Job ID = 1298537 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:29:31 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 ) 2019-06-03T08:29:31 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 ) 2019-06-03T08:29:31 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 ) 2019-06-03T08:33:20 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 ) 2019-06-03T08:33:20 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 ) 2019-06-03T08:35:06 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 ) 2019-06-03T08:35:06 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 ) 2019-06-03T08:37:41 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 ) 2019-06-03T08:40:30 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 : 24,099,633 reads read : 24,099,633 reads written : 24,099,633 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: 00:05:56 24099633 reads; of these: 24099633 (100.00%) were unpaired; of these: 1769610 (7.34%) aligned 0 times 20296759 (84.22%) aligned exactly 1 time 2033264 (8.44%) aligned >1 times 92.66% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 4996046 / 22330023 = 0.2237 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 17:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.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 17:53:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:53:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.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 17:53:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:53:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.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 17:53:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:53:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:54:00: 1000000 INFO @ Mon, 03 Jun 2019 17:54:01: 1000000 INFO @ Mon, 03 Jun 2019 17:54:05: 1000000 INFO @ Mon, 03 Jun 2019 17:54:09: 2000000 INFO @ Mon, 03 Jun 2019 17:54:11: 2000000 INFO @ Mon, 03 Jun 2019 17:54:18: 2000000 INFO @ Mon, 03 Jun 2019 17:54:18: 3000000 INFO @ Mon, 03 Jun 2019 17:54:21: 3000000 INFO @ Mon, 03 Jun 2019 17:54:27: 4000000 INFO @ Mon, 03 Jun 2019 17:54:31: 4000000 INFO @ Mon, 03 Jun 2019 17:54:32: 3000000 INFO @ Mon, 03 Jun 2019 17:54:36: 5000000 INFO @ Mon, 03 Jun 2019 17:54:41: 5000000 INFO @ Mon, 03 Jun 2019 17:54:45: 4000000 INFO @ Mon, 03 Jun 2019 17:54:45: 6000000 INFO @ Mon, 03 Jun 2019 17:54:51: 6000000 INFO @ Mon, 03 Jun 2019 17:54:54: 7000000 INFO @ Mon, 03 Jun 2019 17:55:00: 5000000 INFO @ Mon, 03 Jun 2019 17:55:01: 7000000 INFO @ Mon, 03 Jun 2019 17:55:03: 8000000 INFO @ Mon, 03 Jun 2019 17:55:10: 8000000 INFO @ Mon, 03 Jun 2019 17:55:11: 9000000 INFO @ Mon, 03 Jun 2019 17:55:14: 6000000 INFO @ Mon, 03 Jun 2019 17:55:21: 10000000 INFO @ Mon, 03 Jun 2019 17:55:21: 9000000 INFO @ Mon, 03 Jun 2019 17:55:27: 7000000 INFO @ Mon, 03 Jun 2019 17:55:29: 11000000 INFO @ Mon, 03 Jun 2019 17:55:31: 10000000 INFO @ Mon, 03 Jun 2019 17:55:38: 12000000 INFO @ Mon, 03 Jun 2019 17:55:42: 8000000 INFO @ Mon, 03 Jun 2019 17:55:42: 11000000 INFO @ Mon, 03 Jun 2019 17:55:46: 13000000 INFO @ Mon, 03 Jun 2019 17:55:52: 12000000 INFO @ Mon, 03 Jun 2019 17:55:55: 14000000 INFO @ Mon, 03 Jun 2019 17:55:56: 9000000 INFO @ Mon, 03 Jun 2019 17:56:03: 13000000 INFO @ Mon, 03 Jun 2019 17:56:04: 15000000 INFO @ Mon, 03 Jun 2019 17:56:10: 10000000 INFO @ Mon, 03 Jun 2019 17:56:13: 16000000 INFO @ Mon, 03 Jun 2019 17:56:13: 14000000 INFO @ Mon, 03 Jun 2019 17:56:22: 17000000 INFO @ Mon, 03 Jun 2019 17:56:23: 15000000 INFO @ Mon, 03 Jun 2019 17:56:24: 11000000 INFO @ Mon, 03 Jun 2019 17:56:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:56:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:56:25: #1 total tags in treatment: 17333977 INFO @ Mon, 03 Jun 2019 17:56:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:56:25: #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 17:56:25: #1 tags after filtering in treatment: 17333977 INFO @ Mon, 03 Jun 2019 17:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:56:25: #1 finished! INFO @ Mon, 03 Jun 2019 17:56:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:56:27: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 17:56:27: Too few paired peaks (51) 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 17:56:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.05_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/SRX467039/SRX467039.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:56:34: 16000000 INFO @ Mon, 03 Jun 2019 17:56:37: 12000000 INFO @ Mon, 03 Jun 2019 17:56:45: 17000000 INFO @ Mon, 03 Jun 2019 17:56:48: 13000000 INFO @ Mon, 03 Jun 2019 17:56:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:56:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:56:49: #1 total tags in treatment: 17333977 INFO @ Mon, 03 Jun 2019 17:56:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:56:49: #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 17:56:49: #1 tags after filtering in treatment: 17333977 INFO @ Mon, 03 Jun 2019 17:56:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:56:49: #1 finished! INFO @ Mon, 03 Jun 2019 17:56:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:56:51: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 17:56:51: Too few paired peaks (51) 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 17:56:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.20_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/SRX467039/SRX467039.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:56:59: 14000000 INFO @ Mon, 03 Jun 2019 17:57:10: 15000000 INFO @ Mon, 03 Jun 2019 17:57:21: 16000000 INFO @ Mon, 03 Jun 2019 17:57:33: 17000000 INFO @ Mon, 03 Jun 2019 17:57:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:57:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:57:36: #1 total tags in treatment: 17333977 INFO @ Mon, 03 Jun 2019 17:57:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:57:36: #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 17:57:37: #1 tags after filtering in treatment: 17333977 INFO @ Mon, 03 Jun 2019 17:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:57:37: #1 finished! INFO @ Mon, 03 Jun 2019 17:57:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:57:38: #2 number of paired peaks: 51 WARNING @ Mon, 03 Jun 2019 17:57:38: Too few paired peaks (51) 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 17:57:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.10_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/SRX467039/SRX467039.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467039/SRX467039.10_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。