Job ID = 1298355 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:18:07 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 ) 2019-06-03T08:18:26 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 ) 2019-06-03T08:21:33 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 ) 2019-06-03T08:21:33 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 ) 2019-06-03T08:26:24 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 ) 2019-06-03T08:35:06 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 ) spots read : 26,982,774 reads read : 26,982,774 reads written : 26,982,774 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: 00:08:54 26982774 reads; of these: 26982774 (100.00%) were unpaired; of these: 4621565 (17.13%) aligned 0 times 17995139 (66.69%) aligned exactly 1 time 4366070 (16.18%) aligned >1 times 82.87% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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] 5981713 / 22361209 = 0.2675 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 17:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.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 17:50:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:50:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.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 17:50:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:50:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.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 17:50:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:50:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:50:25: 1000000 INFO @ Mon, 03 Jun 2019 17:50:25: 1000000 INFO @ Mon, 03 Jun 2019 17:50:26: 1000000 INFO @ Mon, 03 Jun 2019 17:50:33: 2000000 INFO @ Mon, 03 Jun 2019 17:50:33: 2000000 INFO @ Mon, 03 Jun 2019 17:50:35: 2000000 INFO @ Mon, 03 Jun 2019 17:50:41: 3000000 INFO @ Mon, 03 Jun 2019 17:50:41: 3000000 INFO @ Mon, 03 Jun 2019 17:50:43: 3000000 INFO @ Mon, 03 Jun 2019 17:50:49: 4000000 INFO @ Mon, 03 Jun 2019 17:50:50: 4000000 INFO @ Mon, 03 Jun 2019 17:50:52: 4000000 INFO @ Mon, 03 Jun 2019 17:50:57: 5000000 INFO @ Mon, 03 Jun 2019 17:50:57: 5000000 INFO @ Mon, 03 Jun 2019 17:51:01: 5000000 INFO @ Mon, 03 Jun 2019 17:51:05: 6000000 INFO @ Mon, 03 Jun 2019 17:51:05: 6000000 INFO @ Mon, 03 Jun 2019 17:51:09: 6000000 INFO @ Mon, 03 Jun 2019 17:51:13: 7000000 INFO @ Mon, 03 Jun 2019 17:51:13: 7000000 INFO @ Mon, 03 Jun 2019 17:51:18: 7000000 INFO @ Mon, 03 Jun 2019 17:51:21: 8000000 INFO @ Mon, 03 Jun 2019 17:51:21: 8000000 INFO @ Mon, 03 Jun 2019 17:51:27: 8000000 INFO @ Mon, 03 Jun 2019 17:51:29: 9000000 INFO @ Mon, 03 Jun 2019 17:51:29: 9000000 INFO @ Mon, 03 Jun 2019 17:51:35: 9000000 INFO @ Mon, 03 Jun 2019 17:51:36: 10000000 INFO @ Mon, 03 Jun 2019 17:51:37: 10000000 INFO @ Mon, 03 Jun 2019 17:51:44: 10000000 INFO @ Mon, 03 Jun 2019 17:51:45: 11000000 INFO @ Mon, 03 Jun 2019 17:51:46: 11000000 INFO @ Mon, 03 Jun 2019 17:51:52: 11000000 INFO @ Mon, 03 Jun 2019 17:51:54: 12000000 INFO @ Mon, 03 Jun 2019 17:51:54: 12000000 INFO @ Mon, 03 Jun 2019 17:52:01: 12000000 INFO @ Mon, 03 Jun 2019 17:52:03: 13000000 INFO @ Mon, 03 Jun 2019 17:52:03: 13000000 INFO @ Mon, 03 Jun 2019 17:52:10: 13000000 INFO @ Mon, 03 Jun 2019 17:52:12: 14000000 INFO @ Mon, 03 Jun 2019 17:52:12: 14000000 INFO @ Mon, 03 Jun 2019 17:52:18: 14000000 INFO @ Mon, 03 Jun 2019 17:52:21: 15000000 INFO @ Mon, 03 Jun 2019 17:52:21: 15000000 INFO @ Mon, 03 Jun 2019 17:52:27: 15000000 INFO @ Mon, 03 Jun 2019 17:52:29: 16000000 INFO @ Mon, 03 Jun 2019 17:52:30: 16000000 INFO @ Mon, 03 Jun 2019 17:52:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:52:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:52:33: #1 total tags in treatment: 16379496 INFO @ Mon, 03 Jun 2019 17:52:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:52:33: #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 17:52:33: #1 tags after filtering in treatment: 16379496 INFO @ Mon, 03 Jun 2019 17:52:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:52:33: #1 finished! INFO @ Mon, 03 Jun 2019 17:52:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:52:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:52:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:52:33: #1 total tags in treatment: 16379496 INFO @ Mon, 03 Jun 2019 17:52:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:52:33: #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 17:52:33: #1 tags after filtering in treatment: 16379496 INFO @ Mon, 03 Jun 2019 17:52:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:52:33: #1 finished! INFO @ Mon, 03 Jun 2019 17:52:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:52:34: #2 number of paired peaks: 48 WARNING @ Mon, 03 Jun 2019 17:52:34: Too few paired peaks (48) 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 17:52:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.05_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/SRX467025/SRX467025.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:52:35: #2 number of paired peaks: 48 WARNING @ Mon, 03 Jun 2019 17:52:35: Too few paired peaks (48) 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 17:52:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis INFO @ Mon, 03 Jun 2019 17:52:35: 16000000 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:52:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:52:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:52:38: #1 total tags in treatment: 16379496 INFO @ Mon, 03 Jun 2019 17:52:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:52:38: #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 17:52:38: #1 tags after filtering in treatment: 16379496 INFO @ Mon, 03 Jun 2019 17:52:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:52:38: #1 finished! INFO @ Mon, 03 Jun 2019 17:52:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:52:40: #2 number of paired peaks: 48 WARNING @ Mon, 03 Jun 2019 17:52:40: Too few paired peaks (48) 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 17:52:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.10_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/SRX467025/SRX467025.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467025/SRX467025.10_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。