Job ID = 2641040 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T11:53:50 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 ) 2019-08-24T11:53:50 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 ) 2019-08-24T11:53:50 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 ) 2019-08-24T11:53:50 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 ) 2019-08-24T11:53:50 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 : 22,183,762 reads read : 44,367,524 reads written : 22,183,762 reads 0-length : 22,183,762 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:03:49 22183762 reads; of these: 22183762 (100.00%) were unpaired; of these: 2017145 (9.09%) aligned 0 times 18234706 (82.20%) aligned exactly 1 time 1931911 (8.71%) aligned >1 times 90.91% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 10969748 / 20166617 = 0.5440 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.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 21:08:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:08:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:08:08: 1000000 INFO @ Sat, 24 Aug 2019 21:08:15: 2000000 INFO @ Sat, 24 Aug 2019 21:08:21: 3000000 INFO @ Sat, 24 Aug 2019 21:08:28: 4000000 INFO @ Sat, 24 Aug 2019 21:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.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 21:08:30: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:08:30: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:08:35: 5000000 INFO @ Sat, 24 Aug 2019 21:08:39: 1000000 INFO @ Sat, 24 Aug 2019 21:08:42: 6000000 INFO @ Sat, 24 Aug 2019 21:08:47: 2000000 INFO @ Sat, 24 Aug 2019 21:08:48: 7000000 INFO @ Sat, 24 Aug 2019 21:08:55: 3000000 INFO @ Sat, 24 Aug 2019 21:08:55: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.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 21:09:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:09:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:09:02: 9000000 INFO @ Sat, 24 Aug 2019 21:09:02: 4000000 INFO @ Sat, 24 Aug 2019 21:09:03: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:09:03: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:09:03: #1 total tags in treatment: 9196869 INFO @ Sat, 24 Aug 2019 21:09:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:09:03: #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 21:09:04: #1 tags after filtering in treatment: 9196869 INFO @ Sat, 24 Aug 2019 21:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:09:04: #1 finished! INFO @ Sat, 24 Aug 2019 21:09:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:09:04: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:09:04: 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 21:09:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.05_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/SRX5257237/SRX5257237.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:09:07: 1000000 INFO @ Sat, 24 Aug 2019 21:09:10: 5000000 INFO @ Sat, 24 Aug 2019 21:09:14: 2000000 INFO @ Sat, 24 Aug 2019 21:09:18: 6000000 INFO @ Sat, 24 Aug 2019 21:09:20: 3000000 INFO @ Sat, 24 Aug 2019 21:09:26: 7000000 INFO @ Sat, 24 Aug 2019 21:09:26: 4000000 INFO @ Sat, 24 Aug 2019 21:09:33: 5000000 INFO @ Sat, 24 Aug 2019 21:09:34: 8000000 INFO @ Sat, 24 Aug 2019 21:09:39: 6000000 INFO @ Sat, 24 Aug 2019 21:09:42: 9000000 INFO @ Sat, 24 Aug 2019 21:09:43: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:09:43: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:09:43: #1 total tags in treatment: 9196869 INFO @ Sat, 24 Aug 2019 21:09:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:09:43: #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 21:09:43: #1 tags after filtering in treatment: 9196869 INFO @ Sat, 24 Aug 2019 21:09:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:09:43: #1 finished! INFO @ Sat, 24 Aug 2019 21:09:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:09:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:09:44: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:09:44: 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 21:09:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.10_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/SRX5257237/SRX5257237.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:09:45: 7000000 INFO @ Sat, 24 Aug 2019 21:09:52: 8000000 INFO @ Sat, 24 Aug 2019 21:09:58: 9000000 INFO @ Sat, 24 Aug 2019 21:09:59: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 21:09:59: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 21:09:59: #1 total tags in treatment: 9196869 INFO @ Sat, 24 Aug 2019 21:09:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:09:59: #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 21:09:59: #1 tags after filtering in treatment: 9196869 INFO @ Sat, 24 Aug 2019 21:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:09:59: #1 finished! INFO @ Sat, 24 Aug 2019 21:09:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:10:00: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:10:00: 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 21:10:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.20_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/SRX5257237/SRX5257237.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5257237/SRX5257237.20_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。