Job ID = 1293672 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:27:48 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 : 36,013,387 reads read : 36,013,387 reads written : 36,013,387 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: 00:15:38 36013387 reads; of these: 36013387 (100.00%) were unpaired; of these: 2483380 (6.90%) aligned 0 times 24236418 (67.30%) aligned exactly 1 time 9293589 (25.81%) aligned >1 times 93.10% overall alignment rate Time searching: 00:15:38 Overall time: 00:15:38 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] 4972096 / 33530007 = 0.1483 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 02:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.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 02:09:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:09:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.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 02:09:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:09:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.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 02:09:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:09:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:09:56: 1000000 INFO @ Mon, 03 Jun 2019 02:09:56: 1000000 INFO @ Mon, 03 Jun 2019 02:09:57: 1000000 INFO @ Mon, 03 Jun 2019 02:10:04: 2000000 INFO @ Mon, 03 Jun 2019 02:10:05: 2000000 INFO @ Mon, 03 Jun 2019 02:10:05: 2000000 INFO @ Mon, 03 Jun 2019 02:10:12: 3000000 INFO @ Mon, 03 Jun 2019 02:10:13: 3000000 INFO @ Mon, 03 Jun 2019 02:10:14: 3000000 INFO @ Mon, 03 Jun 2019 02:10:19: 4000000 INFO @ Mon, 03 Jun 2019 02:10:22: 4000000 INFO @ Mon, 03 Jun 2019 02:10:22: 4000000 INFO @ Mon, 03 Jun 2019 02:10:27: 5000000 INFO @ Mon, 03 Jun 2019 02:10:30: 5000000 INFO @ Mon, 03 Jun 2019 02:10:31: 5000000 INFO @ Mon, 03 Jun 2019 02:10:35: 6000000 INFO @ Mon, 03 Jun 2019 02:10:39: 6000000 INFO @ Mon, 03 Jun 2019 02:10:40: 6000000 INFO @ Mon, 03 Jun 2019 02:10:43: 7000000 INFO @ Mon, 03 Jun 2019 02:10:48: 7000000 INFO @ Mon, 03 Jun 2019 02:10:48: 7000000 INFO @ Mon, 03 Jun 2019 02:10:51: 8000000 INFO @ Mon, 03 Jun 2019 02:10:56: 8000000 INFO @ Mon, 03 Jun 2019 02:10:57: 8000000 INFO @ Mon, 03 Jun 2019 02:10:59: 9000000 INFO @ Mon, 03 Jun 2019 02:11:05: 9000000 INFO @ Mon, 03 Jun 2019 02:11:06: 9000000 INFO @ Mon, 03 Jun 2019 02:11:07: 10000000 INFO @ Mon, 03 Jun 2019 02:11:14: 10000000 INFO @ Mon, 03 Jun 2019 02:11:15: 10000000 INFO @ Mon, 03 Jun 2019 02:11:16: 11000000 INFO @ Mon, 03 Jun 2019 02:11:22: 11000000 INFO @ Mon, 03 Jun 2019 02:11:23: 11000000 INFO @ Mon, 03 Jun 2019 02:11:23: 12000000 INFO @ Mon, 03 Jun 2019 02:11:31: 13000000 INFO @ Mon, 03 Jun 2019 02:11:31: 12000000 INFO @ Mon, 03 Jun 2019 02:11:32: 12000000 INFO @ Mon, 03 Jun 2019 02:11:39: 14000000 INFO @ Mon, 03 Jun 2019 02:11:40: 13000000 INFO @ Mon, 03 Jun 2019 02:11:40: 13000000 INFO @ Mon, 03 Jun 2019 02:11:48: 15000000 INFO @ Mon, 03 Jun 2019 02:11:48: 14000000 INFO @ Mon, 03 Jun 2019 02:11:48: 14000000 INFO @ Mon, 03 Jun 2019 02:11:55: 16000000 INFO @ Mon, 03 Jun 2019 02:11:57: 15000000 INFO @ Mon, 03 Jun 2019 02:11:57: 15000000 INFO @ Mon, 03 Jun 2019 02:12:03: 17000000 INFO @ Mon, 03 Jun 2019 02:12:06: 16000000 INFO @ Mon, 03 Jun 2019 02:12:06: 16000000 INFO @ Mon, 03 Jun 2019 02:12:10: 18000000 INFO @ Mon, 03 Jun 2019 02:12:14: 17000000 INFO @ Mon, 03 Jun 2019 02:12:15: 17000000 INFO @ Mon, 03 Jun 2019 02:12:18: 19000000 INFO @ Mon, 03 Jun 2019 02:12:23: 18000000 INFO @ Mon, 03 Jun 2019 02:12:23: 18000000 INFO @ Mon, 03 Jun 2019 02:12:26: 20000000 INFO @ Mon, 03 Jun 2019 02:12:31: 19000000 INFO @ Mon, 03 Jun 2019 02:12:32: 19000000 INFO @ Mon, 03 Jun 2019 02:12:34: 21000000 INFO @ Mon, 03 Jun 2019 02:12:39: 20000000 INFO @ Mon, 03 Jun 2019 