Job ID = 1294059 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:33:29 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 ) 2019-06-02T19:37:19 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 ) 2019-06-02T19:37:19 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 ) 2019-06-02T19:41:20 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 ) 2019-06-02T19:43:08 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 : 60,802,012 reads read : 60,802,012 reads written : 60,802,012 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: 00:20:51 60802012 reads; of these: 60802012 (100.00%) were unpaired; of these: 12624689 (20.76%) aligned 0 times 31023870 (51.02%) aligned exactly 1 time 17153453 (28.21%) aligned >1 times 79.24% overall alignment rate Time searching: 00:20:51 Overall time: 00:20:51 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 20 files... [bam_rmdupse_core] 9517926 / 48177323 = 0.1976 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 05:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.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 05:33:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:33:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.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 05:33:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:33:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.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 05:33:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:33:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:34:05: 1000000 INFO @ Mon, 03 Jun 2019 05:34:07: 1000000 INFO @ Mon, 03 Jun 2019 05:34:07: 1000000 INFO @ Mon, 03 Jun 2019 05:34:14: 2000000 INFO @ Mon, 03 Jun 2019 05:34:18: 2000000 INFO @ Mon, 03 Jun 2019 05:34:18: 2000000 INFO @ Mon, 03 Jun 2019 05:34:23: 3000000 INFO @ Mon, 03 Jun 2019 05:34:28: 3000000 INFO @ Mon, 03 Jun 2019 05:34:29: 3000000 INFO @ Mon, 03 Jun 2019 05:34:31: 4000000 INFO @ Mon, 03 Jun 2019 05:34:38: 4000000 INFO @ Mon, 03 Jun 2019 05:34:39: 4000000 INFO @ Mon, 03 Jun 2019 05:34:40: 5000000 INFO @ Mon, 03 Jun 2019 05:34:48: 5000000 INFO @ Mon, 03 Jun 2019 05:34:49: 6000000 INFO @ Mon, 03 Jun 2019 05:34:50: 5000000 INFO @ Mon, 03 Jun 2019 05:34:58: 7000000 INFO @ Mon, 03 Jun 2019 05:34:59: 6000000 INFO @ Mon, 03 Jun 2019 05:35:00: 6000000 INFO @ Mon, 03 Jun 2019 05:35:06: 8000000 INFO @ Mon, 03 Jun 2019 05:35:09: 7000000 INFO @ Mon, 03 Jun 2019 05:35:10: 7000000 INFO @ Mon, 03 Jun 2019 05:35:15: 9000000 INFO @ Mon, 03 Jun 2019 05:35:19: 8000000 INFO @ Mon, 03 Jun 2019 05:35:20: 8000000 INFO @ Mon, 03 Jun 2019 05:35:23: 10000000 INFO @ Mon, 03 Jun 2019 05:35:29: 9000000 INFO @ Mon, 03 Jun 2019 05:35:31: 9000000 INFO @ Mon, 03 Jun 2019 05:35:32: 11000000 INFO @ Mon, 03 Jun 2019 05:35:39: 10000000 INFO @ Mon, 03 Jun 2019 05:35:41: 10000000 INFO @ Mon, 03 Jun 2019 05:35:41: 12000000 INFO @ Mon, 03 Jun 2019 05:35:49: 11000000 INFO @ Mon, 03 Jun 2019 05:35:50: 13000000 INFO @ Mon, 03 Jun 2019 05:35:51: 11000000 INFO @ Mon, 03 Jun 2019 05:35:58: 14000000 INFO @ Mon, 03 Jun 2019 05:35:59: 12000000 INFO @ Mon, 03 Jun 2019 05:36:02: 12000000 INFO @ Mon, 03 Jun 2019 05:36:07: 15000000 INFO @ Mon, 03 Jun 2019 05:36:09: 13000000 INFO @ Mon, 03 Jun 2019 05:36:12: 13000000 INFO @ Mon, 03 Jun 2019 05:36:15: 16000000 INFO @ Mon, 03 Jun 2019 05:36:19: 14000000 INFO @ Mon, 03 Jun 2019 05:36:23: 14000000 INFO @ Mon, 03 Jun 2019 05:36:24: 17000000 INFO @ Mon, 03 Jun 2019 05:36:29: 15000000 INFO @ Mon, 03 Jun 2019 05:36:33: 18000000 INFO @ Mon, 03 Jun 2019 05:36:33: 15000000 INFO @ Mon, 03 Jun 2019 05:36:39: 16000000 INFO @ Mon, 03 Jun 2019 05:36:41: 19000000 INFO @ Mon, 03 Jun 2019 05:36:43: 16000000 INFO @ Mon, 03 Jun 2019 05:36:49: 17000000 INFO @ Mon, 03 Jun 2019 05:36:50: 20000000 INFO @ Mon, 03 Jun 2019 05:36:53: 17000000 INFO @ Mon, 03 Jun 2019 05:36:59: 21000000 INFO @ Mon, 03 Jun 2019 05:36:59: 18000000 INFO @ Mon, 03 Jun 2019 05:37:03: 18000000 INFO @ Mon, 03 Jun 2019 05:37:07: 22000000 INFO @ Mon, 03 Jun 2019 05:37:09: 19000000 INFO @ Mon, 03 Jun 2019 05:37:14: 19000000 INFO @ Mon, 03 Jun 2019 05:37:16: 23000000 INFO @ Mon, 03 Jun 2019 05:37:19: 20000000 INFO @ Mon, 03 Jun 2019 05:37:24: 20000000 INFO @ Mon, 03 Jun 2019 05:37:25: 24000000 INFO @ Mon, 03 Jun 2019 05:37:29: 21000000 INFO @ Mon, 03 Jun 2019 05:37:34: 25000000 INFO @ Mon, 03 Jun 2019 05:37:34: 21000000 INFO @ Mon, 03 Jun 2019 05:37:39: 22000000 INFO @ Mon, 03 Jun 2019 05:37:43: 26000000 INFO @ Mon, 03 Jun 2019 05:37:45: 22000000 INFO @ Mon, 03 Jun 2019 05:37:49: 23000000 INFO @ Mon, 