Job ID = 1293789 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,754,690 reads read : 21,754,690 reads written : 21,754,690 2019-06-02T17:34:31 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 ) spots read : 22,157,841 reads read : 22,157,841 reads written : 22,157,841 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: 00:12:03 43912531 reads; of these: 43912531 (100.00%) were unpaired; of these: 9069580 (20.65%) aligned 0 times 26464370 (60.27%) aligned exactly 1 time 8378581 (19.08%) aligned >1 times 79.35% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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] 10155812 / 34842951 = 0.2915 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 02:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.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 02:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.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 02:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.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 02:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:58:29: 1000000 INFO @ Mon, 03 Jun 2019 02:58:29: 1000000 INFO @ Mon, 03 Jun 2019 02:58:30: 1000000 INFO @ Mon, 03 Jun 2019 02:58:37: 2000000 INFO @ Mon, 03 Jun 2019 02:58:37: 2000000 INFO @ Mon, 03 Jun 2019 02:58:38: 2000000 INFO @ Mon, 03 Jun 2019 02:58:44: 3000000 INFO @ Mon, 03 Jun 2019 02:58:44: 3000000 INFO @ Mon, 03 Jun 2019 02:58:46: 3000000 INFO @ Mon, 03 Jun 2019 02:58:51: 4000000 INFO @ Mon, 03 Jun 2019 02:58:51: 4000000 INFO @ Mon, 03 Jun 2019 02:58:54: 4000000 INFO @ Mon, 03 Jun 2019 02:58:58: 5000000 INFO @ Mon, 03 Jun 2019 02:58:58: 5000000 INFO @ Mon, 03 Jun 2019 02:59:02: 5000000 INFO @ Mon, 03 Jun 2019 02:59:05: 6000000 INFO @ Mon, 03 Jun 2019 02:59:05: 6000000 INFO @ Mon, 03 Jun 2019 02:59:10: 6000000 INFO @ Mon, 03 Jun 2019 02:59:12: 7000000 INFO @ Mon, 03 Jun 2019 02:59:13: 7000000 INFO @ Mon, 03 Jun 2019 02:59:17: 7000000 INFO @ Mon, 03 Jun 2019 02:59:20: 8000000 INFO @ Mon, 03 Jun 2019 02:59:20: 8000000 INFO @ Mon, 03 Jun 2019 02:59:25: 8000000 INFO @ Mon, 03 Jun 2019 02:59:27: 9000000 INFO @ Mon, 03 Jun 2019 02:59:27: 9000000 INFO @ Mon, 03 Jun 2019 02:59:33: 9000000 INFO @ Mon, 03 Jun 2019 02:59:34: 10000000 INFO @ Mon, 03 Jun 2019 02:59:34: 10000000 INFO @ Mon, 03 Jun 2019 02:59:41: 10000000 INFO @ Mon, 03 Jun 2019 02:59:41: 11000000 INFO @ Mon, 03 Jun 2019 02:59:42: 11000000 INFO @ Mon, 03 Jun 2019 02:59:48: 11000000 INFO @ Mon, 03 Jun 2019 02:59:49: 12000000 INFO @ Mon, 03 Jun 2019 02:59:49: 12000000 INFO @ Mon, 03 Jun 2019 02:59:56: 12000000 INFO @ Mon, 03 Jun 2019 02:59:56: 13000000 INFO @ Mon, 03 Jun 2019 02:59:56: 13000000 INFO @ Mon, 03 Jun 2019 03:00:03: 14000000 INFO @ Mon, 03 Jun 2019 03:00:03: 14000000 INFO @ Mon, 03 Jun 2019 03:00:04: 13000000 INFO @ Mon, 03 Jun 2019 03:00:10: 15000000 INFO @ Mon, 03 Jun 2019 03:00:10: 15000000 INFO @ Mon, 03 Jun 2019 03:00:11: 14000000 INFO @ Mon, 03 Jun 2019 03:00:17: 16000000 INFO @ Mon, 03 Jun 2019 03:00:17: 16000000 INFO @ Mon, 03 Jun 2019 03:00:19: 15000000 INFO @ Mon, 03 Jun 2019 03:00:24: 17000000 INFO @ Mon, 03 Jun 2019 03:00:24: 17000000 INFO @ Mon, 03 Jun 2019 03:00:27: 16000000 INFO @ Mon, 03 Jun 2019 03:00:31: 18000000 INFO @ Mon, 03 Jun 2019 03:00:31: 18000000 INFO @ Mon, 03 Jun 2019 03:00:34: 17000000 INFO @ Mon, 03 Jun 2019 03:00:38: 19000000 INFO @ Mon, 03 Jun 2019 03:00:38: 19000000 INFO @ Mon, 03 Jun 2019 03:00:42: 18000000 INFO @ Mon, 03 Jun 2019 03:00:45: 20000000 INFO @ Mon, 03 Jun 2019 03:00:45: 20000000 INFO @ Mon, 03 Jun 2019 03:00:50: 19000000 INFO @ Mon, 03 Jun 2019 03:00:52: 21000000 INFO @ Mon, 03 Jun 2019 03:00:52: 21000000 INFO @ Mon, 03 Jun 2019 03:00:58: 20000000 INFO @ Mon, 03 Jun 2019 03:00:59: 22000000 INFO @ Mon, 03 Jun 2019 03:00:59: 22000000 INFO @ Mon, 03 Jun 2019 03:01:05: 21000000 INFO @ Mon, 03 Jun 2019 03:01:06: 23000000 INFO @ Mon, 03 Jun 2019 03:01:06: 23000000 INFO @ Mon, 03 Jun 2019 03:01:13: 24000000 INFO @ Mon, 03 Jun 2019 03:01:13: 22000000 INFO @ Mon, 03 Jun 2019 03:01:13: 24000000 INFO @ Mon, 03 Jun 2019 03:01:18: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 03:01:18: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 03:01:18: #1 total tags in treatment: 24687139 INFO @ Mon, 03 Jun 2019 03:01:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:01:18: #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 03:01:18: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 03:01:18: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 03:01:18: #1 total tags in treatment: 24687139 INFO @ Mon, 03 Jun 2019 03:01:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:01:18: #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 03:01:18: #1 tags after filtering in treatment: 24687139 INFO @ Mon, 03 Jun 2019 03:01:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:01:18: #1 finished! INFO @ Mon, 03 Jun 2019 03:01:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:01:19: #1 tags after filtering in treatment: 24687139 INFO @ Mon, 03 Jun 2019 03:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:01:19: #1 finished! INFO @ Mon, 03 Jun 2019 03:01:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:01:20: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 03:01:20: 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 @ Mon, 03 Jun 2019 03:01:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.05_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/SRX113338/SRX113338.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:01:21: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 03:01:21: 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 @ Mon, 03 Jun 2019 03:01:21: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 03:01:21: 23000000 cut: /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.10_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/SRX113338/SRX113338.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:01:28: 24000000 INFO @ Mon, 03 Jun 2019 03:01:34: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 03:01:34: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 03:01:34: #1 total tags in treatment: 24687139 INFO @ Mon, 03 Jun 2019 03:01:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:01:34: #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 03:01:34: #1 tags after filtering in treatment: 24687139 INFO @ Mon, 03 Jun 2019 03:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:01:34: #1 finished! INFO @ Mon, 03 Jun 2019 03:01:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:01:36: #2 number of paired peaks: 41 WARNING @ Mon, 03 Jun 2019 03:01:36: 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 @ Mon, 03 Jun 2019 03:01:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.20_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/SRX113338/SRX113338.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113338/SRX113338.20_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。