Job ID = 1293710 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,673,993 reads read : 25,673,993 reads written : 25,673,993 2019-06-02T17:00:01 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 : 20,946,942 reads read : 20,946,942 reads written : 20,946,942 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: 00:13:11 46620935 reads; of these: 46620935 (100.00%) were unpaired; of these: 5646495 (12.11%) aligned 0 times 32599747 (69.93%) aligned exactly 1 time 8374693 (17.96%) aligned >1 times 87.89% overall alignment rate Time searching: 00:13:11 Overall time: 00:13:11 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] 13389311 / 40974440 = 0.3268 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 02:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.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 02:25:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:25:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.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 02:25:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:25:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.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 02:25:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:25:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:25:43: 1000000 INFO @ Mon, 03 Jun 2019 02:25:43: 1000000 INFO @ Mon, 03 Jun 2019 02:25:44: 1000000 INFO @ Mon, 03 Jun 2019 02:25:52: 2000000 INFO @ Mon, 03 Jun 2019 02:25:52: 2000000 INFO @ Mon, 03 Jun 2019 02:25:53: 2000000 INFO @ Mon, 03 Jun 2019 02:26:01: 3000000 INFO @ Mon, 03 Jun 2019 02:26:01: 3000000 INFO @ Mon, 03 Jun 2019 02:26:03: 3000000 INFO @ Mon, 03 Jun 2019 02:26:09: 4000000 INFO @ Mon, 03 Jun 2019 02:26:09: 4000000 INFO @ Mon, 03 Jun 2019 02:26:12: 4000000 INFO @ Mon, 03 Jun 2019 02:26:18: 5000000 INFO @ Mon, 03 Jun 2019 02:26:18: 5000000 INFO @ Mon, 03 Jun 2019 02:26:22: 5000000 INFO @ Mon, 03 Jun 2019 02:26:26: 6000000 INFO @ Mon, 03 Jun 2019 02:26:26: 6000000 INFO @ Mon, 03 Jun 2019 02:26:33: 6000000 INFO @ Mon, 03 Jun 2019 02:26:34: 7000000 INFO @ Mon, 03 Jun 2019 02:26:34: 7000000 INFO @ Mon, 03 Jun 2019 02:26:42: 7000000 INFO @ Mon, 03 Jun 2019 02:26:43: 8000000 INFO @ Mon, 03 Jun 2019 02:26:43: 8000000 INFO @ Mon, 03 Jun 2019 02:26:51: 9000000 INFO @ Mon, 03 Jun 2019 02:26:51: 9000000 INFO @ Mon, 03 Jun 2019 02:26:52: 8000000 INFO @ Mon, 03 Jun 2019 02:27:00: 10000000 INFO @ Mon, 03 Jun 2019 02:27:00: 10000000 INFO @ Mon, 03 Jun 2019 02:27:02: 9000000 INFO @ Mon, 03 Jun 2019 02:27:08: 11000000 INFO @ Mon, 03 Jun 2019 02:27:08: 11000000 INFO @ Mon, 03 Jun 2019 02:27:12: 10000000 INFO @ Mon, 03 Jun 2019 02:27:16: 12000000 INFO @ Mon, 03 Jun 2019 02:27:17: 12000000 INFO @ Mon, 03 Jun 2019 02:27:21: 11000000 INFO @ Mon, 03 Jun 2019 02:27:25: 13000000 INFO @ Mon, 03 Jun 2019 02:27:26: 13000000 INFO @ Mon, 03 Jun 2019 02:27:32: 12000000 INFO @ Mon, 03 Jun 2019 02:27:33: 14000000 INFO @ Mon, 03 Jun 2019 02:27:35: 14000000 INFO @ Mon, 03 Jun 2019 02:27:41: 15000000 INFO @ Mon, 03 Jun 2019 02:27:43: 13000000 INFO @ Mon, 03 Jun 2019 02:27:44: 15000000 INFO @ Mon, 03 Jun 2019 02:27:49: 16000000 INFO @ Mon, 03 Jun 2019 02:27:52: 16000000 INFO @ Mon, 03 Jun 2019 02:27:53: 14000000 INFO @ Mon, 03 Jun 2019 02:27:57: 17000000 INFO @ Mon, 03 Jun 2019 02:28:01: 17000000 INFO @ Mon, 03 Jun 2019 02:28:03: 15000000 INFO @ Mon, 03 Jun 2019 02:28:05: 18000000 INFO @ Mon, 03 Jun 2019 02:28:10: 18000000 INFO @ Mon, 03 Jun 2019 02:28:13: 16000000 INFO @ Mon, 03 Jun 2019 02:28:13: 19000000 INFO @ Mon, 03 Jun 2019 02:28:19: 19000000 INFO @ Mon, 03 Jun 2019 02:28:21: 20000000 INFO @ Mon, 03 Jun 2019 02:28:22: 17000000 INFO @ Mon, 03 Jun 2019 02:28:27: 20000000 