Job ID = 4178626 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T04:28:20 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 ) 2019-12-05T04:28:20 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 ) 2019-12-05T04:28:20 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 ) 2019-12-05T04:29:10 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 : 27,543,813 reads read : 27,543,813 reads written : 27,543,813 rm: cannot remove ‘[DSE]RR*’: 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: 00:10:47 27543813 reads; of these: 27543813 (100.00%) were unpaired; of these: 4258732 (15.46%) aligned 0 times 16507592 (59.93%) aligned exactly 1 time 6777489 (24.61%) aligned >1 times 84.54% overall alignment rate Time searching: 00:10:47 Overall time: 00:10:47 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] 9913600 / 23285081 = 0.4257 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.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 @ Thu, 05 Dec 2019 13:49:11: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:49:11: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:49:20: 1000000 INFO @ Thu, 05 Dec 2019 13:49:28: 2000000 INFO @ Thu, 05 Dec 2019 13:49:36: 3000000 INFO @ Thu, 05 Dec 2019 13:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.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 @ Thu, 05 Dec 2019 13:49:42: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:49:42: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:49:44: 4000000 INFO @ Thu, 05 Dec 2019 13:49:51: 1000000 INFO @ Thu, 05 Dec 2019 13:49:52: 5000000 INFO @ Thu, 05 Dec 2019 13:50:00: 2000000 INFO @ Thu, 05 Dec 2019 13:50:01: 6000000 INFO @ Thu, 05 Dec 2019 13:50:09: 3000000 INFO @ Thu, 05 Dec 2019 13:50:09: 7000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.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 @ Thu, 05 Dec 2019 13:50:12: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:50:12: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:50:17: 8000000 INFO @ Thu, 05 Dec 2019 13:50:18: 4000000 INFO @ Thu, 05 Dec 2019 13:50:20: 1000000 INFO @ Thu, 05 Dec 2019 13:50:26: 9000000 INFO @ Thu, 05 Dec 2019 13:50:26: 5000000 INFO @ Thu, 05 Dec 2019 13:50:28: 2000000 INFO @ Thu, 05 Dec 2019 13:50:34: 10000000 INFO @ Thu, 05 Dec 2019 13:50:36: 6000000 INFO @ Thu, 05 Dec 2019 13:50:37: 3000000 INFO @ Thu, 05 Dec 2019 13:50:43: 11000000 INFO @ Thu, 05 Dec 2019 13:50:45: 4000000 INFO @ Thu, 05 Dec 2019 13:50:45: 7000000 INFO @ Thu, 05 Dec 2019 13:50:51: 12000000 INFO @ Thu, 05 Dec 2019 13:50:53: 5000000 INFO @ Thu, 05 Dec 2019 13:50:54: 8000000 INFO @ Thu, 05 Dec 2019 13:51:01: 13000000 INFO @ Thu, 05 Dec 2019 13:51:01: 6000000 INFO @ Thu, 05 Dec 2019 13:51:03: 9000000 INFO @ Thu, 05 Dec 2019 13:51:04: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:51:04: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:51:04: #1 total tags in treatment: 13371481 INFO @ Thu, 05 Dec 2019 13:51:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:51:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:51:04: #1 tags after filtering in treatment: 13371481 INFO @ Thu, 05 Dec 2019 13:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:51:04: #1 finished! INFO @ Thu, 05 Dec 2019 13:51:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:51:06: #2 number of paired peaks: 41 WARNING @ Thu, 05 Dec 2019 13:51:06: Too few paired peaks (41) 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 @ Thu, 05 Dec 2019 13:51:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:51:09: 7000000 INFO @ Thu, 05 Dec 2019 13:51:12: 10000000 INFO @ Thu, 05 Dec 2019 13:51:17: 8000000 INFO @ Thu, 05 Dec 2019 13:51:21: 11000000 INFO @ Thu, 05 Dec 2019 13:51:25: 9000000 INFO @ Thu, 05 Dec 2019 13:51:29: 12000000 INFO @ Thu, 05 Dec 2019 13:51:33: 10000000 INFO @ Thu, 05 Dec 2019 13:51:37: 13000000 INFO @ Thu, 05 Dec 2019 13:51:40: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:51:40: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:51:40: #1 total tags in treatment: 13371481 INFO @ Thu, 05 Dec 2019 13:51:40: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:51:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:51:40: #1 tags after filtering in treatment: 13371481 INFO @ Thu, 05 Dec 2019 13:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:51:40: #1 finished! INFO @ Thu, 05 Dec 2019 13:51:40: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:51:41: 11000000 INFO @ Thu, 05 Dec 2019 13:51:42: #2 number of paired peaks: 41 WARNING @ Thu, 05 Dec 2019 13:51:42: Too few paired peaks (41) 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 @ Thu, 05 Dec 2019 13:51:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.10_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/SRX6468500/SRX6468500.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:51:48: 12000000 INFO @ Thu, 05 Dec 2019 13:51:58: 13000000 INFO @ Thu, 05 Dec 2019 13:52:01: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:52:01: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:52:01: #1 total tags in treatment: 13371481 INFO @ Thu, 05 Dec 2019 13:52:01: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:52:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:52:01: #1 tags after filtering in treatment: 13371481 INFO @ Thu, 05 Dec 2019 13:52:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:52:01: #1 finished! INFO @ Thu, 05 Dec 2019 13:52:01: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:52:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:52:03: #2 number of paired peaks: 41 WARNING @ Thu, 05 Dec 2019 13:52:03: Too few paired peaks (41) 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 @ Thu, 05 Dec 2019 13:52:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.20_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/SRX6468500/SRX6468500.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX6468500/SRX6468500.20_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。