Job ID = 1308874 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:11:57 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 : 47,077,808 reads read : 94,155,616 reads written : 47,077,808 reads 0-length : 47,077,808 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: 00:36:08 47077808 reads; of these: 47077808 (100.00%) were unpaired; of these: 2761547 (5.87%) aligned 0 times 25259302 (53.65%) aligned exactly 1 time 19056959 (40.48%) aligned >1 times 94.13% overall alignment rate Time searching: 00:36:08 Overall time: 00:36:08 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] 11290137 / 44316261 = 0.2548 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 @ Tue, 04 Jun 2019 00:01:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.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 @ Tue, 04 Jun 2019 00:01:39: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:01:39: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:01:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.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 @ Tue, 04 Jun 2019 00:01:39: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:01:39: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:01:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.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 @ Tue, 04 Jun 2019 00:01:39: #1 read tag files... INFO @ Tue, 04 Jun 2019 00:01:39: #1 read treatment tags... INFO @ Tue, 04 Jun 2019 00:01:47: 1000000 INFO @ Tue, 04 Jun 2019 00:01:47: 1000000 INFO @ Tue, 04 Jun 2019 00:01:48: 1000000 INFO @ Tue, 04 Jun 2019 00:01:54: 2000000 INFO @ Tue, 04 Jun 2019 00:01:55: 2000000 INFO @ Tue, 04 Jun 2019 00:01:55: 2000000 INFO @ Tue, 04 Jun 2019 00:02:00: 3000000 INFO @ Tue, 04 Jun 2019 00:02:02: 3000000 INFO @ Tue, 04 Jun 2019 00:02:03: 3000000 INFO @ Tue, 04 Jun 2019 00:02:07: 4000000 INFO @ Tue, 04 Jun 2019 00:02:10: 4000000 INFO @ Tue, 04 Jun 2019 00:02:11: 4000000 INFO @ Tue, 04 Jun 2019 00:02:14: 5000000 INFO @ Tue, 04 Jun 2019 00:02:17: 5000000 INFO @ Tue, 04 Jun 2019 00:02:18: 5000000 INFO @ Tue, 04 Jun 2019 00:02:20: 6000000 INFO @ Tue, 04 Jun 2019 00:02:24: 6000000 INFO @ Tue, 04 Jun 2019 00:02:26: 6000000 INFO @ Tue, 04 Jun 2019 00:02:27: 7000000 INFO @ Tue, 04 Jun 2019 00:02:32: 7000000 INFO @ Tue, 04 Jun 2019 00:02:33: 7000000 INFO @ Tue, 04 Jun 2019 00:02:34: 8000000 INFO @ Tue, 04 Jun 2019 00:02:39: 8000000 INFO @ Tue, 04 Jun 2019 00:02:41: 9000000 INFO @ Tue, 04 Jun 2019 00:02:41: 8000000 INFO @ Tue, 04 Jun 2019 00:02:46: 9000000 INFO @ Tue, 04 Jun 2019 00:02:47: 10000000 INFO @ Tue, 04 Jun 2019 00:02:48: 9000000 INFO @ Tue, 04 Jun 2019 00:02:53: 10000000 INFO @ Tue, 04 Jun 2019 00:02:54: 11000000 INFO @ Tue, 04 Jun 2019 00:02:56: 10000000 INFO @ Tue, 04 Jun 2019 00:03:01: 11000000 INFO @ Tue, 04 Jun 2019 00:03:02: 12000000 INFO @ Tue, 04 Jun 2019 00:03:03: 11000000 INFO @ Tue, 04 Jun 2019 00:03:09: 13000000 INFO @ Tue, 04 Jun 2019 00:03:09: 12000000 INFO @ Tue, 04 Jun 2019 00:03:12: 12000000 INFO @ Tue, 04 Jun 2019 00:03:16: 13000000 INFO @ Tue, 04 Jun 2019 00:03:17: 14000000 INFO @ Tue, 04 Jun 2019 00:03:20: 13000000 INFO @ Tue, 04 Jun 2019 00:03:25: 15000000 INFO @ Tue, 04 Jun 2019 00:03:25: 14000000 INFO @ Tue, 04 Jun 2019 00:03:29: 14000000 INFO @ Tue, 04 Jun 2019 00:03:33: 16000000 INFO @ Tue, 04 Jun 2019 00:03:33: 15000000 INFO @ Tue, 04 Jun 2019 00:03:37: 15000000 INFO @ Tue, 04 Jun 2019 00:03:41: 17000000 INFO @ Tue, 04 Jun 2019 00:03:42: 16000000 INFO @ Tue, 04 Jun 2019 00:03:46: 16000000 INFO @ Tue, 04 Jun 2019 00:03:49: 18000000 INFO @ Tue, 04 Jun 2019 00:03:50: 17000000 INFO @ Tue, 04 Jun 2019 00:03:55: 17000000 INFO @ Tue, 04 Jun 2019 00:03:57: 19000000 INFO @ Tue, 04 Jun 2019 00:03:59: 18000000 INFO @ Tue, 04 Jun 2019 00:04:04: 18000000 INFO @ Tue, 04 Jun 2019 00:04:05: 20000000 INFO @ Tue, 04 Jun 2019 00:04:07: 19000000 INFO @ Tue, 04 Jun 2019 00:04:12: 21000000 INFO @ Tue, 04 Jun 2019 00:04:13: 19000000 INFO @ Tue, 04 Jun 2019 00:04:15: 20000000 INFO @ Tue, 04 Jun 2019 00:04:18: 22000000 INFO @ Tue, 04 Jun 2019 00:04:22: 20000000 INFO @ Tue, 04 Jun 2019 00:04:23: 21000000 INFO @ Tue, 04 Jun 2019 00:04:25: 23000000 INFO @ Tue, 04 Jun 2019 00:04:29: 21000000 INFO @ Tue, 04 Jun 2019 00:04:30: 22000000 INFO @ Tue, 04 Jun 2019 00:04:31: 24000000 INFO @ Tue, 04 Jun 2019 00:04:37: 