Job ID = 1302895 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:20:41 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 ) 2019-06-03T11:20:41 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 ) 2019-06-03T11:27:28 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 ) 2019-06-03T11:33:16 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T11:36:57 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 : 50,628,630 reads read : 50,628,630 reads written : 50,628,630 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: 00:21:20 50628630 reads; of these: 50628630 (100.00%) were unpaired; of these: 1379393 (2.72%) aligned 0 times 34910619 (68.95%) aligned exactly 1 time 14338618 (28.32%) aligned >1 times 97.28% overall alignment rate Time searching: 00:21:20 Overall time: 00:21:20 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 24 files... [bam_rmdupse_core] 9586627 / 49249237 = 0.1947 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 21:20:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.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 21:20:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:20:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.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 21:20:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:20:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.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 21:20:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:20:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:20:43: 1000000 INFO @ Mon, 03 Jun 2019 21:20:46: 1000000 INFO @ Mon, 03 Jun 2019 21:20:47: 1000000 INFO @ Mon, 03 Jun 2019 21:20:52: 2000000 INFO @ Mon, 03 Jun 2019 21:20:57: 2000000 INFO @ Mon, 03 Jun 2019 21:20:59: 2000000 INFO @ Mon, 03 Jun 2019 21:21:01: 3000000 INFO @ Mon, 03 Jun 2019 21:21:06: 3000000 INFO @ Mon, 03 Jun 2019 21:21:09: 4000000 INFO @ Mon, 03 Jun 2019 21:21:11: 3000000 INFO @ Mon, 03 Jun 2019 21:21:16: 5000000 INFO @ Mon, 03 Jun 2019 21:21:17: 4000000 INFO @ Mon, 03 Jun 2019 21:21:23: 4000000 INFO @ Mon, 03 Jun 2019 21:21:24: 6000000 INFO @ Mon, 03 Jun 2019 21:21:28: 5000000 INFO @ Mon, 03 Jun 2019 21:21:32: 7000000 INFO @ Mon, 03 Jun 2019 21:21:34: 5000000 INFO @ Mon, 03 Jun 2019 21:21:39: 6000000 INFO @ Mon, 03 Jun 2019 21:21:40: 8000000 INFO @ Mon, 03 Jun 2019 21:21:46: 6000000 INFO @ Mon, 03 Jun 2019 21:21:48: 9000000 INFO @ Mon, 03 Jun 2019 21:21:51: 7000000 INFO @ Mon, 03 Jun 2019 21:21:56: 10000000 INFO @ Mon, 03 Jun 2019 21:21:58: 7000000 INFO @ Mon, 03 Jun 2019 21:22:02: 8000000 INFO @ Mon, 03 Jun 2019 21:22:04: 11000000 INFO @ Mon, 03 Jun 2019 21:22:10: 8000000 INFO @ Mon, 03 Jun 2019 21:22:12: 9000000 INFO @ Mon, 03 Jun 2019 21:22:12: 12000000 INFO @ Mon, 03 Jun 2019 21:22:20: 9000000 INFO @ Mon, 03 Jun 2019 21:22:20: 13000000 INFO @ Mon, 03 Jun 2019 21:22:22: 10000000 INFO @ Mon, 03 Jun 2019 21:22:28: 14000000 INFO @ Mon, 03 Jun 2019 21:22:31: 10000000 INFO @ Mon, 03 Jun 2019 21:22:33: 11000000 INFO @ Mon, 03 Jun 2019 21:22:36: 15000000 INFO @ Mon, 03 Jun 2019 21:22:43: 12000000 INFO @ Mon, 03 Jun 2019 21:22:43: 11000000 INFO @ Mon, 03 Jun 2019 21:22:44: 16000000 INFO @ Mon, 03 Jun 2019 21:22:52: 17000000 INFO @ Mon, 03 Jun 2019 21:22:53: 13000000 INFO @ Mon, 03 Jun 2019 21:22:55: 12000000 INFO @ Mon, 03 Jun 2019 21:23:00: 18000000 INFO @ Mon, 03 Jun 2019 21:23:03: 14000000 INFO @ Mon, 03 Jun 2019 21:23:07: 13000000 INFO @ Mon, 03 Jun 2019 21:23:08: 19000000 INFO @ Mon, 03 Jun 2019 21:23:14: 15000000 INFO @ Mon, 03 Jun 2019 21:23:16: 20000000 INFO @ Mon, 03 Jun 2019 21:23:18: 14000000 INFO @ Mon, 03 Jun 2019 21:23:24: 16000000 INFO @ Mon, 03 Jun 2019 21:23:24: 21000000 INFO @ Mon, 03 Jun 2019 21:23:30: 15000000 INFO @ Mon, 03 Jun 2019 21:23:32: 22000000 INFO @ Mon, 03 Jun 2019 21:23:34: 17000000 INFO @ Mon, 03 Jun 2019 21:23:40: 23000000 INFO @ Mon, 03 Jun 2019 21:23:42: 16000000 INFO @ Mon, 03 Jun 2019 21:23:43: 18000000 INFO @ Mon, 03 Jun 2019 21:23:48: 24000000 INFO @ Mon, 03 Jun 2019 21:23:53: 17000000 INFO @ Mon, 03 Jun 2019 21:23:54: 19000000 INFO @ Mon, 03 Jun 2019 21:23:55: 25000000 INFO @ Mon, 03 Jun 2019 21:24:03: 26000000 INFO @ Mon, 03 Jun 2019 21:24:04: 20000000 INFO @ Mon, 03 Jun 2019 21:24:04: 18000000 INFO @ Mon, 03 Jun 2019 21:24:11: 27000000 INFO @ Mon, 03 Jun 2019 21:24:14: 21000000 INFO @ Mon, 03 Jun 2019 21:24:17: 19000000 INFO @ Mon, 03 Jun 2019 21:24:19: 28000000 INFO @ Mon, 03 Jun 2019 21:24:24: 22000000 INFO @ Mon, 03 Jun 2019 21:24:27: 29000000 INFO @ Mon, 03 Jun 2019 21:24:29: 20000000 INFO @ Mon, 03 Jun 2019 21:24:35: 30000000 INFO @ Mon, 03 Jun 2019 21:24:35: 23000000 INFO @ Mon, 03 Jun 2019 21:24:41: 21000000 INFO @ Mon, 03 Jun 2019 21:24:43: 31000000 INFO @ Mon, 03 Jun 2019 21:24:45: 24000000 INFO @ Mon, 03 Jun 2019 21:24:51: 32000000 INFO @ Mon, 03 Jun 2019 21:24:53: 22000000 INFO @ Mon, 03 Jun 2019 21:24:56: 25000000 INFO @ Mon, 03 Jun 2019 21:24:59: 33000000 INFO @ Mon, 03 Jun 2019 21:25:05: 23000000 INFO @ Mon, 03 Jun 2019 21:25:06: 26000000 INFO @ Mon, 03 Jun 2019 21:25:07: 34000000 INFO @ Mon, 03 Jun 2019 21:25:15: 35000000 INFO @ Mon, 03 Jun 2019 21:25:16: 24000000 INFO @ Mon, 03 Jun 2019 21:25:16: 27000000 INFO @ Mon, 03 Jun 2019 21:25:23: 36000000 INFO @ Mon, 03 Jun 2019 21:25:26: 28000000 INFO @ Mon, 03 Jun 2019 21:25:27: 25000000 INFO @ Mon, 03 Jun 2019 21:25:31: 37000000 INFO @ Mon, 03 Jun 2019 21:25:36: 29000000 INFO @ Mon, 03 Jun 2019 21:25:38: 26000000 INFO @ Mon, 03 Jun 2019 21:25:39: 38000000 INFO @ Mon, 03 Jun 2019 21:25:46: 30000000 INFO @ Mon, 03 Jun 2019 21:25:47: 39000000 INFO @ Mon, 03 Jun 2019 21:25:49: 27000000 INFO @ Mon, 03 Jun 2019 21:25:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:25:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:25:53: #1 total tags in treatment: 39662610 INFO @ Mon, 03 Jun 2019 21:25:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:25:53: #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 21:25:54: #1 tags after filtering in treatment: 39662610 INFO @ Mon, 03 Jun 2019 21:25:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:25:54: #1 finished! INFO @ Mon, 03 Jun 2019 21:25:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:25:57: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 21:25:57: Too few paired peaks (2) 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 21:25:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.05_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/SRX4933896/SRX4933896.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:25:57: 31000000 INFO @ Mon, 03 Jun 2019 21:26:00: 28000000 INFO @ Mon, 03 Jun 2019 21:26:08: 32000000 INFO @ Mon, 03 Jun 2019 21:26:10: 29000000 INFO @ Mon, 03 Jun 2019 21:26:18: 33000000 INFO @ Mon, 03 Jun 2019 21:26:22: 30000000 INFO @ Mon, 03 Jun 2019 21:26:28: 34000000 INFO @ Mon, 03 Jun 2019 21:26:33: 31000000 INFO @ Mon, 03 Jun 2019 21:26:38: 35000000 INFO @ Mon, 03 Jun 2019 21:26:44: 32000000 INFO @ Mon, 03 Jun 2019 21:26:48: 36000000 INFO @ Mon, 03 Jun 2019 21:26:55: 33000000 INFO @ Mon, 03 Jun 2019 21:26:58: 37000000 INFO @ Mon, 03 Jun 2019 21:27:06: 34000000 INFO @ Mon, 03 Jun 2019 21:27:08: 38000000 INFO @ Mon, 03 Jun 2019 21:27:17: 35000000 INFO @ Mon, 03 Jun 2019 21:27:18: 39000000 INFO @ Mon, 03 Jun 2019 21:27:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:27:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:27:25: #1 total tags in treatment: 39662610 INFO @ Mon, 03 Jun 2019 21:27:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:27:25: #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 21:27:25: #1 tags after filtering in treatment: 39662610 INFO @ Mon, 03 Jun 2019 21:27:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:27:25: #1 finished! INFO @ Mon, 03 Jun 2019 21:27:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:27:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:27:28: 36000000 INFO @ Mon, 03 Jun 2019 21:27:29: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 21:27:29: Too few paired peaks (2) 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 21:27:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.20_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/SRX4933896/SRX4933896.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:27:39: 37000000 INFO @ Mon, 03 Jun 2019 21:27:49: 38000000 INFO @ Mon, 03 Jun 2019 21:28:00: 39000000 INFO @ Mon, 03 Jun 2019 21:28:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 21:28:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 21:28:08: #1 total tags in treatment: 39662610 INFO @ Mon, 03 Jun 2019 21:28:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:28:08: #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 21:28:08: #1 tags after filtering in treatment: 39662610 INFO @ Mon, 03 Jun 2019 21:28:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:28:08: #1 finished! INFO @ Mon, 03 Jun 2019 21:28:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:28:12: #2 number of paired peaks: 2 WARNING @ Mon, 03 Jun 2019 21:28:12: Too few paired peaks (2) 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 21:28:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.10_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/SRX4933896/SRX4933896.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4933896/SRX4933896.10_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。