Job ID = 2011719 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T17:12:21 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 ) 2019-07-05T17:12:26 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 ) 2019-07-05T17:12:28 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 ) 2019-07-05T17:22:49 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 : 24,035,727 reads read : 24,035,727 reads written : 24,035,727 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: 00:03:33 24035727 reads; of these: 24035727 (100.00%) were unpaired; of these: 10192391 (42.41%) aligned 0 times 11155652 (46.41%) aligned exactly 1 time 2687684 (11.18%) aligned >1 times 57.59% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 8421459 / 13843336 = 0.6083 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 02:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.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, 06 Jul 2019 02:32:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:32:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.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, 06 Jul 2019 02:32:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:32:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:32:38: 1000000 INFO @ Sat, 06 Jul 2019 02:32:39: 1000000 INFO @ Sat, 06 Jul 2019 02:32:44: 2000000 INFO @ Sat, 06 Jul 2019 02:32:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.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, 06 Jul 2019 02:32:44: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:32:44: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:32:45: 2000000 INFO @ Sat, 06 Jul 2019 02:32:50: 3000000 INFO @ Sat, 06 Jul 2019 02:32:51: 3000000 INFO @ Sat, 06 Jul 2019 02:32:51: 1000000 INFO @ Sat, 06 Jul 2019 02:32:56: 4000000 INFO @ Sat, 06 Jul 2019 02:32:57: 4000000 INFO @ Sat, 06 Jul 2019 02:32:58: 2000000 INFO @ Sat, 06 Jul 2019 02:33:03: 5000000 INFO @ Sat, 06 Jul 2019 02:33:03: 5000000 INFO @ Sat, 06 Jul 2019 02:33:05: 3000000 INFO @ Sat, 06 Jul 2019 02:33:05: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:33:05: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:33:05: #1 total tags in treatment: 5421877 INFO @ Sat, 06 Jul 2019 02:33:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:33:05: #1 tags after filtering in treatment: 5421877 INFO @ Sat, 06 Jul 2019 02:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:33:05: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:33:06: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:06: 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, 06 Jul 2019 02:33:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.05_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 02:33:06: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:33:06: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:33:06: #1 total tags in treatment: 5421877 INFO @ Sat, 06 Jul 2019 02:33:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:33:06: #1 tags after filtering in treatment: 5421877 INFO @ Sat, 06 Jul 2019 02:33:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:33:06: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:06: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 2 millis INFO @ Sat, 06 Jul 2019 02:33:07: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:07: 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, 06 Jul 2019 02:33:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.10_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/SRX4726618/SRX4726618.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:33:11: 4000000 INFO @ Sat, 06 Jul 2019 02:33:18: 5000000 INFO @ Sat, 06 Jul 2019 02:33:21: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:33:21: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:33:21: #1 total tags in treatment: 5421877 INFO @ Sat, 06 Jul 2019 02:33:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:33:21: #1 tags after filtering in treatment: 5421877 INFO @ Sat, 06 Jul 2019 02:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:33:21: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:33:21: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:21: 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, 06 Jul 2019 02:33:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.20_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/SRX4726618/SRX4726618.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4726618/SRX4726618.20_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。