Job ID = 2009863 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T11:25:14 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from t : NET - Reading information from the socket failed ) 1900-01-00T00:00:00 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from t : NET - Reading information from the socket failed ) 2019-07-05T11:27:29 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 : 28,422,081 reads read : 28,422,081 reads written : 28,422,081 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:02 28422081 reads; of these: 28422081 (100.00%) were unpaired; of these: 6948077 (24.45%) aligned 0 times 16031188 (56.40%) aligned exactly 1 time 5442816 (19.15%) aligned >1 times 75.55% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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 12 files... [bam_rmdupse_core] 12128370 / 21474004 = 0.5648 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 21:03:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.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 @ Fri, 05 Jul 2019 21:03:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.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 @ Fri, 05 Jul 2019 21:03:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.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 @ Fri, 05 Jul 2019 21:03:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:19: 1000000 INFO @ Fri, 05 Jul 2019 21:03:20: 1000000 INFO @ Fri, 05 Jul 2019 21:03:20: 1000000 INFO @ Fri, 05 Jul 2019 21:03:27: 2000000 INFO @ Fri, 05 Jul 2019 21:03:28: 2000000 INFO @ Fri, 05 Jul 2019 21:03:28: 2000000 INFO @ Fri, 05 Jul 2019 21:03:33: 3000000 INFO @ Fri, 05 Jul 2019 21:03:35: 3000000 INFO @ Fri, 05 Jul 2019 21:03:36: 3000000 INFO @ Fri, 05 Jul 2019 21:03:40: 4000000 INFO @ Fri, 05 Jul 2019 21:03:42: 4000000 INFO @ Fri, 05 Jul 2019 21:03:44: 4000000 INFO @ Fri, 05 Jul 2019 21:03:47: 5000000 INFO @ Fri, 05 Jul 2019 21:03:49: 5000000 INFO @ Fri, 05 Jul 2019 21:03:52: 5000000 INFO @ Fri, 05 Jul 2019 21:03:54: 6000000 INFO @ Fri, 05 Jul 2019 21:03:56: 6000000 INFO @ Fri, 05 Jul 2019 21:04:00: 6000000 INFO @ Fri, 05 Jul 2019 21:04:01: 7000000 INFO @ Fri, 05 Jul 2019 21:04:03: 7000000 INFO @ Fri, 05 Jul 2019 21:04:08: 7000000 INFO @ Fri, 05 Jul 2019 21:04:10: 8000000 INFO @ Fri, 05 Jul 2019 21:04:10: 8000000 INFO @ Fri, 05 Jul 2019 21:04:16: 8000000 INFO @ Fri, 05 Jul 2019 21:04:17: 9000000 INFO @ Fri, 05 Jul 2019 21:04:17: 9000000 INFO @ Fri, 05 Jul 2019 21:04:19: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:04:19: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:04:19: #1 total tags in treatment: 9345634 INFO @ Fri, 05 Jul 2019 21:04:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:04:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:04:19: #1 tags after filtering in treatment: 9345634 INFO @ Fri, 05 Jul 2019 21:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:04:19: #1 finished! INFO @ Fri, 05 Jul 2019 21:04:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:04:20: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:04:20: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:04:20: #1 total tags in treatment: 9345634 INFO @ Fri, 05 Jul 2019 21:04:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:04:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:04:20: #1 tags after filtering in treatment: 9345634 INFO @ Fri, 05 Jul 2019 21:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:04:20: #1 finished! INFO @ Fri, 05 Jul 2019 21:04:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:04:20: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:04:20: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 05 Jul 2019 21:04:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:04:21: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:04:21: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 05 Jul 2019 21:04:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 7 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:04:24: 9000000 INFO @ Fri, 05 Jul 2019 21:04:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:04:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:04:27: #1 total tags in treatment: 9345634 INFO @ Fri, 05 Jul 2019 21:04:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:04:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:04:27: #1 tags after filtering in treatment: 9345634 INFO @ Fri, 05 Jul 2019 21:04:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:04:27: #1 finished! INFO @ Fri, 05 Jul 2019 21:04:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:04:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:04:28: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 21:04:28: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 05 Jul 2019 21:04:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX2070409/SRX2070409.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。