Job ID = 2010736 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:17:06 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 : 7,753,672 reads read : 15,507,344 reads written : 15,507,344 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: 00:07:03 7753672 reads; of these: 7753672 (100.00%) were paired; of these: 1096557 (14.14%) aligned concordantly 0 times 5806871 (74.89%) aligned concordantly exactly 1 time 850244 (10.97%) aligned concordantly >1 times ---- 1096557 pairs aligned concordantly 0 times; of these: 127530 (11.63%) aligned discordantly 1 time ---- 969027 pairs aligned 0 times concordantly or discordantly; of these: 1938054 mates make up the pairs; of these: 1681411 (86.76%) aligned 0 times 164315 (8.48%) aligned exactly 1 time 92328 (4.76%) aligned >1 times 89.16% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 120373 / 6760502 = 0.0178 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 00:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.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 00:33:22: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:33:22: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:33:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.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 00:33:23: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:33:23: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:33:32: 1000000 INFO @ Sat, 06 Jul 2019 00:33:33: 1000000 INFO @ Sat, 06 Jul 2019 00:33:42: 2000000 INFO @ Sat, 06 Jul 2019 00:33:43: 2000000 INFO @ Sat, 06 Jul 2019 00:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.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 00:33:52: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:33:52: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:33:52: 3000000 INFO @ Sat, 06 Jul 2019 00:33:53: 3000000 INFO @ Sat, 06 Jul 2019 00:34:03: 1000000 INFO @ Sat, 06 Jul 2019 00:34:03: 4000000 INFO @ Sat, 06 Jul 2019 00:34:03: 4000000 INFO @ Sat, 06 Jul 2019 00:34:13: 5000000 INFO @ Sat, 06 Jul 2019 00:34:13: 2000000 INFO @ Sat, 06 Jul 2019 00:34:14: 5000000 INFO @ Sat, 06 Jul 2019 00:34:24: 6000000 INFO @ Sat, 06 Jul 2019 00:34:24: 6000000 INFO @ Sat, 06 Jul 2019 00:34:24: 3000000 INFO @ Sat, 06 Jul 2019 00:34:34: 7000000 INFO @ Sat, 06 Jul 2019 00:34:35: 7000000 INFO @ Sat, 06 Jul 2019 00:34:35: 4000000 INFO @ Sat, 06 Jul 2019 00:34:44: 8000000 INFO @ Sat, 06 Jul 2019 00:34:45: 8000000 INFO @ Sat, 06 Jul 2019 00:34:46: 5000000 INFO @ Sat, 06 Jul 2019 00:34:53: 9000000 INFO @ Sat, 06 Jul 2019 00:34:54: 9000000 INFO @ Sat, 06 Jul 2019 00:34:57: 6000000 INFO @ Sat, 06 Jul 2019 00:35:03: 10000000 INFO @ Sat, 06 Jul 2019 00:35:03: 10000000 INFO @ Sat, 06 Jul 2019 00:35:08: 7000000 INFO @ Sat, 06 Jul 2019 00:35:12: 11000000 INFO @ Sat, 06 Jul 2019 00:35:13: 11000000 INFO @ Sat, 06 Jul 2019 00:35:19: 8000000 INFO @ Sat, 06 Jul 2019 00:35:21: 12000000 INFO @ Sat, 06 Jul 2019 00:35:22: 12000000 INFO @ Sat, 06 Jul 2019 00:35:30: 9000000 INFO @ Sat, 06 Jul 2019 00:35:31: 13000000 INFO @ Sat, 06 Jul 2019 00:35:31: 13000000 INFO @ Sat, 06 Jul 2019 00:35:36: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:35:36: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:35:36: #1 total tags in treatment: 6537981 INFO @ Sat, 06 Jul 2019 00:35:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:35:36: #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 00:35:36: #1 tags after filtering in treatment: 5281574 INFO @ Sat, 06 Jul 2019 00:35:36: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 06 Jul 2019 00:35:36: #1 finished! INFO @ Sat, 06 Jul 2019 00:35:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:35:37: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:35:37: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:35:37: #1 total tags in treatment: 6537981 INFO @ Sat, 06 Jul 2019 00:35:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:35:37: #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 00:35:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:35:37: 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 00:35:37: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:35:37: #1 tags after filtering in treatment: 5281574 INFO @ Sat, 06 Jul 2019 00:35:37: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 06 Jul 2019 00:35:37: #1 finished! INFO @ Sat, 06 Jul 2019 00:35:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:35:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:35:37: 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 00:35:37: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:35:40: 10000000 INFO @ Sat, 06 Jul 2019 00:35:51: 11000000 INFO @ Sat, 06 Jul 2019 00:36:01: 12000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.10_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/SRX386917/SRX386917.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:36:11: 13000000 INFO @ Sat, 06 Jul 2019 00:36:17: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:36:17: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:36:17: #1 total tags in treatment: 6537981 INFO @ Sat, 06 Jul 2019 00:36:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:36:17: #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 00:36:17: #1 tags after filtering in treatment: 5281574 INFO @ Sat, 06 Jul 2019 00:36:17: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 06 Jul 2019 00:36:17: #1 finished! INFO @ Sat, 06 Jul 2019 00:36:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:36:17: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:36:17: 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 00:36:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.20_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/SRX386917/SRX386917.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386917/SRX386917.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。