INFO @ Mon, 03 Jun 2019 02:28:29: 21000000 INFO @ Mon, 03 Jun 2019 02:28:32: 18000000 INFO @ Mon, 03 Jun 2019 02:28:36: 21000000 INFO @ Mon, 03 Jun 2019 02:28:37: 22000000 INFO @ Mon, 03 Jun 2019 02:28:42: 19000000 INFO @ Mon, 03 Jun 2019 02:28:45: 22000000 INFO @ Mon, 03 Jun 2019 02:28:46: 23000000 INFO @ Mon, 03 Jun 2019 02:28:51: 20000000 INFO @ Mon, 03 Jun 2019 02:28:54: 23000000 INFO @ Mon, 03 Jun 2019 02:28:54: 24000000 INFO @ Mon, 03 Jun 2019 02:29:01: 21000000 INFO @ Mon, 03 Jun 2019 02:29:02: 25000000 INFO @ Mon, 03 Jun 2019 02:29:02: 24000000 INFO @ Mon, 03 Jun 2019 02:29:10: 26000000 INFO @ Mon, 03 Jun 2019 02:29:11: 25000000 INFO @ Mon, 03 Jun 2019 02:29:11: 22000000 INFO @ Mon, 03 Jun 2019 02:29:18: 27000000 INFO @ Mon, 03 Jun 2019 02:29:19: 26000000 INFO @ Mon, 03 Jun 2019 02:29:21: 23000000 INFO @ Mon, 03 Jun 2019 02:29:23: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:29:23: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:29:23: #1 total tags in treatment: 27585129 INFO @ Mon, 03 Jun 2019 02:29:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:29:23: #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 02:29:23: #1 tags after filtering in treatment: 27585129 INFO @ Mon, 03 Jun 2019 02:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:29:23: #1 finished! INFO @ Mon, 03 Jun 2019 02:29:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:29:25: #2 number of paired peaks: 10 WARNING @ Mon, 03 Jun 2019 02:29:25: Too few paired peaks (10) 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 02:29:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.05_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/SRX111789/SRX111789.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:29:27: 27000000 INFO @ Mon, 03 Jun 2019 02:29:30: 24000000 INFO @ Mon, 03 Jun 2019 02:29:32: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:29:32: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:29:32: #1 total tags in treatment: 27585129 INFO @ Mon, 03 Jun 2019 02:29:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:29:32: #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 02:29:32: #1 tags after filtering in treatment: 27585129 INFO @ Mon, 03 Jun 2019 02:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:29:32: #1 finished! INFO @ Mon, 03 Jun 2019 02:29:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:29:35: #2 number of paired peaks: 10 WARNING @ Mon, 03 Jun 2019 02:29:35: Too few paired peaks (10) 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 02:29:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.10_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/SRX111789/SRX111789.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:29:38: 25000000 INFO @ Mon, 03 Jun 2019 02:29:48: 26000000 INFO @ Mon, 03 Jun 2019 02:29:57: 27000000 INFO @ Mon, 03 Jun 2019 02:30:02: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:30:02: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:30:02: #1 total tags in treatment: 27585129 INFO @ Mon, 03 Jun 2019 02:30:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:30:02: #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 02:30:02: #1 tags after filtering in treatment: 27585129 INFO @ Mon, 03 Jun 2019 02:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:30:02: #1 finished! INFO @ Mon, 03 Jun 2019 02:30:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:30:05: #2 number of paired peaks: 10 WARNING @ Mon, 03 Jun 2019 02:30:05: Too few paired peaks (10) 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 02:30:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111789/SRX111789.20_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。