Job ID = 1293874 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:02:09 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 ) 2019-06-02T18:02:10 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 : 49,215,113 reads read : 49,215,113 reads written : 49,215,113 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: 00:13:58 49215113 reads; of these: 49215113 (100.00%) were unpaired; of these: 5459538 (11.09%) aligned 0 times 36642798 (74.45%) aligned exactly 1 time 7112777 (14.45%) aligned >1 times 88.91% overall alignment rate Time searching: 00:13:58 Overall time: 00:13:58 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 20 files... [bam_rmdupse_core] 18088965 / 43755575 = 0.4134 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 03:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.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 03:27:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:27:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.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 03:27:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:27:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.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 03:27:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:27:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:27:26: 1000000 INFO @ Mon, 03 Jun 2019 03:27:27: 1000000 INFO @ Mon, 03 Jun 2019 03:27:27: 1000000 INFO @ Mon, 03 Jun 2019 03:27:35: 2000000 INFO @ Mon, 03 Jun 2019 03:27:36: 2000000 INFO @ Mon, 03 Jun 2019 03:27:36: 2000000 INFO @ Mon, 03 Jun 2019 03:27:43: 3000000 INFO @ Mon, 03 Jun 2019 03:27:46: 3000000 INFO @ Mon, 03 Jun 2019 03:27:47: 3000000 INFO @ Mon, 03 Jun 2019 03:27:52: 4000000 INFO @ Mon, 03 Jun 2019 03:27:55: 4000000 INFO @ Mon, 03 Jun 2019 03:27:57: 4000000 INFO @ Mon, 03 Jun 2019 03:28:01: 5000000 INFO @ Mon, 03 Jun 2019 03:28:05: 5000000 INFO @ Mon, 03 Jun 2019 03:28:06: 5000000 INFO @ Mon, 03 Jun 2019 03:28:09: 6000000 INFO @ Mon, 03 Jun 2019 03:28:14: 6000000 INFO @ Mon, 03 Jun 2019 03:28:16: 6000000 INFO @ Mon, 03 Jun 2019 03:28:18: 7000000 INFO @ Mon, 03 Jun 2019 03:28:23: 7000000 INFO @ Mon, 03 Jun 2019 03:28:25: 7000000 INFO @ Mon, 03 Jun 2019 03:28:26: 8000000 INFO @ Mon, 03 Jun 2019 03:28:32: 8000000 INFO @ Mon, 03 Jun 2019 03:28:35: 8000000 INFO @ Mon, 03 Jun 2019 03:28:35: 9000000 INFO @ Mon, 03 Jun 2019 03:28:41: 9000000 INFO @ Mon, 03 Jun 2019 03:28:44: 10000000 INFO @ Mon, 03 Jun 2019 03:28:45: 9000000 INFO @ Mon, 03 Jun 2019 03:28:50: 10000000 INFO @ Mon, 03 Jun 2019 03:28:52: 11000000 INFO @ Mon, 03 Jun 2019 03:28:54: 10000000 INFO @ Mon, 03 Jun 2019 03:28:58: 11000000 INFO @ Mon, 03 Jun 2019 03:29:01: 12000000 INFO @ Mon, 03 Jun 2019 03:29:03: 11000000 INFO @ Mon, 03 Jun 2019 03:29:07: 12000000 INFO @ Mon, 03 Jun 2019 03:29:09: 13000000 INFO @ Mon, 03 Jun 2019 03:29:13: 12000000 INFO @ Mon, 03 Jun 2019 03:29:15: 13000000 INFO @ Mon, 03 Jun 2019 03:29:18: 14000000 INFO @ Mon, 03 Jun 2019 03:29:23: 13000000 INFO @ Mon, 03 Jun 2019 03:29:24: 14000000 INFO @ Mon, 03 Jun 2019 03:29:26: 15000000 INFO @ Mon, 03 Jun 2019 03:29:32: 14000000 INFO @ Mon, 03 Jun 2019 03:29:32: 15000000 INFO @ Mon, 03 Jun 2019 03:29:35: 16000000 INFO @ Mon, 03 Jun 2019 03:29:41: 16000000 INFO @ Mon, 03 Jun 2019 03:29:41: 15000000 INFO @ Mon, 03 Jun 2019 03:29:43: 17000000 INFO @ Mon, 03 Jun 2019 03:29:49: 17000000 INFO @ Mon, 03 Jun 2019 03:29:50: 16000000 INFO @ Mon, 03 Jun 2019 03:29:52: 18000000 INFO @ Mon, 03 Jun 2019 03:29:58: 18000000 INFO @ Mon, 03 Jun 2019 03:29:59: 17000000 INFO @ Mon, 03 Jun 2019 03:30:00: 19000000 INFO @ Mon, 03 Jun 2019 03:30:07: 