Job ID = 2590335 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,536,788 reads read : 27,073,576 reads written : 13,536,788 reads 0-length : 13,536,788 2019-08-12T11:53:18 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 ) 2019-08-12T11:53:18 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 ) 2019-08-12T11:53:18 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 ) 2019-08-12T11:53:18 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 : 13,320,276 reads read : 26,640,552 reads written : 13,320,276 reads 0-length : 13,320,276 spots read : 13,518,222 reads read : 27,036,444 reads written : 13,518,222 reads 0-length : 13,518,222 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: 00:15:22 40375286 reads; of these: 40375286 (100.00%) were unpaired; of these: 1275672 (3.16%) aligned 0 times 28342137 (70.20%) aligned exactly 1 time 10757477 (26.64%) aligned >1 times 96.84% overall alignment rate Time searching: 00:15:22 Overall time: 00:15:22 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 16 files... [bam_rmdupse_core] 4438965 / 39099614 = 0.1135 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, 12 Aug 2019 21:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.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, 12 Aug 2019 21:26:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.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, 12 Aug 2019 21:26:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.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, 12 Aug 2019 21:26:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:26:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:26:49: 1000000 INFO @ Mon, 12 Aug 2019 21:26:49: 1000000 INFO @ Mon, 12 Aug 2019 21:26:50: 1000000 INFO @ Mon, 12 Aug 2019 21:26:57: 2000000 INFO @ Mon, 12 Aug 2019 21:26:58: 2000000 INFO @ Mon, 12 Aug 2019 21:26:59: 2000000 INFO @ Mon, 12 Aug 2019 21:27:03: 3000000 INFO @ Mon, 12 Aug 2019 21:27:07: 3000000 INFO @ Mon, 12 Aug 2019 21:27:08: 3000000 INFO @ Mon, 12 Aug 2019 21:27:10: 4000000 INFO @ Mon, 12 Aug 2019 21:27:16: 4000000 INFO @ Mon, 12 Aug 2019 21:27:17: 4000000 INFO @ Mon, 12 Aug 2019 21:27:17: 5000000 INFO @ Mon, 12 Aug 2019 21:27:24: 6000000 INFO @ Mon, 12 Aug 2019 21:27:25: 5000000 INFO @ Mon, 12 Aug 2019 21:27:26: 5000000 INFO @ Mon, 12 Aug 2019 21:27:31: 7000000 INFO @ Mon, 12 Aug 2019 21:27:34: 6000000 INFO @ Mon, 12 Aug 2019 21:27:35: 6000000 INFO @ Mon, 12 Aug 2019 21:27:38: 8000000 INFO @ Mon, 12 Aug 2019 21:27:43: 7000000 INFO @ Mon, 12 Aug 2019 21:27:44: 7000000 INFO @ Mon, 12 Aug 2019 21:27:45: 9000000 INFO @ Mon, 12 Aug 2019 21:27:51: 8000000 INFO @ Mon, 12 Aug 2019 21:27:52: 10000000 INFO @ Mon, 12 Aug 2019 21:27:53: 8000000 INFO @ Mon, 12 Aug 2019 21:27:58: 11000000 INFO @ Mon, 12 Aug 2019 21:28:00: 9000000 INFO @ Mon, 12 Aug 2019 21:28:02: 9000000 INFO @ Mon, 12 Aug 2019 21:28:05: 12000000 INFO @ Mon, 12 Aug 2019 21:28:09: 10000000 INFO @ Mon, 12 Aug 2019 21:28:11: 10000000 INFO @ Mon, 12 Aug 2019 21:28:12: 13000000 INFO @ Mon, 12 Aug 2019 21:28:18: 11000000 INFO @ Mon, 12 Aug 2019 21:28:19: 14000000 INFO @ Mon, 12 Aug 2019 21:28:20: 11000000 INFO @ Mon, 12 Aug 2019 21:28:26: 15000000 INFO @ Mon, 12 Aug 2019 21:28:27: 12000000 INFO @ Mon, 12 Aug 2019 21:28:29: 12000000 INFO @ Mon, 12 Aug 2019 21:28:33: 16000000 INFO @ Mon, 12 Aug 2019 21:28:36: 13000000 INFO @ Mon, 12 Aug 2019 21:28:38: 13000000 INFO @ Mon, 12 Aug 2019 21:28:40: 17000000 INFO @ Mon, 12 Aug 2019 21:28:44: 14000000 INFO @ Mon, 12 Aug 2019 21:28:46: 14000000 INFO @ Mon, 12 Aug 2019 21:28:47: 18000000 INFO @ Mon, 12 Aug 2019 21:28:53: 15000000 INFO @ Mon, 12 Aug 2019 21:28:53: 19000000 INFO @ Mon, 12 Aug 2019 21:28:55: 15000000 INFO @ Mon, 12 Aug 2019 21:29:00: 20000000 INFO @ Mon, 12 Aug 2019 21:29:02: 16000000 INFO @ Mon, 12 Aug 2019 21:29:04: 16000000 INFO @ Mon, 12 Aug 2019 21:29:07: 21000000 INFO @ Mon, 12 Aug 2019 21:29:11: 17000000 INFO @ Mon, 12 Aug 2019 21:29:13: 17000000 INFO @ Mon, 12 Aug 2019 21:29:14: 22000000 INFO @ Mon, 12 Aug 2019 21:29:19: 18000000 INFO @ Mon, 12 Aug 2019 21:29:21: 23000000 INFO @ Mon, 12 Aug 2019 21:29:22: 18000000 INFO @ Mon, 12 Aug 2019 21:29:28: 24000000 INFO @ Mon, 12 Aug 2019 21:29:28: 19000000 INFO @ Mon, 12 Aug 2019 21:29:30: 19000000 INFO @ Mon, 12 Aug 2019 21:29:35: 25000000 INFO @ Mon, 12 Aug 2019 21:29:37: 20000000 INFO @ Mon, 12 Aug 2019 21:29:39: 20000000 INFO @ Mon, 12 Aug 2019 21:29:41: 26000000 INFO @ Mon, 12 Aug 2019 21:29:46: 21000000 INFO @ Mon, 12 Aug 2019 21:29:48: 21000000 INFO @ Mon, 12 Aug 2019 21:29:48: 27000000 INFO @ Mon, 12 Aug 2019 21:29:54: 22000000 INFO @ Mon, 12 Aug 2019 21:29:55: 28000000 INFO @ Mon, 12 Aug 2019 21:29:57: 22000000 INFO @ Mon, 12 Aug 2019 21:30:02: 29000000 INFO @ Mon, 12 Aug 2019 21:30:03: 23000000 INFO @ Mon, 12 Aug 2019 21:30:06: 23000000 INFO @ Mon, 12 Aug 2019 21:30:09: 30000000 INFO @ Mon, 12 Aug 2019 21:30:12: 24000000 INFO @ Mon, 12 Aug 2019 21:30:14: 24000000 INFO @ Mon, 12 Aug 2019 21:30:16: 31000000 INFO @ Mon, 12 Aug 2019 21:30:21: 25000000 INFO @ Mon, 12 Aug 2019 21:30:22: 32000000 INFO @ Mon, 12 Aug 2019 21:30:23: 25000000 INFO @ Mon, 12 Aug 2019 21:30:29: 33000000 INFO @ Mon, 12 Aug 2019 21:30:29: 26000000 INFO @ Mon, 12 Aug 2019 21:30:32: 26000000 INFO @ Mon, 12 Aug 2019 21:30:36: 34000000 INFO @ Mon, 12 Aug 2019 21:30:38: 27000000 INFO @ Mon, 12 Aug 2019 21:30:41: 27000000 INFO @ Mon, 12 Aug 2019 21:30:41: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:30:41: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:30:41: #1 total tags in treatment: 34660649 INFO @ Mon, 12 Aug 2019 21:30:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:30:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:30:42: #1 tags after filtering in treatment: 34660649 INFO @ Mon, 12 Aug 2019 21:30:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:30:42: #1 finished! INFO @ Mon, 12 Aug 2019 21:30:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:30:45: #2 number of paired peaks: 24 WARNING @ Mon, 12 Aug 2019 21:30:45: Too few paired peaks (24) 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, 12 Aug 2019 21:30:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.20_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/SRX3981612/SRX3981612.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:30:47: 28000000 INFO @ Mon, 12 Aug 2019 21:30:49: 28000000 INFO @ Mon, 12 Aug 2019 21:30:56: 29000000 INFO @ Mon, 12 Aug 2019 21:30:58: 29000000 INFO @ Mon, 12 Aug 2019 21:31:04: 30000000 INFO @ Mon, 12 Aug 2019 21:31:07: 30000000 INFO @ Mon, 12 Aug 2019 21:31:13: 31000000 INFO @ Mon, 12 Aug 2019 21:31:16: 31000000 INFO @ Mon, 12 Aug 2019 21:31:22: 32000000 INFO @ Mon, 12 Aug 2019 21:31:24: 32000000 INFO @ Mon, 12 Aug 2019 21:31:31: 33000000 INFO @ Mon, 12 Aug 2019 21:31:33: 33000000 INFO @ Mon, 12 Aug 2019 21:31:39: 34000000 INFO @ Mon, 12 Aug 2019 21:31:42: 34000000 INFO @ Mon, 12 Aug 2019 21:31:45: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:31:45: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:31:45: #1 total tags in treatment: 34660649 INFO @ Mon, 12 Aug 2019 21:31:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:31:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:31:46: #1 tags after filtering in treatment: 34660649 INFO @ Mon, 12 Aug 2019 21:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:31:46: #1 finished! INFO @ Mon, 12 Aug 2019 21:31:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:31:48: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:31:48: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:31:48: #1 total tags in treatment: 34660649 INFO @ Mon, 12 Aug 2019 21:31:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:31:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:31:48: #1 tags after filtering in treatment: 34660649 INFO @ Mon, 12 Aug 2019 21:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:31:48: #1 finished! INFO @ Mon, 12 Aug 2019 21:31:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:31:49: #2 number of paired peaks: 24 WARNING @ Mon, 12 Aug 2019 21:31:49: Too few paired peaks (24) 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, 12 Aug 2019 21:31:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.05_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/SRX3981612/SRX3981612.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:31:51: #2 number of paired peaks: 24 WARNING @ Mon, 12 Aug 2019 21:31:51: Too few paired peaks (24) 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, 12 Aug 2019 21:31:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.10_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/SRX3981612/SRX3981612.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3981612/SRX3981612.10_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。