Job ID = 2640909 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,496,792 reads read : 7,496,792 reads written : 7,496,792 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 ) 2019-08-24T10:56:30 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 : 8,220,814 reads read : 8,220,814 reads written : 8,220,814 spots read : 8,230,081 reads read : 8,230,081 reads written : 8,230,081 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: 00:04:10 23947687 reads; of these: 23947687 (100.00%) were unpaired; of these: 2511708 (10.49%) aligned 0 times 16167594 (67.51%) aligned exactly 1 time 5268385 (22.00%) aligned >1 times 89.51% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 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 12 files... [bam_rmdupse_core] 10996400 / 21435979 = 0.5130 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:15:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.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 20:15:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:15:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:16:07: 1000000 INFO @ Sat, 24 Aug 2019 20:16:14: 2000000 INFO @ Sat, 24 Aug 2019 20:16:21: 3000000 INFO @ Sat, 24 Aug 2019 20:16:27: 4000000 INFO @ Sat, 24 Aug 2019 20:16:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.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 20:16:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:16:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:16:34: 5000000 INFO @ Sat, 24 Aug 2019 20:16:37: 1000000 INFO @ Sat, 24 Aug 2019 20:16:40: 6000000 INFO @ Sat, 24 Aug 2019 20:16:46: 2000000 INFO @ Sat, 24 Aug 2019 20:16:47: 7000000 INFO @ Sat, 24 Aug 2019 20:16:53: 8000000 INFO @ Sat, 24 Aug 2019 20:16:54: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:16:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.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 20:16:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:16:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:17:00: 9000000 INFO @ Sat, 24 Aug 2019 20:17:03: 4000000 INFO @ Sat, 24 Aug 2019 20:17:07: 10000000 INFO @ Sat, 24 Aug 2019 20:17:08: 1000000 INFO @ Sat, 24 Aug 2019 20:17:11: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:17:11: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:17:11: #1 total tags in treatment: 10439579 INFO @ Sat, 24 Aug 2019 20:17:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:17:11: #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 20:17:11: #1 tags after filtering in treatment: 10439579 INFO @ Sat, 24 Aug 2019 20:17:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:17:11: #1 finished! INFO @ Sat, 24 Aug 2019 20:17:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:17:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:17:11: 5000000 INFO @ Sat, 24 Aug 2019 20:17:12: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:17:12: 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 20:17:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.05_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/SRX4292276/SRX4292276.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:17:17: 2000000 INFO @ Sat, 24 Aug 2019 20:17:19: 6000000 INFO @ Sat, 24 Aug 2019 20:17:26: 3000000 INFO @ Sat, 24 Aug 2019 20:17:27: 7000000 INFO @ Sat, 24 Aug 2019 20:17:34: 4000000 INFO @ Sat, 24 Aug 2019 20:17:36: 8000000 INFO @ Sat, 24 Aug 2019 20:17:43: 5000000 INFO @ Sat, 24 Aug 2019 20:17:44: 9000000 INFO @ Sat, 24 Aug 2019 20:17:51: 6000000 INFO @ Sat, 24 Aug 2019 20:17:52: 10000000 INFO @ Sat, 24 Aug 2019 20:17:56: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:17:56: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:17:56: #1 total tags in treatment: 10439579 INFO @ Sat, 24 Aug 2019 20:17:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:17:56: #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 20:17:56: #1 tags after filtering in treatment: 10439579 INFO @ Sat, 24 Aug 2019 20:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:17:56: #1 finished! INFO @ Sat, 24 Aug 2019 20:17:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:17:57: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:17:57: 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 20:17:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.10_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/SRX4292276/SRX4292276.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:18:00: 7000000 INFO @ Sat, 24 Aug 2019 20:18:08: 8000000 INFO @ Sat, 24 Aug 2019 20:18:16: 9000000 INFO @ Sat, 24 Aug 2019 20:18:24: 10000000 INFO @ Sat, 24 Aug 2019 20:18:28: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 20:18:28: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 20:18:28: #1 total tags in treatment: 10439579 INFO @ Sat, 24 Aug 2019 20:18:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:18:28: #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 20:18:28: #1 tags after filtering in treatment: 10439579 INFO @ Sat, 24 Aug 2019 20:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 20:18:28: #1 finished! INFO @ Sat, 24 Aug 2019 20:18:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:18:29: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:18:29: 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 @ Sat, 24 Aug 2019 20:18:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.20_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/SRX4292276/SRX4292276.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4292276/SRX4292276.20_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。