Job ID = 2007936 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:29 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 : 1,823,670 reads read : 3,647,340 reads written : 3,647,340 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: 00:02:06 1823670 reads; of these: 1823670 (100.00%) were paired; of these: 251843 (13.81%) aligned concordantly 0 times 1442830 (79.12%) aligned concordantly exactly 1 time 128997 (7.07%) aligned concordantly >1 times ---- 251843 pairs aligned concordantly 0 times; of these: 156556 (62.16%) aligned discordantly 1 time ---- 95287 pairs aligned 0 times concordantly or discordantly; of these: 190574 mates make up the pairs; of these: 129633 (68.02%) aligned 0 times 28435 (14.92%) aligned exactly 1 time 32506 (17.06%) aligned >1 times 96.45% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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_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] 9380 / 1724727 = 0.0054 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 16:50:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.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 16:50:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:50:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:50:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.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 16:50:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:50:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.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 16:50:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:50:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:50:52: 1000000 INFO @ Fri, 05 Jul 2019 16:50:53: 1000000 INFO @ Fri, 05 Jul 2019 16:50:54: 1000000 INFO @ Fri, 05 Jul 2019 16:51:03: 2000000 INFO @ Fri, 05 Jul 2019 16:51:06: 2000000 INFO @ Fri, 05 Jul 2019 16:51:06: 2000000 INFO @ Fri, 05 Jul 2019 16:51:14: 3000000 INFO @ Fri, 05 Jul 2019 16:51:19: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:51:19: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:51:19: #1 total tags in treatment: 1562914 INFO @ Fri, 05 Jul 2019 16:51:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:51:19: #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 16:51:19: #1 tags after filtering in treatment: 1505046 INFO @ Fri, 05 Jul 2019 16:51:19: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:51:19: #1 finished! INFO @ Fri, 05 Jul 2019 16:51:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:51:19: 3000000 INFO @ Fri, 05 Jul 2019 16:51:19: #2 number of paired peaks: 11 WARNING @ Fri, 05 Jul 2019 16:51:19: Too few paired peaks (11) 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 16:51:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.10_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/ERX471729/ERX471729.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:51:19: 3000000 INFO @ Fri, 05 Jul 2019 16:51:25: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:51:25: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:51:25: #1 total tags in treatment: 1562914 INFO @ Fri, 05 Jul 2019 16:51:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:51:25: #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 16:51:25: #1 tags after filtering in treatment: 1505046 INFO @ Fri, 05 Jul 2019 16:51:25: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:51:27: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:51:27: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:51:27: #1 total tags in treatment: 1562914 INFO @ Fri, 05 Jul 2019 16:51:27: #1 finished! INFO @ Fri, 05 Jul 2019 16:51:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:51:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:51:27: #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 16:51:27: #1 tags after filtering in treatment: 1505046 INFO @ Fri, 05 Jul 2019 16:51:27: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:51:27: #1 finished! INFO @ Fri, 05 Jul 2019 16:51:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:51:27: #2 number of paired peaks: 11 WARNING @ Fri, 05 Jul 2019 16:51:27: Too few paired peaks (11) 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 16:51:27: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 16:51:27: #2 number of paired peaks: 11 WARNING @ Fri, 05 Jul 2019 16:51:27: Too few paired peaks (11) 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 16:51:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.05_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/ERX471729/ERX471729.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.20_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/ERX471729/ERX471729.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471729/ERX471729.20_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。