Job ID = 2640903 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,285,849 reads read : 6,285,849 reads written : 6,285,849 2019-08-24T10:53:40 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 ) 2019-08-24T10:53:40 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 ) 2019-08-24T10:53:40 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 ) 2019-08-24T10:53:40 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 : 6,033,331 reads read : 6,033,331 reads written : 6,033,331 spots read : 6,387,840 reads read : 6,387,840 reads written : 6,387,840 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: 00:03:09 18707020 reads; of these: 18707020 (100.00%) were unpaired; of these: 1108399 (5.93%) aligned 0 times 13497399 (72.15%) aligned exactly 1 time 4101222 (21.92%) aligned >1 times 94.07% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 8318229 / 17598621 = 0.4727 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.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 @ Sat, 24 Aug 2019 20:05:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:05:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:05:56: 1000000 INFO @ Sat, 24 Aug 2019 20:06:04: 2000000 INFO @ Sat, 24 Aug 2019 20:06:12: 3000000 INFO @ Sat, 24 Aug 2019 20:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.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 @ Sat, 24 Aug 2019 20:06:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:06:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:06:19: 4000000 INFO @ Sat, 24 Aug 2019 20:06:26: 1000000 INFO @ Sat, 24 Aug 2019 20:06:27: 5000000 INFO @ Sat, 24 Aug 2019 20:06:33: 2000000 INFO @ Sat, 24 Aug 2019 20:06:35: 6000000 INFO @ Sat, 24 Aug 2019 20:06:40: 3000000 INFO @ Sat, 24 Aug 2019 20:06:43: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:06:47: 4000000 INFO @ Sat, 24 Aug 2019 20:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.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 @ Sat, 24 Aug 2019 20:06:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:06:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:06:51: 8000000 INFO @ Sat, 24 Aug 2019 20:06:54: 5000000 INFO @ Sat, 24 Aug 2019 20:06:57: 1000000 INFO @ Sat, 24 Aug 2019 20:06:59: 9000000 INFO @ Sat, 24 Aug 2019 20:07:01: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:07:01: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:07:01: #1 total tags in treatment: 9280392 INFO @ Sat, 24 Aug 2019 20:07:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:07:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:07:01: #1 tags after filtering in treatment: 9280392 INFO @ Sat, 24 Aug 2019 20:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:07:01: #1 finished! INFO @ Sat, 24 Aug 2019 20:07:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:07:02: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:07:02: 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 @ Sat, 24 Aug 2019 20:07:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.05_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/SRX4292270/SRX4292270.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:07:02: 6000000 INFO @ Sat, 24 Aug 2019 20:07:04: 2000000 INFO @ Sat, 24 Aug 2019 20:07:09: 7000000 INFO @ Sat, 24 Aug 2019 20:07:11: 3000000 INFO @ Sat, 24 Aug 2019 20:07:16: 8000000 INFO @ Sat, 24 Aug 2019 20:07:18: 4000000 INFO @ Sat, 24 Aug 2019 20:07:23: 9000000 INFO @ Sat, 24 Aug 2019 20:07:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:07:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:07:25: #1 total tags in treatment: 9280392 INFO @ Sat, 24 Aug 2019 20:07:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:07:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:07:25: #1 tags after filtering in treatment: 9280392 INFO @ Sat, 24 Aug 2019 20:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:07:25: #1 finished! INFO @ Sat, 24 Aug 2019 20:07:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:07:25: 5000000 INFO @ Sat, 24 Aug 2019 20:07:26: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:07:26: 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 @ Sat, 24 Aug 2019 20:07:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.10_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/SRX4292270/SRX4292270.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:07:33: 6000000 INFO @ Sat, 24 Aug 2019 20:07:40: 7000000 INFO @ Sat, 24 Aug 2019 20:07:47: 8000000 INFO @ Sat, 24 Aug 2019 20:07:54: 9000000 INFO @ Sat, 24 Aug 2019 20:07:56: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:07:56: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:07:56: #1 total tags in treatment: 9280392 INFO @ Sat, 24 Aug 2019 20:07:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:07:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 20:07:56: #1 tags after filtering in treatment: 9280392 INFO @ Sat, 24 Aug 2019 20:07:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:07:56: #1 finished! INFO @ Sat, 24 Aug 2019 20:07:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:07:57: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:07:57: 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 @ Sat, 24 Aug 2019 20:07:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.20_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/SRX4292270/SRX4292270.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292270/SRX4292270.20_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。