03 Jun 2019 05:37:51: 27000000 INFO @ Mon, 03 Jun 2019 05:37:56: 23000000 INFO @ Mon, 03 Jun 2019 05:38:00: 24000000 INFO @ Mon, 03 Jun 2019 05:38:00: 28000000 INFO @ Mon, 03 Jun 2019 05:38:07: 24000000 INFO @ Mon, 03 Jun 2019 05:38:09: 29000000 INFO @ Mon, 03 Jun 2019 05:38:10: 25000000 INFO @ Mon, 03 Jun 2019 05:38:17: 25000000 INFO @ Mon, 03 Jun 2019 05:38:18: 30000000 INFO @ Mon, 03 Jun 2019 05:38:20: 26000000 INFO @ Mon, 03 Jun 2019 05:38:26: 31000000 INFO @ Mon, 03 Jun 2019 05:38:27: 26000000 INFO @ Mon, 03 Jun 2019 05:38:30: 27000000 INFO @ Mon, 03 Jun 2019 05:38:35: 32000000 INFO @ Mon, 03 Jun 2019 05:38:37: 27000000 INFO @ Mon, 03 Jun 2019 05:38:40: 28000000 INFO @ Mon, 03 Jun 2019 05:38:44: 33000000 INFO @ Mon, 03 Jun 2019 05:38:47: 28000000 INFO @ Mon, 03 Jun 2019 05:38:50: 29000000 INFO @ Mon, 03 Jun 2019 05:38:53: 34000000 INFO @ Mon, 03 Jun 2019 05:38:58: 29000000 INFO @ Mon, 03 Jun 2019 05:39:01: 30000000 INFO @ Mon, 03 Jun 2019 05:39:02: 35000000 INFO @ Mon, 03 Jun 2019 05:39:08: 30000000 INFO @ Mon, 03 Jun 2019 05:39:11: 31000000 INFO @ Mon, 03 Jun 2019 05:39:12: 36000000 INFO @ Mon, 03 Jun 2019 05:39:19: 31000000 INFO @ Mon, 03 Jun 2019 05:39:21: 37000000 INFO @ Mon, 03 Jun 2019 05:39:22: 32000000 INFO @ Mon, 03 Jun 2019 05:39:30: 38000000 INFO @ Mon, 03 Jun 2019 05:39:30: 32000000 INFO @ Mon, 03 Jun 2019 05:39:32: 33000000 INFO @ Mon, 03 Jun 2019 05:39:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:39:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:39:36: #1 total tags in treatment: 38659397 INFO @ Mon, 03 Jun 2019 05:39:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:39:36: #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 05:39:37: #1 tags after filtering in treatment: 38659397 INFO @ Mon, 03 Jun 2019 05:39:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:39:37: #1 finished! INFO @ Mon, 03 Jun 2019 05:39:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:39:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:39:40: #2 number of paired peaks: 33 WARNING @ Mon, 03 Jun 2019 05:39:40: Too few paired peaks (33) 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 05:39:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.10_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/SRX177656/SRX177656.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:39:41: 33000000 INFO @ Mon, 03 Jun 2019 05:39:42: 34000000 INFO @ Mon, 03 Jun 2019 05:39:52: 34000000 INFO @ Mon, 03 Jun 2019 05:39:52: 35000000 INFO @ Mon, 03 Jun 2019 05:40:03: 35000000 INFO @ Mon, 03 Jun 2019 05:40:03: 36000000 INFO @ Mon, 03 Jun 2019 05:40:13: 37000000 INFO @ Mon, 03 Jun 2019 05:40:13: 36000000 INFO @ Mon, 03 Jun 2019 05:40:23: 38000000 INFO @ Mon, 03 Jun 2019 05:40:24: 37000000 INFO @ Mon, 03 Jun 2019 05:40:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:40:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:40:30: #1 total tags in treatment: 38659397 INFO @ Mon, 03 Jun 2019 05:40:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:30: #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 05:40:30: #1 tags after filtering in treatment: 38659397 INFO @ Mon, 03 Jun 2019 05:40:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:30: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:33: #2 number of paired peaks: 33 WARNING @ Mon, 03 Jun 2019 05:40:33: Too few paired peaks (33) 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 05:40:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.05_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/SRX177656/SRX177656.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:40:34: 38000000 INFO @ Mon, 03 Jun 2019 05:40:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:40:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:40:41: #1 total tags in treatment: 38659397 INFO @ Mon, 03 Jun 2019 05:40:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:41: #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 05:40:42: #1 tags after filtering in treatment: 38659397 INFO @ Mon, 03 Jun 2019 05:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:42: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:45: #2 number of paired peaks: 33 WARNING @ Mon, 03 Jun 2019 05:40:45: Too few paired peaks (33) 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 05:40:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.20_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/SRX177656/SRX177656.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX177656/SRX177656.20_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。