Job ID = 2640901 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,223,322 reads read : 7,223,322 reads written : 7,223,322 spots read : 8,044,625 reads read : 8,044,625 reads written : 8,044,625 2019-08-24T10:58:16 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 ) 2019-08-24T10:58:58 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 : 8,533,880 reads read : 8,533,880 reads written : 8,533,880 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: 00:04:40 23801827 reads; of these: 23801827 (100.00%) were unpaired; of these: 1101893 (4.63%) aligned 0 times 17180628 (72.18%) aligned exactly 1 time 5519306 (23.19%) aligned >1 times 95.37% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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 12 files... [bam_rmdupse_core] 11259898 / 22699934 = 0.4960 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.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 20:12:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:12:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:12:23: 1000000 INFO @ Sat, 24 Aug 2019 20:12:30: 2000000 INFO @ Sat, 24 Aug 2019 20:12:38: 3000000 INFO @ Sat, 24 Aug 2019 20:12:45: 4000000 INFO @ Sat, 24 Aug 2019 20:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.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 20:12:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:12:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:12:53: 5000000 INFO @ Sat, 24 Aug 2019 20:12:53: 1000000 INFO @ Sat, 24 Aug 2019 20:13:00: 6000000 INFO @ Sat, 24 Aug 2019 20:13:01: 2000000 INFO @ Sat, 24 Aug 2019 20:13:08: 7000000 INFO @ Sat, 24 Aug 2019 20:13:09: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.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 20:13:16: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:13:16: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:13:16: 8000000 INFO @ Sat, 24 Aug 2019 20:13:17: 4000000 INFO @ Sat, 24 Aug 2019 20:13:24: 9000000 INFO @ Sat, 24 Aug 2019 20:13:25: 1000000 INFO @ Sat, 24 Aug 2019 20:13:25: 5000000 INFO @ Sat, 24 Aug 2019 20:13:32: 10000000 INFO @ Sat, 24 Aug 2019 20:13:33: 6000000 INFO @ Sat, 24 Aug 2019 20:13:33: 2000000 INFO @ Sat, 24 Aug 2019 20:13:39: 11000000 INFO @ Sat, 24 Aug 2019 20:13:41: 7000000 INFO @ Sat, 24 Aug 2019 20:13:41: 3000000 INFO @ Sat, 24 Aug 2019 20:13:42: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:13:42: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:13:42: #1 total tags in treatment: 11440036 INFO @ Sat, 24 Aug 2019 20:13:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:13:42: #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 20:13:43: #1 tags after filtering in treatment: 11440036 INFO @ Sat, 24 Aug 2019 20:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:13:43: #1 finished! INFO @ Sat, 24 Aug 2019 20:13:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:13:44: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:13:44: 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 20:13:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.05_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/SRX4292268/SRX4292268.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:13:48: 4000000 INFO @ Sat, 24 Aug 2019 20:13:48: 8000000 INFO @ Sat, 24 Aug 2019 20:13:56: 5000000 INFO @ Sat, 24 Aug 2019 20:13:57: 9000000 INFO @ Sat, 24 Aug 2019 20:14:04: 6000000 INFO @ Sat, 24 Aug 2019 20:14:05: 10000000 INFO @ Sat, 24 Aug 2019 20:14:11: 7000000 INFO @ Sat, 24 Aug 2019 20:14:13: 11000000 INFO @ Sat, 24 Aug 2019 20:14:17: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:14:17: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:14:17: #1 total tags in treatment: 11440036 INFO @ Sat, 24 Aug 2019 20:14:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:14:17: #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 20:14:17: #1 tags after filtering in treatment: 11440036 INFO @ Sat, 24 Aug 2019 20:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:14:17: #1 finished! INFO @ Sat, 24 Aug 2019 20:14:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:14:18: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:14:18: 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 20:14:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.10_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/SRX4292268/SRX4292268.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:14:19: 8000000 INFO @ Sat, 24 Aug 2019 20:14:26: 9000000 INFO @ Sat, 24 Aug 2019 20:14:33: 10000000 INFO @ Sat, 24 Aug 2019 20:14:40: 11000000 INFO @ Sat, 24 Aug 2019 20:14:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:14:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:14:43: #1 total tags in treatment: 11440036 INFO @ Sat, 24 Aug 2019 20:14:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:14:43: #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 20:14:43: #1 tags after filtering in treatment: 11440036 INFO @ Sat, 24 Aug 2019 20:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:14:43: #1 finished! INFO @ Sat, 24 Aug 2019 20:14:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:14:44: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:14:44: 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 20:14:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.20_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/SRX4292268/SRX4292268.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292268/SRX4292268.20_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。