22000000 INFO @ Tue, 04 Jun 2019 00:04:37: 23000000 INFO @ Tue, 04 Jun 2019 00:04:38: 25000000 INFO @ Tue, 04 Jun 2019 00:04:44: 24000000 INFO @ Tue, 04 Jun 2019 00:04:44: 23000000 INFO @ Tue, 04 Jun 2019 00:04:46: 26000000 INFO @ Tue, 04 Jun 2019 00:04:51: 25000000 INFO @ Tue, 04 Jun 2019 00:04:52: 24000000 INFO @ Tue, 04 Jun 2019 00:04:53: 27000000 INFO @ Tue, 04 Jun 2019 00:04:59: 25000000 INFO @ Tue, 04 Jun 2019 00:04:59: 26000000 INFO @ Tue, 04 Jun 2019 00:05:00: 28000000 INFO @ Tue, 04 Jun 2019 00:05:06: 29000000 INFO @ Tue, 04 Jun 2019 00:05:07: 27000000 INFO @ Tue, 04 Jun 2019 00:05:07: 26000000 INFO @ Tue, 04 Jun 2019 00:05:13: 30000000 INFO @ Tue, 04 Jun 2019 00:05:14: 28000000 INFO @ Tue, 04 Jun 2019 00:05:15: 27000000 INFO @ Tue, 04 Jun 2019 00:05:20: 31000000 INFO @ Tue, 04 Jun 2019 00:05:22: 29000000 INFO @ Tue, 04 Jun 2019 00:05:23: 28000000 INFO @ Tue, 04 Jun 2019 00:05:27: 32000000 INFO @ Tue, 04 Jun 2019 00:05:29: 30000000 INFO @ Tue, 04 Jun 2019 00:05:31: 29000000 INFO @ Tue, 04 Jun 2019 00:05:33: 33000000 INFO @ Tue, 04 Jun 2019 00:05:34: #1 tag size is determined as 62 bps INFO @ Tue, 04 Jun 2019 00:05:34: #1 tag size = 62 INFO @ Tue, 04 Jun 2019 00:05:34: #1 total tags in treatment: 33026124 INFO @ Tue, 04 Jun 2019 00:05:34: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:05:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:05:34: #1 tags after filtering in treatment: 33026124 INFO @ Tue, 04 Jun 2019 00:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:05:34: #1 finished! INFO @ Tue, 04 Jun 2019 00:05:34: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:05:36: 31000000 INFO @ Tue, 04 Jun 2019 00:05:37: #2 number of paired peaks: 34 WARNING @ Tue, 04 Jun 2019 00:05:37: Too few paired peaks (34) 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 @ Tue, 04 Jun 2019 00:05:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.05_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/SRX5661478/SRX5661478.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 04 Jun 2019 00:05:38: 30000000 INFO @ Tue, 04 Jun 2019 00:05:43: 32000000 INFO @ Tue, 04 Jun 2019 00:05:45: 31000000 INFO @ Tue, 04 Jun 2019 00:05:50: 33000000 INFO @ Tue, 04 Jun 2019 00:05:50: #1 tag size is determined as 62 bps INFO @ Tue, 04 Jun 2019 00:05:50: #1 tag size = 62 INFO @ Tue, 04 Jun 2019 00:05:50: #1 total tags in treatment: 33026124 INFO @ Tue, 04 Jun 2019 00:05:50: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:05:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:05:51: #1 tags after filtering in treatment: 33026124 INFO @ Tue, 04 Jun 2019 00:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:05:51: #1 finished! INFO @ Tue, 04 Jun 2019 00:05:51: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:05:52: 32000000 INFO @ Tue, 04 Jun 2019 00:05:54: #2 number of paired peaks: 34 WARNING @ Tue, 04 Jun 2019 00:05:54: Too few paired peaks (34) 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 @ Tue, 04 Jun 2019 00:05:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.10_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/SRX5661478/SRX5661478.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 04 Jun 2019 00:05:59: 33000000 INFO @ Tue, 04 Jun 2019 00:06:00: #1 tag size is determined as 62 bps INFO @ Tue, 04 Jun 2019 00:06:00: #1 tag size = 62 INFO @ Tue, 04 Jun 2019 00:06:00: #1 total tags in treatment: 33026124 INFO @ Tue, 04 Jun 2019 00:06:00: #1 user defined the maximum tags... INFO @ Tue, 04 Jun 2019 00:06:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Jun 2019 00:06:00: #1 tags after filtering in treatment: 33026124 INFO @ Tue, 04 Jun 2019 00:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 04 Jun 2019 00:06:00: #1 finished! INFO @ Tue, 04 Jun 2019 00:06:00: #2 Build Peak Model... INFO @ Tue, 04 Jun 2019 00:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Jun 2019 00:06:03: #2 number of paired peaks: 34 WARNING @ Tue, 04 Jun 2019 00:06:03: Too few paired peaks (34) 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 @ Tue, 04 Jun 2019 00:06:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.20_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/SRX5661478/SRX5661478.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5661478/SRX5661478.20_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。