19000000 INFO @ Mon, 03 Jun 2019 03:30:09: 20000000 INFO @ Mon, 03 Jun 2019 03:30:09: 18000000 INFO @ Mon, 03 Jun 2019 03:30:16: 20000000 INFO @ Mon, 03 Jun 2019 03:30:18: 21000000 INFO @ Mon, 03 Jun 2019 03:30:19: 19000000 INFO @ Mon, 03 Jun 2019 03:30:24: 21000000 INFO @ Mon, 03 Jun 2019 03:30:26: 22000000 INFO @ Mon, 03 Jun 2019 03:30:28: 20000000 INFO @ Mon, 03 Jun 2019 03:30:33: 22000000 INFO @ Mon, 03 Jun 2019 03:30:34: 23000000 INFO @ Mon, 03 Jun 2019 03:30:37: 21000000 INFO @ Mon, 03 Jun 2019 03:30:41: 23000000 INFO @ Mon, 03 Jun 2019 03:30:43: 24000000 INFO @ Mon, 03 Jun 2019 03:30:46: 22000000 INFO @ Mon, 03 Jun 2019 03:30:50: 24000000 INFO @ Mon, 03 Jun 2019 03:30:51: 25000000 INFO @ Mon, 03 Jun 2019 03:30:56: 23000000 INFO @ Mon, 03 Jun 2019 03:30:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:30:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:30:57: #1 total tags in treatment: 25666610 INFO @ Mon, 03 Jun 2019 03:30:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:30:57: #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 03:30:58: #1 tags after filtering in treatment: 25666610 INFO @ Mon, 03 Jun 2019 03:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:30:58: #1 finished! INFO @ Mon, 03 Jun 2019 03:30:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:30:58: 25000000 INFO @ Mon, 03 Jun 2019 03:31:00: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 03:31:00: Too few paired peaks (0) 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 03:31:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.20_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/SRX135517/SRX135517.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:31:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:31:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:31:04: #1 total tags in treatment: 25666610 INFO @ Mon, 03 Jun 2019 03:31:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:31:04: #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 03:31:05: 24000000 INFO @ Mon, 03 Jun 2019 03:31:05: #1 tags after filtering in treatment: 25666610 INFO @ Mon, 03 Jun 2019 03:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:31:05: #1 finished! INFO @ Mon, 03 Jun 2019 03:31:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:31:07: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 03:31:07: Too few paired peaks (0) 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 03:31:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.05_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/SRX135517/SRX135517.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:31:14: 25000000 INFO @ Mon, 03 Jun 2019 03:31:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:31:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:31:19: #1 total tags in treatment: 25666610 INFO @ Mon, 03 Jun 2019 03:31:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:31:19: #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 03:31:20: #1 tags after filtering in treatment: 25666610 INFO @ Mon, 03 Jun 2019 03:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:31:20: #1 finished! INFO @ Mon, 03 Jun 2019 03:31:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:31:22: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 03:31:22: Too few paired peaks (0) 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 03:31:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.10_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/SRX135517/SRX135517.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX135517/SRX135517.10_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。