02:12:40: 20000000 INFO @ Mon, 03 Jun 2019 02:12:42: 22000000 INFO @ Mon, 03 Jun 2019 02:12:48: 21000000 INFO @ Mon, 03 Jun 2019 02:12:48: 21000000 INFO @ Mon, 03 Jun 2019 02:12:50: 23000000 INFO @ Mon, 03 Jun 2019 02:12:56: 22000000 INFO @ Mon, 03 Jun 2019 02:12:57: 22000000 INFO @ Mon, 03 Jun 2019 02:12:58: 24000000 INFO @ Mon, 03 Jun 2019 02:13:05: 23000000 INFO @ Mon, 03 Jun 2019 02:13:05: 23000000 INFO @ Mon, 03 Jun 2019 02:13:06: 25000000 INFO @ Mon, 03 Jun 2019 02:13:13: 24000000 INFO @ Mon, 03 Jun 2019 02:13:13: 26000000 INFO @ Mon, 03 Jun 2019 02:13:14: 24000000 INFO @ Mon, 03 Jun 2019 02:13:21: 27000000 INFO @ Mon, 03 Jun 2019 02:13:22: 25000000 INFO @ Mon, 03 Jun 2019 02:13:22: 25000000 INFO @ Mon, 03 Jun 2019 02:13:29: 28000000 INFO @ Mon, 03 Jun 2019 02:13:30: 26000000 INFO @ Mon, 03 Jun 2019 02:13:32: 26000000 INFO @ Mon, 03 Jun 2019 02:13:33: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:13:33: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:13:33: #1 total tags in treatment: 28557911 INFO @ Mon, 03 Jun 2019 02:13:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:13:33: #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 02:13:34: #1 tags after filtering in treatment: 28557911 INFO @ Mon, 03 Jun 2019 02:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:13:34: #1 finished! INFO @ Mon, 03 Jun 2019 02:13:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:13:37: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 02:13:37: 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 @ Mon, 03 Jun 2019 02:13:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.05_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/SRX104983/SRX104983.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:13:39: 27000000 INFO @ Mon, 03 Jun 2019 02:13:40: 27000000 INFO @ Mon, 03 Jun 2019 02:13:47: 28000000 INFO @ Mon, 03 Jun 2019 02:13:49: 28000000 INFO @ Mon, 03 Jun 2019 02:13:51: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:13:51: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:13:51: #1 total tags in treatment: 28557911 INFO @ Mon, 03 Jun 2019 02:13:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:13:51: #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 02:13:52: #1 tags after filtering in treatment: 28557911 INFO @ Mon, 03 Jun 2019 02:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:13:52: #1 finished! INFO @ Mon, 03 Jun 2019 02:13:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:13:54: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:13:54: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:13:54: #1 total tags in treatment: 28557911 INFO @ Mon, 03 Jun 2019 02:13:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:13:54: #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 02:13:55: #1 tags after filtering in treatment: 28557911 INFO @ Mon, 03 Jun 2019 02:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:13:55: #1 finished! INFO @ Mon, 03 Jun 2019 02:13:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:13:55: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 02:13:55: 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 @ Mon, 03 Jun 2019 02:13:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.10_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/SRX104983/SRX104983.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:13:57: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 02:13:57: 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 @ Mon, 03 Jun 2019 02:13:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.20_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/SRX104983/SRX104983.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX104983/SRX104983.20_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。