Job ID = 1303876 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T11:34:55 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 ) 2019-06-03T11:34:55 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 ) 2019-06-03T11:36:36 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 ) 2019-06-03T11:38:35 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 ) 2019-06-03T11:38:35 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 ) 2019-06-03T11:40:06 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 ) 2019-06-03T11:40:06 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 ) 2019-06-03T11:40:06 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 ) 2019-06-03T11:40:55 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 ) 2019-06-03T11:40:55 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 ) 2019-06-03T11:43:16 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 ) 2019-06-03T11:43:23 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 ) 2019-06-03T11:43:34 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 ) 2019-06-03T11:44:46 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 ) 2019-06-03T11:45:55 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 ) 2019-06-03T11:46:07 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 ) spots read : 27,747,945 reads read : 27,747,945 reads written : 27,747,945 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: 00:07:50 27747945 reads; of these: 27747945 (100.00%) were unpaired; of these: 5329247 (19.21%) aligned 0 times 17429944 (62.82%) aligned exactly 1 time 4988754 (17.98%) aligned >1 times 80.79% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:50 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 8 files... [bam_rmdupse_core] 6177895 / 22418698 = 0.2756 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 21:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.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 21:02:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:02:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.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 21:02:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:02:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.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 21:02:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:02:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:02:57: 1000000 INFO @ Mon, 03 Jun 2019 21:02:58: 1000000 INFO @ Mon, 03 Jun 2019 21:02:58: 1000000 INFO @ Mon, 03 Jun 2019 21:03:03: 2000000 INFO @ Mon, 03 Jun 2019 21:03:05: 2000000 INFO @ Mon, 03 Jun 2019 21:03:05: 2000000 INFO @ Mon, 03 Jun 2019 21:03:10: 3000000 INFO @ Mon, 03 Jun 2019 21:03:13: 3000000 INFO @ Mon, 03 Jun 2019 21:03:13: 3000000 INFO @ Mon, 03 Jun 2019 21:03:17: 4000000 INFO @ Mon, 03 Jun 2019 21:03:20: 4000000 INFO @ Mon, 03 Jun 2019 21:03:21: 4000000 INFO @ Mon, 03 Jun 2019 21:03:24: 5000000 INFO @ Mon, 03 Jun 2019 21:03:27: 5000000 INFO @ Mon, 03 Jun 2019 21:03:28: 5000000 INFO @ Mon, 03 Jun 2019 21:03:30: 6000000 INFO @ Mon, 03 Jun 2019 21:03:35: 6000000 INFO @ Mon, 03 Jun 2019 21:03:36: 6000000 INFO @ Mon, 03 Jun 2019 21:03:37: 7000000 INFO @ Mon, 03 Jun 2019 21:03:42: 7000000 INFO @ Mon, 03 Jun 2019 21:03:43: 7000000 INFO @ Mon, 03 Jun 2019 21:03:43: 8000000 INFO @ Mon, 03 Jun 2019 21:03:49: 8000000 INFO @ Mon, 03 Jun 2019 21:03:50: 9000000 INFO @ Mon, 03 Jun 2019 21:03:50: 8000000 INFO @ Mon, 03 Jun 2019 21:03:56: 9000000 INFO @ Mon, 03 Jun 2019 21:03:57: 10000000 INFO @ Mon, 03 Jun 2019 21:03:58: 9000000 INFO @ Mon, 03 Jun 2019 21:04:03: 11000000 INFO @ Mon, 03 Jun 2019 21:04:04: 10000000 INFO @ Mon, 03 Jun 2019 21:04:05: 10000000 INFO @ Mon, 03 Jun 2019 21:04:10: 12000000 INFO @ Mon, 03 Jun 2019 21:04:11: 11000000 INFO @ Mon, 03 Jun 2019 21:04:13: 11000000 INFO @ Mon, 03 Jun 2019 21:04:17: 13000000 INFO @ Mon, 03 Jun 2019 21:04:18: 12000000 INFO @ Mon, 03 Jun 2019 21:04:20: 12000000 INFO @ Mon, 03 Jun 2019 21:04:23: 14000000 INFO @ Mon, 03 Jun 2019 21:04:25: 13000000 INFO @ Mon, 03 Jun 2019 21:04:27: 13000000 INFO @ Mon, 03 Jun 2019 21:04:30: 15000000 INFO @ Mon, 03 Jun 2019 21:04:33: 14000000 INFO @ Mon, 03 Jun 2019 21:04:35: 14000000 INFO @ Mon, 03 Jun 2019 21:04:37: 16000000 INFO @ Mon, 03 Jun 2019 21:04:38: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:04:38: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:04:38: #1 total tags in treatment: 16240803 INFO @ Mon, 03 Jun 2019 21:04:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:04:38: #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 21:04:39: #1 tags after filtering in treatment: 16240803 INFO @ Mon, 03 Jun 2019 21:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:04:39: #1 finished! INFO @ Mon, 03 Jun 2019 21:04:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:04:40: 15000000 INFO @ Mon, 03 Jun 2019 21:04:40: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 21:04:40: Too few paired peaks (49) 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 21:04:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.20_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/SRX495171/SRX495171.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:04:43: 15000000 INFO @ Mon, 03 Jun 2019 21:04:47: 16000000 INFO @ Mon, 03 Jun 2019 21:04:49: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:04:49: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:04:49: #1 total tags in treatment: 16240803 INFO @ Mon, 03 Jun 2019 21:04:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:04:49: #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 21:04:49: #1 tags after filtering in treatment: 16240803 INFO @ Mon, 03 Jun 2019 21:04:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:04:49: #1 finished! INFO @ Mon, 03 Jun 2019 21:04:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:04:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:04:50: 16000000 INFO @ Mon, 03 Jun 2019 21:04:51: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 21:04:51: Too few paired peaks (49) 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 21:04:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.10_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/SRX495171/SRX495171.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:04:52: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:04:52: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:04:52: #1 total tags in treatment: 16240803 INFO @ Mon, 03 Jun 2019 21:04:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:04:52: #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 21:04:52: #1 tags after filtering in treatment: 16240803 INFO @ Mon, 03 Jun 2019 21:04:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:04:52: #1 finished! INFO @ Mon, 03 Jun 2019 21:04:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:04:54: #2 number of paired peaks: 49 WARNING @ Mon, 03 Jun 2019 21:04:54: Too few paired peaks (49) 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 21:04:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.05_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/SRX495171/SRX495171.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX495171/SRX495171.05_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。