAGCTTTGGCTCTCCTTGCAAAGTTATTTCTAGTTAATTCATTATGCAGAAGGTATAGGGGTTAGTCCTTGCTATATTATGCTTGGCTATA ATTTTTCATCTTTCCCTTGCGGTACTATATCTATTGCGCCAGGTTTCAATT +SRR10984982.1.100503440 GWNJ-0842:539:GW1908022346th:1:2208:25641:14195 length=150 AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJJJJJJJJJJJJJJJFJJJJJ JJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJFJJFJJJJFJJJJJJJ

klymenko commented 8 months ago

The sequence identifier in SRR10984982.1_1.fastq（ first environment）（34528.11MB） starts with SRR10984982.1.1. In SRR10984982.1_1.fastq（ second environment）（33761.33MB）- with SRR10984982.1.

Do you run fasterq-dump SRR10984994.1 in first environment and fasterq-dump SRR10984994 in the second one?

yanpinlu commented 8 months ago

The sequence identifier in SRR10984982.1_1.fastq（ first environment）（34528.11MB） starts with SRR10984982.1.1. In SRR10984982.1_1.fastq（ second environment）（33761.33MB）- with SRR10984982.1.

Do you run fasterq-dump SRR10984994.1 in first environment and fasterq-dump SRR10984994 in the second one?

No, the input file name is the same, fasterq-dump SRR10984994.1，all the Rawdata is SRRxxxxxxxx.1

klymenko commented 8 months ago

In both environments:

  1. Remove SRR10984982*fastq;
  2. run fasterq-dump;
  3. head created SRR10984982*fastq files.

Post the output here. Post everything you have on your screen - commands and their output. Don't post screenshots - copy the text and paste here.