Job ID = 2011855 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:53:37 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T18:04:23 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 15,912,140 reads read : 31,824,280 reads written : 31,824,042 reads 0-length : 238 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Warning: skipping mate #1 of read 'SRR8313302.2947563 2947563 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313302.2947563 2947563 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313302.3147708 3147708 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313302.3147708 3147708 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313302.4674913 4674913 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313302.4674913 4674913 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313302.9269513 9269513 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313302.9269513 9269513 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313302.11463992 11463992 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313302.11463992 11463992 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313302.15493606 15493606 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313302.15493606 15493606 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313302.15670768 15670768 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313302.15670768 15670768 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 12713449 / 14936674 = 0.8512 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 03:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 06 Jul 2019 03:29:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 06 Jul 2019 03:29:34: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:34: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 06 Jul 2019 03:29:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:43: 1000000 INFO @ Sat, 06 Jul 2019 03:29:43: 1000000 INFO @ Sat, 06 Jul 2019 03:29:43: 1000000 INFO @ Sat, 06 Jul 2019 03:29:50: 2000000 INFO @ Sat, 06 Jul 2019 03:29:51: 2000000 INFO @ Sat, 06 Jul 2019 03:29:51: 2000000 INFO @ Sat, 06 Jul 2019 03:29:57: 3000000 INFO @ Sat, 06 Jul 2019 03:29:58: 3000000 INFO @ Sat, 06 Jul 2019 03:30:00: 3000000 INFO @ Sat, 06 Jul 2019 03:30:04: 4000000 INFO @ Sat, 06 Jul 2019 03:30:06: 4000000 INFO @ Sat, 06 Jul 2019 03:30:08: 4000000 INFO @ Sat, 06 Jul 2019 03:30:11: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:30:11: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:30:11: #1 total tags in treatment: 2222018 INFO @ Sat, 06 Jul 2019 03:30:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:30:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:30:11: #1 tags after filtering in treatment: 1693339 INFO @ Sat, 06 Jul 2019 03:30:11: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 03:30:11: #1 finished! INFO @ Sat, 06 Jul 2019 03:30:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:30:12: #2 number of paired peaks: 158 WARNING @ Sat, 06 Jul 2019 03:30:12: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 06 Jul 2019 03:30:12: start model_add_line... INFO @ Sat, 06 Jul 2019 03:30:12: start X-correlation... INFO @ Sat, 06 Jul 2019 03:30:12: end of X-cor INFO @ Sat, 06 Jul 2019 03:30:12: #2 finished! INFO @ Sat, 06 Jul 2019 03:30:12: #2 predicted fragment length is 176 bps INFO @ Sat, 06 Jul 2019 03:30:12: #2 alternative fragment length(s) may be 1,19,58,62,70,110,117,132,154,176,205,228,255,284,305,357,393,453,577,593 bps INFO @ Sat, 06 Jul 2019 03:30:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.10_model.r INFO @ Sat, 06 Jul 2019 03:30:12: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:30:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:30:13: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:30:13: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:30:13: #1 total tags in treatment: 2222018 INFO @ Sat, 06 Jul 2019 03:30:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:30:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:30:13: #1 tags after filtering in treatment: 1693339 INFO @ Sat, 06 Jul 2019 03:30:13: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 03:30:13: #1 finished! INFO @ Sat, 06 Jul 2019 03:30:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:30:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:30:13: #2 number of paired peaks: 158 WARNING @ Sat, 06 Jul 2019 03:30:13: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 06 Jul 2019 03:30:13: start model_add_line... INFO @ Sat, 06 Jul 2019 03:30:13: start X-correlation... INFO @ Sat, 06 Jul 2019 03:30:13: end of X-cor INFO @ Sat, 06 Jul 2019 03:30:13: #2 finished! INFO @ Sat, 06 Jul 2019 03:30:13: #2 predicted fragment length is 176 bps INFO @ Sat, 06 Jul 2019 03:30:13: #2 alternative fragment length(s) may be 1,19,58,62,70,110,117,132,154,176,205,228,255,284,305,357,393,453,577,593 bps INFO @ Sat, 06 Jul 2019 03:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.20_model.r INFO @ Sat, 06 Jul 2019 03:30:13: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:30:15: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 03:30:15: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 03:30:15: #1 total tags in treatment: 2222018 INFO @ Sat, 06 Jul 2019 03:30:15: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:30:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:30:15: #1 tags after filtering in treatment: 1693339 INFO @ Sat, 06 Jul 2019 03:30:15: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 03:30:15: #1 finished! INFO @ Sat, 06 Jul 2019 03:30:15: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:30:15: #2 number of paired peaks: 158 WARNING @ Sat, 06 Jul 2019 03:30:15: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 06 Jul 2019 03:30:15: start model_add_line... INFO @ Sat, 06 Jul 2019 03:30:15: start X-correlation... INFO @ Sat, 06 Jul 2019 03:30:16: end of X-cor INFO @ Sat, 06 Jul 2019 03:30:16: #2 finished! INFO @ Sat, 06 Jul 2019 03:30:16: #2 predicted fragment length is 176 bps INFO @ Sat, 06 Jul 2019 03:30:16: #2 alternative fragment length(s) may be 1,19,58,62,70,110,117,132,154,176,205,228,255,284,305,357,393,453,577,593 bps INFO @ Sat, 06 Jul 2019 03:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.05_model.r INFO @ Sat, 06 Jul 2019 03:30:16: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:30:18: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:30:19: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:30:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:30:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:30:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.10_summits.bed INFO @ Sat, 06 Jul 2019 03:30:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.20_summits.bed INFO @ Sat, 06 Jul 2019 03:30:21: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:30:21: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:30:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:30:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:30:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5126610/SRX5126610.05_summits.bed INFO @ Sat, 06 Jul 2019 03:30:23: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。