Job ID = 2008178 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:35:43 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 : 8,245,357 reads read : 16,490,714 reads written : 16,490,714 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: 00:09:29 8245357 reads; of these: 8245357 (100.00%) were paired; of these: 279612 (3.39%) aligned concordantly 0 times 7379501 (89.50%) aligned concordantly exactly 1 time 586244 (7.11%) aligned concordantly >1 times ---- 279612 pairs aligned concordantly 0 times; of these: 137782 (49.28%) aligned discordantly 1 time ---- 141830 pairs aligned 0 times concordantly or discordantly; of these: 283660 mates make up the pairs; of these: 191123 (67.38%) aligned 0 times 66441 (23.42%) aligned exactly 1 time 26096 (9.20%) aligned >1 times 98.84% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 1516061 / 8086704 = 0.1875 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 18:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.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 18:07:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:07:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.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 18:08:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:08:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.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 18:08:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:08:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:08:09: 1000000 INFO @ Fri, 05 Jul 2019 18:08:09: 1000000 INFO @ Fri, 05 Jul 2019 18:08:10: 1000000 INFO @ Fri, 05 Jul 2019 18:08:18: 2000000 INFO @ Fri, 05 Jul 2019 18:08:19: 2000000 INFO @ Fri, 05 Jul 2019 18:08:20: 2000000 INFO @ Fri, 05 Jul 2019 18:08:27: 3000000 INFO @ Fri, 05 Jul 2019 18:08:29: 3000000 INFO @ Fri, 05 Jul 2019 18:08:30: 3000000 INFO @ Fri, 05 Jul 2019 18:08:36: 4000000 INFO @ Fri, 05 Jul 2019 18:08:40: 4000000 INFO @ Fri, 05 Jul 2019 18:08:40: 4000000 INFO @ Fri, 05 Jul 2019 18:08:44: 5000000 INFO @ Fri, 05 Jul 2019 18:08:50: 5000000 INFO @ Fri, 05 Jul 2019 18:08:51: 5000000 INFO @ Fri, 05 Jul 2019 18:08:53: 6000000 INFO @ Fri, 05 Jul 2019 18:09:00: 6000000 INFO @ Fri, 05 Jul 2019 18:09:01: 6000000 INFO @ Fri, 05 Jul 2019 18:09:02: 7000000 INFO @ Fri, 05 Jul 2019 18:09:09: 7000000 INFO @ Fri, 05 Jul 2019 18:09:10: 8000000 INFO @ Fri, 05 Jul 2019 18:09:11: 7000000 INFO @ Fri, 05 Jul 2019 18:09:19: 9000000 INFO @ Fri, 05 Jul 2019 18:09:19: 8000000 INFO @ Fri, 05 Jul 2019 18:09:21: 8000000 INFO @ Fri, 05 Jul 2019 18:09:28: 10000000 INFO @ Fri, 05 Jul 2019 18:09:29: 9000000 INFO @ Fri, 05 Jul 2019 18:09:31: 9000000 INFO @ Fri, 05 Jul 2019 18:09:36: 11000000 INFO @ Fri, 05 Jul 2019 18:09:39: 10000000 INFO @ Fri, 05 Jul 2019 18:09:42: 10000000 INFO @ Fri, 05 Jul 2019 18:09:43: 12000000 INFO @ Fri, 05 Jul 2019 18:09:50: 11000000 INFO @ Fri, 05 Jul 2019 18:09:51: 13000000 INFO @ Fri, 05 Jul 2019 18:09:52: 11000000 INFO @ Fri, 05 Jul 2019 18:09:53: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:09:53: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:09:53: #1 total tags in treatment: 6454108 INFO @ Fri, 05 Jul 2019 18:09:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:09:53: #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 18:09:53: #1 tags after filtering in treatment: 3491903 INFO @ Fri, 05 Jul 2019 18:09:53: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 18:09:53: #1 finished! INFO @ Fri, 05 Jul 2019 18:09:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:09:53: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:09:53: 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 18:09:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.10_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/ERX585713/ERX585713.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:10:00: 12000000 INFO @ Fri, 05 Jul 2019 18:10:03: 12000000 INFO @ Fri, 05 Jul 2019 18:10:11: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:10:13: 13000000 INFO @ Fri, 05 Jul 2019 18:10:14: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:10:14: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:10:14: #1 total tags in treatment: 6454108 INFO @ Fri, 05 Jul 2019 18:10:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:14: #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 18:10:14: #1 tags after filtering in treatment: 3491903 INFO @ Fri, 05 Jul 2019 18:10:14: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 18:10:14: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:14: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:10:14: 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 18:10:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.20_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/ERX585713/ERX585713.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:10:16: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:10:16: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:10:16: #1 total tags in treatment: 6454108 INFO @ Fri, 05 Jul 2019 18:10:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:16: #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 18:10:17: #1 tags after filtering in treatment: 3491903 INFO @ Fri, 05 Jul 2019 18:10:17: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 18:10:17: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:17: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:10:17: 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 @ Fri, 05 Jul 2019 18:10:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.05_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/ERX585713/ERX585713.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585713/ERX585713.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。