Job ID = 1298910 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:39:52 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 ) 2019-06-03T08:39:56 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 : 29,206,592 reads read : 29,206,592 reads written : 29,206,592 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: 00:10:16 29206592 reads; of these: 29206592 (100.00%) were unpaired; of these: 909580 (3.11%) aligned 0 times 22185886 (75.96%) aligned exactly 1 time 6111126 (20.92%) aligned >1 times 96.89% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:16 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] 6073503 / 28297012 = 0.2146 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 18:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.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 18:10:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:10:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.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 18:10:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:10:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.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 18:10:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:10:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:10:53: 1000000 INFO @ Mon, 03 Jun 2019 18:10:54: 1000000 INFO @ Mon, 03 Jun 2019 18:10:54: 1000000 INFO @ Mon, 03 Jun 2019 18:11:02: 2000000 INFO @ Mon, 03 Jun 2019 18:11:02: 2000000 INFO @ Mon, 03 Jun 2019 18:11:03: 2000000 INFO @ Mon, 03 Jun 2019 18:11:11: 3000000 INFO @ Mon, 03 Jun 2019 18:11:11: 3000000 INFO @ Mon, 03 Jun 2019 18:11:13: 3000000 INFO @ Mon, 03 Jun 2019 18:11:20: 4000000 INFO @ Mon, 03 Jun 2019 18:11:20: 4000000 INFO @ Mon, 03 Jun 2019 18:11:23: 4000000 INFO @ Mon, 03 Jun 2019 18:11:29: 5000000 INFO @ Mon, 03 Jun 2019 18:11:30: 5000000 INFO @ Mon, 03 Jun 2019 18:11:33: 5000000 INFO @ Mon, 03 Jun 2019 18:11:39: 6000000 INFO @ Mon, 03 Jun 2019 18:11:40: 6000000 INFO @ Mon, 03 Jun 2019 18:11:44: 6000000 INFO @ Mon, 03 Jun 2019 18:11:48: 7000000 INFO @ Mon, 03 Jun 2019 18:11:49: 7000000 INFO @ Mon, 03 Jun 2019 18:11:56: 7000000 INFO @ Mon, 03 Jun 2019 18:11:56: 8000000 INFO @ Mon, 03 Jun 2019 18:11:59: 8000000 INFO @ Mon, 03 Jun 2019 18:12:05: 9000000 INFO @ Mon, 03 Jun 2019 18:12:07: 8000000 INFO @ Mon, 03 Jun 2019 18:12:09: 9000000 INFO @ Mon, 03 Jun 2019 18:12:14: 10000000 INFO @ Mon, 03 Jun 2019 18:12:18: 9000000 INFO @ Mon, 03 Jun 2019 18:12:19: 10000000 INFO @ Mon, 03 Jun 2019 18:12:23: 11000000 INFO @ Mon, 03 Jun 2019 18:12:29: 10000000 INFO @ Mon, 03 Jun 2019 18:12:29: 11000000 INFO @ Mon, 03 Jun 2019 18:12:32: 12000000 INFO @ Mon, 03 Jun 2019 18:12:40: 12000000 INFO @ Mon, 03 Jun 2019 18:12:40: 13000000 INFO @ Mon, 03 Jun 2019 18:12:41: 11000000 INFO @ Mon, 03 Jun 2019 18:12:49: 14000000 INFO @ Mon, 03 Jun 2019 18:12:49: 13000000 INFO @ Mon, 03 Jun 2019 18:12:51: 12000000 INFO @ Mon, 03 Jun 2019 18:12:57: 15000000 INFO @ Mon, 03 Jun 2019 18:12:59: 14000000 INFO @ Mon, 03 Jun 2019 18:13:02: 13000000 INFO @ Mon, 03 Jun 2019 18:13:06: 16000000 INFO @ Mon, 03 Jun 2019 18:13:08: 15000000 INFO @ Mon, 03 Jun 2019 18:13:12: 14000000 INFO @ Mon, 03 Jun 2019 18:13:15: 17000000 INFO @ Mon, 03 Jun 2019 18:13:18: 16000000 INFO @ Mon, 03 Jun 2019 18:13:22: 15000000 INFO @ Mon, 03 Jun 2019 18:13:24: 18000000 INFO @ Mon, 03 Jun 2019 18:13:28: 17000000 INFO @ Mon, 03 Jun 2019 18:13:32: 19000000 INFO @ Mon, 03 Jun 2019 18:13:33: 16000000 INFO @ Mon, 03 Jun 2019 18:13:37: 18000000 INFO @ Mon, 03 Jun 2019 18:13:42: 20000000 INFO @ Mon, 03 Jun 2019 18:13:43: 17000000 INFO @ Mon, 03 Jun 2019 18:13:46: 19000000 INFO @ Mon, 03 Jun 2019 18:13:51: 21000000 INFO @ Mon, 03 Jun 2019 18:13:54: 18000000 INFO @ Mon, 03 Jun 2019 18:13:55: 20000000 INFO @ Mon, 03 Jun 2019 18:14:00: 22000000 INFO @ Mon, 03 Jun 2019 18:14:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:14:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:14:02: #1 total tags in treatment: 22223509 INFO @ Mon, 03 Jun 2019 18:14:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:14:02: #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 18:14:03: #1 tags after filtering in treatment: 22223509 INFO @ Mon, 03 Jun 2019 18:14:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:14:03: #1 finished! INFO @ Mon, 03 Jun 2019 18:14:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:14:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:14:03: 21000000 INFO @ Mon, 03 Jun 2019 18:14:04: 19000000 INFO @ Mon, 03 Jun 2019 18:14:05: #2 number of paired peaks: 29 WARNING @ Mon, 03 Jun 2019 18:14:05: Too few paired peaks (29) 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 18:14:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.05_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/SRX467058/SRX467058.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:14:12: 22000000 INFO @ Mon, 03 Jun 2019 18:14:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:14:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:14:14: #1 total tags in treatment: 22223509 INFO @ Mon, 03 Jun 2019 18:14:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:14:14: #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 18:14:14: 20000000 INFO @ Mon, 03 Jun 2019 18:14:14: #1 tags after filtering in treatment: 22223509 INFO @ Mon, 03 Jun 2019 18:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:14:14: #1 finished! INFO @ Mon, 03 Jun 2019 18:14:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:14:16: #2 number of paired peaks: 29 WARNING @ Mon, 03 Jun 2019 18:14:16: Too few paired peaks (29) 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 18:14:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.10_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/SRX467058/SRX467058.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:14:24: 21000000 INFO @ Mon, 03 Jun 2019 18:14:33: 22000000 INFO @ Mon, 03 Jun 2019 18:14:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:14:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:14:35: #1 total tags in treatment: 22223509 INFO @ Mon, 03 Jun 2019 18:14:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:14:35: #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 18:14:36: #1 tags after filtering in treatment: 22223509 INFO @ Mon, 03 Jun 2019 18:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:14:36: #1 finished! INFO @ Mon, 03 Jun 2019 18:14:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:14:38: #2 number of paired peaks: 29 WARNING @ Mon, 03 Jun 2019 18:14:38: Too few paired peaks (29) 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 18:14:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.20_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/SRX467058/SRX467058.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467058/SRX467058.20_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。