Job ID = 1293703 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,529,054 reads read : 22,529,054 reads written : 22,529,054 2019-06-02T16:58:07 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 ) 2019-06-02T16:58:07 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 ) 2019-06-02T16:58:07 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 ) 2019-06-02T16:58:07 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 ) 2019-06-02T17:00:01 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 ) 2019-06-02T17:05:33 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 : 23,821,087 reads read : 23,821,087 reads written : 23,821,087 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: 00:13:35 46350141 reads; of these: 46350141 (100.00%) were unpaired; of these: 4933579 (10.64%) aligned 0 times 31950016 (68.93%) aligned exactly 1 time 9466546 (20.42%) aligned >1 times 89.36% overall alignment rate Time searching: 00:13:35 Overall time: 00:13:35 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] 13800455 / 41416562 = 0.3332 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 02:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.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 02:31:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:31:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.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 02:31:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:31:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.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 02:31:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:31:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:31:18: 1000000 INFO @ Mon, 03 Jun 2019 02:31:18: 1000000 INFO @ Mon, 03 Jun 2019 02:31:18: 1000000 INFO @ Mon, 03 Jun 2019 02:31:26: 2000000 INFO @ Mon, 03 Jun 2019 02:31:26: 2000000 INFO @ Mon, 03 Jun 2019 02:31:26: 2000000 INFO @ Mon, 03 Jun 2019 02:31:33: 3000000 INFO @ Mon, 03 Jun 2019 02:31:34: 3000000 INFO @ Mon, 03 Jun 2019 02:31:34: 3000000 INFO @ Mon, 03 Jun 2019 02:31:41: 4000000 INFO @ Mon, 03 Jun 2019 02:31:42: 4000000 INFO @ Mon, 03 Jun 2019 02:31:42: 4000000 INFO @ Mon, 03 Jun 2019 02:31:48: 5000000 INFO @ Mon, 03 Jun 2019 02:31:49: 5000000 INFO @ Mon, 03 Jun 2019 02:31:49: 5000000 INFO @ Mon, 03 Jun 2019 02:31:56: 6000000 INFO @ Mon, 03 Jun 2019 02:31:57: 6000000 INFO @ Mon, 03 Jun 2019 02:31:57: 6000000 INFO @ Mon, 03 Jun 2019 02:32:04: 7000000 INFO @ Mon, 03 Jun 2019 02:32:05: 7000000 INFO @ Mon, 03 Jun 2019 02:32:05: 7000000 INFO @ Mon, 03 Jun 2019 02:32:11: 8000000 INFO @ Mon, 03 Jun 2019 02:32:13: 8000000 INFO @ Mon, 03 Jun 2019 02:32:13: 8000000 INFO @ Mon, 03 Jun 2019 02:32:19: 9000000 INFO @ Mon, 03 Jun 2019 02:32:21: 9000000 INFO @ Mon, 03 Jun 2019 02:32:22: 9000000 INFO @ Mon, 03 Jun 2019 02:32:27: 10000000 INFO @ Mon, 03 Jun 2019 02:32:30: 10000000 INFO @ Mon, 03 Jun 2019 02:32:30: 10000000 INFO @ Mon, 03 Jun 2019 02:32:34: 11000000 INFO @ Mon, 03 Jun 2019 02:32:37: 11000000 INFO @ Mon, 03 Jun 2019 02:32:38: 11000000 INFO @ Mon, 03 Jun 2019 02:32:42: 12000000 INFO @ Mon, 03 Jun 2019 02:32:45: 12000000 INFO @ Mon, 03 Jun 2019 02:32:45: 12000000 INFO @ Mon, 03 Jun 2019 02:32:49: 13000000 INFO @ Mon, 03 Jun 2019 02:32:53: 13000000 INFO @ Mon, 03 Jun 2019 02:32:53: 13000000 INFO @ Mon, 03 Jun 2019 02:32:57: 14000000 INFO @ Mon, 03 Jun 2019 02:33:01: 14000000 INFO @ Mon, 03 Jun 2019 02:33:01: 14000000 INFO @ Mon, 03 Jun 2019 02:33:05: 15000000 INFO @ Mon, 03 Jun 2019 02:33:09: 15000000 INFO @ Mon, 03 Jun 2019 02:33:09: 15000000 INFO @ Mon, 03 Jun 2019 02:33:13: 16000000 INFO @ Mon, 03 Jun 2019 02:33:16: 16000000 INFO @ Mon, 03 Jun 2019 02:33:17: 16000000 INFO @ Mon, 03 Jun 2019 02:33:21: 17000000 INFO @ Mon, 03 Jun 2019 02:33:24: 17000000 INFO @ Mon, 03 Jun 2019 