Job ID = 2640914 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,528,991 reads read : 5,528,991 reads written : 5,528,991 2019-08-24T10:55:11 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 : 6,571,350 reads read : 6,571,350 reads written : 6,571,350 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: 00:02:10 12100341 reads; of these: 12100341 (100.00%) were unpaired; of these: 158818 (1.31%) aligned 0 times 10224569 (84.50%) aligned exactly 1 time 1716954 (14.19%) aligned >1 times 98.69% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 4887994 / 11941523 = 0.4093 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.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 20:02:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:02:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:02:26: 1000000 INFO @ Sat, 24 Aug 2019 20:02:33: 2000000 INFO @ Sat, 24 Aug 2019 20:02:40: 3000000 INFO @ Sat, 24 Aug 2019 20:02:47: 4000000 INFO @ Sat, 24 Aug 2019 20:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.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 20:02:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:02:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:02:53: 5000000 INFO @ Sat, 24 Aug 2019 20:02:56: 1000000 INFO @ Sat, 24 Aug 2019 20:03:00: 6000000 INFO @ Sat, 24 Aug 2019 20:03:05: 2000000 INFO @ Sat, 24 Aug 2019 20:03:07: 7000000 INFO @ Sat, 24 Aug 2019 20:03:08: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:03:08: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:03:08: #1 total tags in treatment: 7053529 INFO @ Sat, 24 Aug 2019 20:03:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:03:08: #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 20:03:08: #1 tags after filtering in treatment: 7053529 INFO @ Sat, 24 Aug 2019 20:03:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:03:08: #1 finished! INFO @ Sat, 24 Aug 2019 20:03:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:03:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:03:08: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:03:08: 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 20:03:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.05_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/SRX4292278/SRX4292278.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:03:13: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.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 20:03:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:03:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:03:21: 4000000 INFO @ Sat, 24 Aug 2019 20:03:25: 1000000 INFO @ Sat, 24 Aug 2019 20:03:29: 5000000 INFO @ Sat, 24 Aug 2019 20:03:32: 2000000 INFO @ Sat, 24 Aug 2019 20:03:37: 6000000 INFO @ Sat, 24 Aug 2019 20:03:39: 3000000 INFO @ Sat, 24 Aug 2019 20:03:45: 7000000 INFO @ Sat, 24 Aug 2019 20:03:45: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:03:45: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:03:45: #1 total tags in treatment: 7053529 INFO @ Sat, 24 Aug 2019 20:03:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:03:45: #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 20:03:45: #1 tags after filtering in treatment: 7053529 INFO @ Sat, 24 Aug 2019 20:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:03:45: #1 finished! INFO @ Sat, 24 Aug 2019 20:03:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:03:46: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:03:46: 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 20:03:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.10_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/SRX4292278/SRX4292278.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:03:46: 4000000 INFO @ Sat, 24 Aug 2019 20:03:53: 5000000 INFO @ Sat, 24 Aug 2019 20:04:00: 6000000 INFO @ Sat, 24 Aug 2019 20:04:07: 7000000 INFO @ Sat, 24 Aug 2019 20:04:07: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:04:07: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:04:07: #1 total tags in treatment: 7053529 INFO @ Sat, 24 Aug 2019 20:04:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:04:07: #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 20:04:07: #1 tags after filtering in treatment: 7053529 INFO @ Sat, 24 Aug 2019 20:04:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:04:07: #1 finished! INFO @ Sat, 24 Aug 2019 20:04:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:04:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:04:08: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:04:08: 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 20:04:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.20_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/SRX4292278/SRX4292278.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292278/SRX4292278.20_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。