Job ID = 1294270 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:06:53 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 ) 2019-06-02T21:06:53 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 : 28,554,254 reads read : 28,554,254 reads written : 28,554,254 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:06 28554254 reads; of these: 28554254 (100.00%) were unpaired; of these: 2688956 (9.42%) aligned 0 times 23235369 (81.37%) aligned exactly 1 time 2629929 (9.21%) aligned >1 times 90.58% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 3724453 / 25865298 = 0.1440 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 06:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.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 06:28:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:28:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.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 06:28:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:28:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.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 06:28:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:28:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:28:41: 1000000 INFO @ Mon, 03 Jun 2019 06:28:41: 1000000 INFO @ Mon, 03 Jun 2019 06:28:42: 1000000 INFO @ Mon, 03 Jun 2019 06:28:48: 2000000 INFO @ Mon, 03 Jun 2019 06:28:48: 2000000 INFO @ Mon, 03 Jun 2019 06:28:51: 2000000 INFO @ Mon, 03 Jun 2019 06:28:56: 3000000 INFO @ Mon, 03 Jun 2019 06:28:56: 3000000 INFO @ Mon, 03 Jun 2019 06:29:00: 3000000 INFO @ Mon, 03 Jun 2019 06:29:04: 4000000 INFO @ Mon, 03 Jun 2019 06:29:04: 4000000 INFO @ Mon, 03 Jun 2019 06:29:09: 4000000 INFO @ Mon, 03 Jun 2019 06:29:12: 5000000 INFO @ Mon, 03 Jun 2019 06:29:12: 5000000 INFO @ Mon, 03 Jun 2019 06:29:18: 5000000 INFO @ Mon, 03 Jun 2019 06:29:19: 6000000 INFO @ Mon, 03 Jun 2019 06:29:20: 6000000 INFO @ Mon, 03 Jun 2019 06:29:27: 6000000 INFO @ Mon, 03 Jun 2019 06:29:27: 7000000 INFO @ Mon, 03 Jun 2019 06:29:28: 7000000 INFO @ Mon, 03 Jun 2019 06:29:35: 8000000 INFO @ Mon, 03 Jun 2019 06:29:35: 8000000 INFO @ Mon, 03 Jun 2019 06:29:35: 7000000 INFO @ Mon, 03 Jun 2019 06:29:42: 9000000 INFO @ Mon, 03 Jun 2019 06:29:43: 9000000 INFO @ Mon, 03 Jun 2019 06:29:44: 8000000 INFO @ Mon, 03 Jun 2019 06:29:50: 10000000 INFO @ Mon, 03 Jun 2019 06:29:51: 10000000 INFO @ Mon, 03 Jun 2019 06:29:53: 9000000 INFO @ Mon, 03 Jun 2019 06:29:57: 11000000 INFO @ Mon, 03 Jun 2019 06:29:58: 11000000 INFO @ Mon, 03 Jun 2019 06:30:02: 10000000 INFO @ Mon, 03 Jun 2019 06:30:05: 12000000 INFO @ Mon, 03 Jun 2019 06:30:06: 12000000 INFO @ Mon, 03 Jun 2019 06:30:11: 11000000 INFO @ Mon, 03 Jun 2019 06:30:12: 13000000 INFO @ Mon, 03 Jun 2019 06:30:13: 13000000 INFO @ Mon, 03 Jun 2019 06:30:20: 12000000 INFO @ Mon, 03 Jun 2019 06:30:20: 14000000 INFO @ Mon, 03 Jun 2019 06:30:21: 14000000 INFO @ Mon, 03 Jun 2019 06:30:28: 15000000 INFO @ Mon, 03 Jun 2019 06:30:29: 13000000 INFO @ Mon, 03 Jun 2019 06:30:29: 15000000 INFO @ Mon, 03 Jun 2019 06:30:35: 16000000 INFO @ Mon, 03 Jun 2019 06:30:37: 16000000 INFO @ Mon, 03 Jun 2019 06:30:38: 14000000 INFO @ Mon, 03 Jun 2019 06:30:43: 17000000 INFO @ Mon, 03 Jun 2019 06:30:45: 17000000 INFO @ Mon, 03 Jun 2019 06:30:47: 15000000 INFO @ Mon, 03 Jun 2019 06:30:50: 18000000 INFO @ Mon, 03 Jun 2019 06:30:53: 18000000 INFO @ Mon, 03 Jun 2019 06:30:55: 16000000 INFO @ Mon, 03 Jun 2019 06:30:58: 19000000 INFO @ Mon, 03 Jun 2019 06:31:00: 19000000 INFO @ Mon, 03 Jun 2019 06:31:04: 17000000 INFO @ Mon, 03 Jun 2019 06:31:05: 20000000 INFO @ Mon, 03 Jun 2019 06:31:08: 20000000 INFO @ Mon, 03 Jun 2019 06:31:13: 21000000 INFO @ Mon, 03 Jun 2019 06:31:13: 18000000 INFO @ Mon, 03 Jun 2019 06:31:15: 21000000 INFO @ Mon, 03 Jun 2019 06:31:20: 22000000 INFO @ Mon, 03 Jun 2019 06:31:22: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:31:22: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:31:22: #1 total tags in treatment: 22140845 INFO @ Mon, 03 Jun 2019 06:31:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:31:22: #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 06:31:22: 19000000 INFO @ Mon, 03 Jun 2019 06:31:22: #1 tags after filtering in treatment: 22140845 INFO @ Mon, 03 Jun 2019 06:31:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:31:22: #1 finished! INFO @ Mon, 03 Jun 2019 06:31:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:31:23: 22000000 INFO @ Mon, 03 Jun 2019 06:31:24: #2 number of paired peaks: 52 WARNING @ Mon, 03 Jun 2019 06:31:24: 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 06:31:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.20_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/SRX220296/SRX220296.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:31:24: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:31:24: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:31:24: #1 total tags in treatment: 22140845 INFO @ Mon, 03 Jun 2019 06:31:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:31:24: #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 06:31:25: #1 tags after filtering in treatment: 22140845 INFO @ Mon, 03 Jun 2019 06:31:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:31:25: #1 finished! INFO @ Mon, 03 Jun 2019 06:31:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:31:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:31:27: #2 number of paired peaks: 52 WARNING @ Mon, 03 Jun 2019 06:31:27: 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 06:31:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.10_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/SRX220296/SRX220296.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:31:31: 20000000 INFO @ Mon, 03 Jun 2019 06:31:39: 21000000 INFO @ Mon, 03 Jun 2019 06:31:48: 22000000 INFO @ Mon, 03 Jun 2019 06:31:49: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 06:31:49: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 06:31:49: #1 total tags in treatment: 22140845 INFO @ Mon, 03 Jun 2019 06:31:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:31:49: #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 06:31:49: #1 tags after filtering in treatment: 22140845 INFO @ Mon, 03 Jun 2019 06:31:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:31:49: #1 finished! INFO @ Mon, 03 Jun 2019 06:31:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:31:51: #2 number of paired peaks: 52 WARNING @ Mon, 03 Jun 2019 06:31:51: 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 06:31:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.05_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/SRX220296/SRX220296.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX220296/SRX220296.05_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。