02:33:24: 17000000 INFO @ Mon, 03 Jun 2019 02:33:29: 18000000 INFO @ Mon, 03 Jun 2019 02:33:31: 18000000 INFO @ Mon, 03 Jun 2019 02:33:31: 18000000 INFO @ Mon, 03 Jun 2019 02:33:36: 19000000 INFO @ Mon, 03 Jun 2019 02:33:40: 19000000 INFO @ Mon, 03 Jun 2019 02:33:40: 19000000 INFO @ Mon, 03 Jun 2019 02:33:44: 20000000 INFO @ Mon, 03 Jun 2019 02:33:48: 20000000 INFO @ Mon, 03 Jun 2019 02:33:48: 20000000 INFO @ Mon, 03 Jun 2019 02:33:52: 21000000 INFO @ Mon, 03 Jun 2019 02:33:56: 21000000 INFO @ Mon, 03 Jun 2019 02:33:56: 21000000 INFO @ Mon, 03 Jun 2019 02:34:00: 22000000 INFO @ Mon, 03 Jun 2019 02:34:05: 22000000 INFO @ Mon, 03 Jun 2019 02:34:05: 22000000 INFO @ Mon, 03 Jun 2019 02:34:08: 23000000 INFO @ Mon, 03 Jun 2019 02:34:13: 23000000 INFO @ Mon, 03 Jun 2019 02:34:13: 23000000 INFO @ Mon, 03 Jun 2019 02:34:16: 24000000 INFO @ Mon, 03 Jun 2019 02:34:21: 24000000 INFO @ Mon, 03 Jun 2019 02:34:22: 24000000 INFO @ Mon, 03 Jun 2019 02:34:23: 25000000 INFO @ Mon, 03 Jun 2019 02:34:29: 25000000 INFO @ Mon, 03 Jun 2019 02:34:30: 25000000 INFO @ Mon, 03 Jun 2019 02:34:31: 26000000 INFO @ Mon, 03 Jun 2019 02:34:37: 26000000 INFO @ Mon, 03 Jun 2019 02:34:37: 26000000 INFO @ Mon, 03 Jun 2019 02:34:39: 27000000 INFO @ Mon, 03 Jun 2019 02:34:44: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:34:44: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:34:44: #1 total tags in treatment: 27616107 INFO @ Mon, 03 Jun 2019 02:34:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:44: #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 02:34:44: #1 tags after filtering in treatment: 27616107 INFO @ Mon, 03 Jun 2019 02:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:44: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:45: 27000000 INFO @ Mon, 03 Jun 2019 02:34:45: 27000000 INFO @ Mon, 03 Jun 2019 02:34:46: #2 number of paired peaks: 1 WARNING @ Mon, 03 Jun 2019 02:34:46: Too few paired peaks (1) 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 02:34:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:34:50: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:34:50: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:34:50: #1 total tags in treatment: 27616107 INFO @ Mon, 03 Jun 2019 02:34:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:50: #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 02:34:50: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:34:50: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:34:50: #1 total tags in treatment: 27616107 INFO @ Mon, 03 Jun 2019 02:34:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:34:50: #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 02:34:51: #1 tags after filtering in treatment: 27616107 INFO @ Mon, 03 Jun 2019 02:34:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:51: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:51: #1 tags after filtering in treatment: 27616107 INFO @ Mon, 03 Jun 2019 02:34:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:34:51: #1 finished! INFO @ Mon, 03 Jun 2019 02:34:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:34:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:34:53: #2 number of paired peaks: 1 WARNING @ Mon, 03 Jun 2019 02:34:53: Too few paired peaks (1) 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 02:34:53: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 02:34:53: #2 number of paired peaks: 1 WARNING @ Mon, 03 Jun 2019 02:34:53: Too few paired peaks (1) 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 02:34:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.10_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/SRX111783/SRX111783.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111783/SRX111783.10_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。