Job ID = 1294664 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:33:13 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 ) 2019-06-03T00:33:13 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 ) 2019-06-03T00:33:58 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 ) 2019-06-03T00:33:58 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 ) 2019-06-03T00:35:44 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 ) 2019-06-03T00:35:44 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 ) 2019-06-03T00:37:07 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 : 17,745,143 reads read : 17,745,143 reads written : 17,745,143 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: 00:06:39 17745143 reads; of these: 17745143 (100.00%) were unpaired; of these: 836743 (4.72%) aligned 0 times 14423673 (81.28%) aligned exactly 1 time 2484727 (14.00%) aligned >1 times 95.28% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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] 1624217 / 16908400 = 0.0961 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 09:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.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 09:52:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:52:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.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 09:52:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:52:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.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 09:52:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:52:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:52:50: 1000000 INFO @ Mon, 03 Jun 2019 09:52:52: 1000000 INFO @ Mon, 03 Jun 2019 09:52:52: 1000000 INFO @ Mon, 03 Jun 2019 09:52:58: 2000000 INFO @ Mon, 03 Jun 2019 09:53:00: 2000000 INFO @ Mon, 03 Jun 2019 09:53:00: 2000000 INFO @ Mon, 03 Jun 2019 09:53:06: 3000000 INFO @ Mon, 03 Jun 2019 09:53:09: 3000000 INFO @ Mon, 03 Jun 2019 09:53:09: 3000000 INFO @ Mon, 03 Jun 2019 09:53:14: 4000000 INFO @ Mon, 03 Jun 2019 09:53:17: 4000000 INFO @ Mon, 03 Jun 2019 09:53:17: 4000000 INFO @ Mon, 03 Jun 2019 09:53:21: 5000000 INFO @ Mon, 03 Jun 2019 09:53:25: 5000000 INFO @ Mon, 03 Jun 2019 09:53:26: 5000000 INFO @ Mon, 03 Jun 2019 09:53:29: 6000000 INFO @ Mon, 03 Jun 2019 09:53:34: 6000000 INFO @ Mon, 03 Jun 2019 09:53:35: 6000000 INFO @ Mon, 03 Jun 2019 09:53:37: 7000000 INFO @ Mon, 03 Jun 2019 09:53:43: 7000000 INFO @ Mon, 03 Jun 2019 09:53:43: 7000000 INFO @ Mon, 03 Jun 2019 09:53:45: 8000000 INFO @ Mon, 03 Jun 2019 09:53:51: 8000000 INFO @ Mon, 03 Jun 2019 09:53:52: 8000000 INFO @ Mon, 03 Jun 2019 09:53:52: 9000000 INFO @ Mon, 03 Jun 2019 09:53:59: 9000000 INFO @ Mon, 03 Jun 2019 09:53:59: 10000000 INFO @ Mon, 03 Jun 2019 09:54:00: 9000000 INFO @ Mon, 03 Jun 2019 09:54:07: 11000000 INFO @ Mon, 03 Jun 2019 09:54:07: 10000000 INFO @ Mon, 03 Jun 2019 09:54:08: 10000000 INFO @ Mon, 03 Jun 2019 09:54:14: 12000000 INFO @ Mon, 03 Jun 2019 09:54:15: 11000000 INFO @ Mon, 03 Jun 2019 09:54:17: 11000000 INFO @ Mon, 03 Jun 2019 09:54:22: 13000000 INFO @ Mon, 03 Jun 2019 09:54:23: 12000000 INFO @ Mon, 03 Jun 2019 09:54:25: 12000000 INFO @ Mon, 03 Jun 2019 09:54:29: 14000000 INFO @ Mon, 03 Jun 2019 09:54:32: 13000000 INFO @ Mon, 03 Jun 2019 09:54:33: 13000000 INFO @ Mon, 03 Jun 2019 09:54:37: 15000000 INFO @ Mon, 03 Jun 2019 09:54:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:54:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:54:39: #1 total tags in treatment: 15284183 INFO @ Mon, 03 Jun 2019 09:54:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:54:39: #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 09:54:39: #1 tags after filtering in treatment: 15284183 INFO @ Mon, 03 Jun 2019 09:54:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:54:39: #1 finished! INFO @ Mon, 03 Jun 2019 09:54:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:54:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:54:40: 14000000 INFO @ Mon, 03 Jun 2019 09:54:41: #2 number of paired peaks: 52 WARNING @ Mon, 03 Jun 2019 09:54:41: Too few paired peaks (52) 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 09:54:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.05_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/SRX287812/SRX287812.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:54:41: 14000000 INFO @ Mon, 03 Jun 2019 09:54:48: 15000000 INFO @ Mon, 03 Jun 2019 09:54:50: 15000000 INFO @ Mon, 03 Jun 2019 09:54:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:54:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:54:50: #1 total tags in treatment: 15284183 INFO @ Mon, 03 Jun 2019 09:54:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:54:50: #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 09:54:50: #1 tags after filtering in treatment: 15284183 INFO @ Mon, 03 Jun 2019 09:54:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:54:50: #1 finished! INFO @ Mon, 03 Jun 2019 09:54:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:54:52: #2 number of paired peaks: 52 WARNING @ Mon, 03 Jun 2019 09:54:52: Too few paired peaks (52) 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 09:54:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.20_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/SRX287812/SRX287812.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:54:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:54:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:54:52: #1 total tags in treatment: 15284183 INFO @ Mon, 03 Jun 2019 09:54:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:54:52: #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 09:54:53: #1 tags after filtering in treatment: 15284183 INFO @ Mon, 03 Jun 2019 09:54:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:54:53: #1 finished! INFO @ Mon, 03 Jun 2019 09:54:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:54:54: #2 number of paired peaks: 52 WARNING @ Mon, 03 Jun 2019 09:54:54: Too few paired peaks (52) 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 09:54:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.10_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/SRX287812/SRX287812.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287812/SRX287812.10_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。