Job ID = 2640755 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T10:04:29 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 7,610,948 reads read : 15,221,896 reads written : 15,221,896 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: 00:02:31 7610948 reads; of these: 7610948 (100.00%) were paired; of these: 5111232 (67.16%) aligned concordantly 0 times 2085952 (27.41%) aligned concordantly exactly 1 time 413764 (5.44%) aligned concordantly >1 times ---- 5111232 pairs aligned concordantly 0 times; of these: 4922 (0.10%) aligned discordantly 1 time ---- 5106310 pairs aligned 0 times concordantly or discordantly; of these: 10212620 mates make up the pairs; of these: 10183934 (99.72%) aligned 0 times 11548 (0.11%) aligned exactly 1 time 17138 (0.17%) aligned >1 times 33.10% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 773828 / 2504097 = 0.3090 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.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, 24 Aug 2019 19:09:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:09:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:09:17: 1000000 INFO @ Sat, 24 Aug 2019 19:09:24: 2000000 INFO @ Sat, 24 Aug 2019 19:09:30: 3000000 INFO @ Sat, 24 Aug 2019 19:09:33: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 19:09:33: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 19:09:33: #1 total tags in treatment: 1726180 INFO @ Sat, 24 Aug 2019 19:09:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:09:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:09:33: #1 tags after filtering in treatment: 1498102 INFO @ Sat, 24 Aug 2019 19:09:33: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 24 Aug 2019 19:09:33: #1 finished! INFO @ Sat, 24 Aug 2019 19:09:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:09:33: #2 number of paired peaks: 38 WARNING @ Sat, 24 Aug 2019 19:09:33: Too few paired peaks (38) 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, 24 Aug 2019 19:09:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.05_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/ERX2732446/ERX2732446.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.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, 24 Aug 2019 19:09:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:09:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:09:48: 1000000 INFO @ Sat, 24 Aug 2019 19:09:56: 2000000 INFO @ Sat, 24 Aug 2019 19:10:05: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:10:09: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 19:10:09: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 19:10:09: #1 total tags in treatment: 1726180 INFO @ Sat, 24 Aug 2019 19:10:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:10:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:10:09: #1 tags after filtering in treatment: 1498102 INFO @ Sat, 24 Aug 2019 19:10:09: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 24 Aug 2019 19:10:09: #1 finished! INFO @ Sat, 24 Aug 2019 19:10:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:10:09: #2 number of paired peaks: 38 WARNING @ Sat, 24 Aug 2019 19:10:09: Too few paired peaks (38) 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, 24 Aug 2019 19:10:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.10_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/ERX2732446/ERX2732446.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.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, 24 Aug 2019 19:10:10: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:10:10: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:10:17: 1000000 INFO @ Sat, 24 Aug 2019 19:10:23: 2000000 INFO @ Sat, 24 Aug 2019 19:10:29: 3000000 INFO @ Sat, 24 Aug 2019 19:10:32: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 19:10:32: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 19:10:32: #1 total tags in treatment: 1726180 INFO @ Sat, 24 Aug 2019 19:10:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:10:32: #1 tags after filtering in treatment: 1498102 INFO @ Sat, 24 Aug 2019 19:10:32: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 24 Aug 2019 19:10:32: #1 finished! INFO @ Sat, 24 Aug 2019 19:10:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:10:32: #2 number of paired peaks: 38 WARNING @ Sat, 24 Aug 2019 19:10:32: Too few paired peaks (38) 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, 24 Aug 2019 19:10:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.20_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/ERX2732446/ERX2732446.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732446/ERX2732446.20_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。