Job ID = 4289136 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T04:40:09 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 ) spots read : 22,976,810 reads read : 45,953,620 reads written : 22,976,810 reads 0-length : 22,976,810 2019-12-10T04:50:47 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 : 26,123,577 reads read : 52,247,154 reads written : 26,123,577 reads 0-length : 26,123,577 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: 00:05:26 49100387 reads; of these: 49100387 (100.00%) were unpaired; of these: 29704631 (60.50%) aligned 0 times 13186939 (26.86%) aligned exactly 1 time 6208817 (12.65%) aligned >1 times 39.50% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9728627 / 19395756 = 0.5016 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:04:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.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 14:04:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:04:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:04:26: 1000000 INFO @ Tue, 10 Dec 2019 14:04:33: 2000000 INFO @ Tue, 10 Dec 2019 14:04:40: 3000000 INFO @ Tue, 10 Dec 2019 14:04:48: 4000000 INFO @ Tue, 10 Dec 2019 14:04:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.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 14:04:48: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:04:48: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:04:55: 5000000 INFO @ Tue, 10 Dec 2019 14:04:56: 1000000 INFO @ Tue, 10 Dec 2019 14:05:03: 6000000 INFO @ Tue, 10 Dec 2019 14:05:03: 2000000 INFO @ Tue, 10 Dec 2019 14:05:11: 7000000 INFO @ Tue, 10 Dec 2019 14:05:12: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:05:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.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 14:05:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:05:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:05:21: 8000000 INFO @ Tue, 10 Dec 2019 14:05:22: 4000000 INFO @ Tue, 10 Dec 2019 14:05:26: 1000000 INFO @ Tue, 10 Dec 2019 14:05:30: 9000000 INFO @ Tue, 10 Dec 2019 14:05:32: 5000000 INFO @ Tue, 10 Dec 2019 14:05:34: 2000000 INFO @ Tue, 10 Dec 2019 14:05:35: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:05:35: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:05:35: #1 total tags in treatment: 9667129 INFO @ Tue, 10 Dec 2019 14:05:35: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:05:35: #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 14:05:35: #1 tags after filtering in treatment: 9667129 INFO @ Tue, 10 Dec 2019 14:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:05:35: #1 finished! INFO @ Tue, 10 Dec 2019 14:05:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:05:36: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:05:36: 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 @ Tue, 10 Dec 2019 14:05:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.05_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/sacCer3/SRX5486256/SRX5486256.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:05:42: 3000000 INFO @ Tue, 10 Dec 2019 14:05:43: 6000000 INFO @ Tue, 10 Dec 2019 14:05:50: 4000000 INFO @ Tue, 10 Dec 2019 14:05:56: 7000000 INFO @ Tue, 10 Dec 2019 14:05:58: 5000000 INFO @ Tue, 10 Dec 2019 14:06:06: 6000000 INFO @ Tue, 10 Dec 2019 14:06:08: 8000000 INFO @ Tue, 10 Dec 2019 14:06:14: 7000000 INFO @ Tue, 10 Dec 2019 14:06:21: 9000000 INFO @ Tue, 10 Dec 2019 14:06:22: 8000000 INFO @ Tue, 10 Dec 2019 14:06:28: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:06:28: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:06:28: #1 total tags in treatment: 9667129 INFO @ Tue, 10 Dec 2019 14:06:28: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:06:28: #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 14:06:28: #1 tags after filtering in treatment: 9667129 INFO @ Tue, 10 Dec 2019 14:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:06:28: #1 finished! INFO @ Tue, 10 Dec 2019 14:06:28: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:06:29: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:06:29: 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 @ Tue, 10 Dec 2019 14:06:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.10_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/sacCer3/SRX5486256/SRX5486256.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:06:30: 9000000 INFO @ Tue, 10 Dec 2019 14:06:36: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 14:06:36: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 14:06:36: #1 total tags in treatment: 9667129 INFO @ Tue, 10 Dec 2019 14:06:36: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:06:36: #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 14:06:36: #1 tags after filtering in treatment: 9667129 INFO @ Tue, 10 Dec 2019 14:06:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:06:36: #1 finished! INFO @ Tue, 10 Dec 2019 14:06:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:06:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:06:37: #2 number of paired peaks: 0 WARNING @ Tue, 10 Dec 2019 14:06:37: 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 @ Tue, 10 Dec 2019 14:06:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.20_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/SRX5486256/SRX5486256.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5486256/SRX5486256.20_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。