Job ID = 4289154 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,221,352 reads read : 22,442,704 reads written : 11,221,352 reads 0-length : 11,221,352 2019-12-10T04:44:36 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 : 10,927,152 reads read : 21,854,304 reads written : 10,927,152 reads 0-length : 10,927,152 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: 00:03:15 22148504 reads; of these: 22148504 (100.00%) were unpaired; of these: 14013641 (63.27%) aligned 0 times 5226375 (23.60%) aligned exactly 1 time 2908488 (13.13%) aligned >1 times 36.73% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 3469833 / 8134863 = 0.4265 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Dec 2019 13:51:55: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:51:55: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:02: 1000000 INFO @ Tue, 10 Dec 2019 13:52:08: 2000000 INFO @ Tue, 10 Dec 2019 13:52:14: 3000000 INFO @ Tue, 10 Dec 2019 13:52:21: 4000000 INFO @ Tue, 10 Dec 2019 13:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Dec 2019 13:52:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:52:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:26: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:52:26: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:52:26: #1 total tags in treatment: 4665030 INFO @ Tue, 10 Dec 2019 13:52:26: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:52:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:52:26: #1 tags after filtering in treatment: 4665030 INFO @ Tue, 10 Dec 2019 13:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:52:26: #1 finished! INFO @ Tue, 10 Dec 2019 13:52:26: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:52:26: #2 number of paired peaks: 29 WARNING @ Tue, 10 Dec 2019 13:52:26: 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 @ Tue, 10 Dec 2019 13:52:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.05_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/sacCer3/SRX6616768/SRX6616768.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:52:32: 1000000 INFO @ Tue, 10 Dec 2019 13:52:40: 2000000 INFO @ Tue, 10 Dec 2019 13:52:46: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:52:53: 4000000 INFO @ Tue, 10 Dec 2019 13:52:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 10 Dec 2019 13:52:57: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:52:57: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:52:59: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:52:59: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:52:59: #1 total tags in treatment: 4665030 INFO @ Tue, 10 Dec 2019 13:52:59: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:52:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:52:59: #1 tags after filtering in treatment: 4665030 INFO @ Tue, 10 Dec 2019 13:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:52:59: #1 finished! INFO @ Tue, 10 Dec 2019 13:52:59: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:52:59: #2 number of paired peaks: 29 WARNING @ Tue, 10 Dec 2019 13:52:59: 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 @ Tue, 10 Dec 2019 13:52:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.10_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/sacCer3/SRX6616768/SRX6616768.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:53:05: 1000000 INFO @ Tue, 10 Dec 2019 13:53:14: 2000000 INFO @ Tue, 10 Dec 2019 13:53:20: 3000000 INFO @ Tue, 10 Dec 2019 13:53:27: 4000000 INFO @ Tue, 10 Dec 2019 13:53:32: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:53:32: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:53:32: #1 total tags in treatment: 4665030 INFO @ Tue, 10 Dec 2019 13:53:32: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:53:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:53:32: #1 tags after filtering in treatment: 4665030 INFO @ Tue, 10 Dec 2019 13:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:53:32: #1 finished! INFO @ Tue, 10 Dec 2019 13:53:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:53:33: #2 number of paired peaks: 29 WARNING @ Tue, 10 Dec 2019 13:53:33: 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 @ Tue, 10 Dec 2019 13:53:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.20_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/sacCer3/SRX6616768/SRX6616768.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6616768/SRX6616768.20_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。