Job ID = 1295316 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:10:20 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 : 30,649,765 reads read : 30,649,765 reads written : 30,649,765 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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 Multiseed full-index search: 00:09:32 30649765 reads; of these: 30649765 (100.00%) were unpaired; of these: 4064672 (13.26%) aligned 0 times 21462551 (70.03%) aligned exactly 1 time 5122542 (16.71%) aligned >1 times 86.74% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7133918 / 26585093 = 0.2683 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 @ Mon, 03 Jun 2019 13:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 13:36:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:36:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 13:36:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:36:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 13:36:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:36:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:37:01: 1000000 INFO @ Mon, 03 Jun 2019 13:37:03: 1000000 INFO @ Mon, 03 Jun 2019 13:37:03: 1000000 INFO @ Mon, 03 Jun 2019 13:37:09: 2000000 INFO @ Mon, 03 Jun 2019 13:37:13: 2000000 INFO @ Mon, 03 Jun 2019 13:37:14: 2000000 INFO @ Mon, 03 Jun 2019 13:37:19: 3000000 INFO @ Mon, 03 Jun 2019 13:37:24: 3000000 INFO @ Mon, 03 Jun 2019 13:37:25: 3000000 INFO @ Mon, 03 Jun 2019 13:37:28: 4000000 INFO @ Mon, 03 Jun 2019 13:37:35: 4000000 INFO @ Mon, 03 Jun 2019 13:37:35: 4000000 INFO @ Mon, 03 Jun 2019 13:37:37: 5000000 INFO @ Mon, 03 Jun 2019 13:37:45: 5000000 INFO @ Mon, 03 Jun 2019 13:37:45: 6000000 INFO @ Mon, 03 Jun 2019 13:37:46: 5000000 INFO @ Mon, 03 Jun 2019 13:37:54: 7000000 INFO @ Mon, 03 Jun 2019 13:37:56: 6000000 INFO @ Mon, 03 Jun 2019 13:37:57: 6000000 INFO @ Mon, 03 Jun 2019 13:38:04: 8000000 INFO @ Mon, 03 Jun 2019 13:38:07: 7000000 INFO @ Mon, 03 Jun 2019 13:38:08: 7000000 INFO @ Mon, 03 Jun 2019 13:38:12: 9000000 INFO @ Mon, 03 Jun 2019 13:38:18: 8000000 INFO @ Mon, 03 Jun 2019 13:38:19: 8000000 INFO @ Mon, 03 Jun 2019 13:38:21: 10000000 INFO @ Mon, 03 Jun 2019 13:38:27: 9000000 INFO @ Mon, 03 Jun 2019 13:38:28: 9000000 INFO @ Mon, 03 Jun 2019 13:38:29: 11000000 INFO @ Mon, 03 Jun 2019 13:38:37: 12000000 INFO @ Mon, 03 Jun 2019 13:38:37: 10000000 INFO @ Mon, 03 Jun 2019 13:38:38: 10000000 INFO @ Mon, 03 Jun 2019 13:38:47: 13000000 INFO @ Mon, 03 Jun 2019 13:38:48: 11000000 INFO @ Mon, 03 Jun 2019 13:38:49: 11000000 INFO @ Mon, 03 Jun 2019 13:38:56: 14000000 INFO @ Mon, 03 Jun 2019 13:38:58: 12000000 INFO @ Mon, 03 Jun 2019 13:38:59: 12000000 INFO @ Mon, 03 Jun 2019 13:39:04: 15000000 INFO @ Mon, 03 Jun 2019 13:39:07: 13000000 INFO @ Mon, 03 Jun 2019 13:39:09: 13000000 INFO @ Mon, 03 Jun 2019 13:39:12: 16000000 INFO @ Mon, 03 Jun 2019 13:39:18: 14000000 INFO @ Mon, 03 Jun 2019 13:39:19: 14000000 INFO @ Mon, 03 Jun 2019 13:39:21: 17000000 INFO @ Mon, 03 Jun 2019 13:39:29: 15000000 INFO @ Mon, 03 Jun 2019 13:39:30: 15000000 INFO @ Mon, 03 Jun 2019 13:39:31: 18000000 INFO @ Mon, 03 Jun 2019 13:39:39: 19000000 INFO @ Mon, 03 Jun 2019 13:39:39: 16000000 INFO @ Mon, 03 Jun 2019 13:39:40: 16000000 INFO @ Mon, 03 Jun 2019 13:39:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:39:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:39:43: #1 total tags in treatment: 19451175 INFO @ Mon, 03 Jun 2019 13:39:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:39:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:39:43: #1 tags after filtering in treatment: 19451175 INFO @ Mon, 03 Jun 2019 13:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:39:43: #1 finished! INFO @ Mon, 03 Jun 2019 13:39:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:39:45: #2 number of paired peaks: 43 WARNING @ Mon, 03 Jun 2019 13:39:45: Too few paired peaks (43) 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 @ Mon, 03 Jun 2019 13:39:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.10_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/dm3/SRX335488/SRX335488.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:39:50: 17000000 INFO @ Mon, 03 Jun 2019 13:39:50: 17000000 INFO @ Mon, 03 Jun 2019 13:39:59: 18000000 INFO @ Mon, 03 Jun 2019 13:40:00: 18000000 INFO @ Mon, 03 Jun 2019 13:40:09: 19000000 INFO @ Mon, 03 Jun 2019 13:40:10: 19000000 INFO @ Mon, 03 Jun 2019 13:40:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:40:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:40:14: #1 total tags in treatment: 19451175 INFO @ Mon, 03 Jun 2019 13:40:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:40:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:40:14: #1 tags after filtering in treatment: 19451175 INFO @ Mon, 03 Jun 2019 13:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:40:14: #1 finished! INFO @ Mon, 03 Jun 2019 13:40:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:40:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:40:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:40:15: #1 total tags in treatment: 19451175 INFO @ Mon, 03 Jun 2019 13:40:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:40:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:40:15: #1 tags after filtering in treatment: 19451175 INFO @ Mon, 03 Jun 2019 13:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:40:15: #1 finished! INFO @ Mon, 03 Jun 2019 13:40:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:40:16: #2 number of paired peaks: 43 WARNING @ Mon, 03 Jun 2019 13:40:16: Too few paired peaks (43) 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 @ Mon, 03 Jun 2019 13:40:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.05_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/dm3/SRX335488/SRX335488.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:40:17: #2 number of paired peaks: 43 WARNING @ Mon, 03 Jun 2019 13:40:17: Too few paired peaks (43) 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 @ Mon, 03 Jun 2019 13:40:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.20_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/dm3/SRX335488/SRX335488.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX335488/SRX335488.20_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。