Job ID = 2009688 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T10:25:57 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 ) 2019-07-05T10:25:57 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 ) 2019-07-05T10:27:14 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 : 20,518,451 reads read : 20,518,451 reads written : 20,518,451 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364344.sra.cache’: 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: 00:02:24 20518451 reads; of these: 20518451 (100.00%) were unpaired; of these: 7892451 (38.47%) aligned 0 times 11000071 (53.61%) aligned exactly 1 time 1625929 (7.92%) aligned >1 times 61.53% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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_rmdupse_core] 4932269 / 12626000 = 0.3906 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 @ Fri, 05 Jul 2019 19:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.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 @ Fri, 05 Jul 2019 19:34:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.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 @ Fri, 05 Jul 2019 19:34:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:16: 1000000 INFO @ Fri, 05 Jul 2019 19:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.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 @ Fri, 05 Jul 2019 19:34:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:18: 1000000 INFO @ Fri, 05 Jul 2019 19:34:22: 2000000 INFO @ Fri, 05 Jul 2019 19:34:23: 1000000 INFO @ Fri, 05 Jul 2019 19:34:26: 2000000 INFO @ Fri, 05 Jul 2019 19:34:29: 3000000 INFO @ Fri, 05 Jul 2019 19:34:29: 2000000 INFO @ Fri, 05 Jul 2019 19:34:33: 3000000 INFO @ Fri, 05 Jul 2019 19:34:36: 4000000 INFO @ Fri, 05 Jul 2019 19:34:36: 3000000 INFO @ Fri, 05 Jul 2019 19:34:40: 4000000 INFO @ Fri, 05 Jul 2019 19:34:42: 5000000 INFO @ Fri, 05 Jul 2019 19:34:43: 4000000 INFO @ Fri, 05 Jul 2019 19:34:48: 5000000 INFO @ Fri, 05 Jul 2019 19:34:49: 6000000 INFO @ Fri, 05 Jul 2019 19:34:49: 5000000 INFO @ Fri, 05 Jul 2019 19:34:55: 6000000 INFO @ Fri, 05 Jul 2019 19:34:56: 7000000 INFO @ Fri, 05 Jul 2019 19:34:56: 6000000 INFO @ Fri, 05 Jul 2019 19:35:00: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:35:00: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:35:00: #1 total tags in treatment: 7693731 INFO @ Fri, 05 Jul 2019 19:35:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:35:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:35:00: #1 tags after filtering in treatment: 7693731 INFO @ Fri, 05 Jul 2019 19:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:35:00: #1 finished! INFO @ Fri, 05 Jul 2019 19:35:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:35:01: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:35:01: 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 @ Fri, 05 Jul 2019 19:35:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.05_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/SRX105558/SRX105558.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:35:03: 7000000 INFO @ Fri, 05 Jul 2019 19:35:03: 7000000 INFO @ Fri, 05 Jul 2019 19:35:07: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:35:07: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:35:07: #1 total tags in treatment: 7693731 INFO @ Fri, 05 Jul 2019 19:35:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:35:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:35:07: #1 tags after filtering in treatment: 7693731 INFO @ Fri, 05 Jul 2019 19:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:35:07: #1 finished! INFO @ Fri, 05 Jul 2019 19:35:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:35:07: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:35:07: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:35:07: #1 total tags in treatment: 7693731 INFO @ Fri, 05 Jul 2019 19:35:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:35:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:35:08: #1 tags after filtering in treatment: 7693731 INFO @ Fri, 05 Jul 2019 19:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:35:08: #1 finished! INFO @ Fri, 05 Jul 2019 19:35:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:35:08: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:35:08: 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 @ Fri, 05 Jul 2019 19:35:08: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:35:08: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:35:08: 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 @ Fri, 05 Jul 2019 19:35:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.10_*.xls’CompletedMACS2peakCalling : No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX105558/SRX105558.10_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。