Job ID = 2640749 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T09:53:37 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 : 11,621,881 reads read : 23,243,762 reads written : 23,243,762 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: 00:07:56 11621881 reads; of these: 11621881 (100.00%) were paired; of these: 643091 (5.53%) aligned concordantly 0 times 9635587 (82.91%) aligned concordantly exactly 1 time 1343203 (11.56%) aligned concordantly >1 times ---- 643091 pairs aligned concordantly 0 times; of these: 121952 (18.96%) aligned discordantly 1 time ---- 521139 pairs aligned 0 times concordantly or discordantly; of these: 1042278 mates make up the pairs; of these: 915640 (87.85%) aligned 0 times 76368 (7.33%) aligned exactly 1 time 50270 (4.82%) aligned >1 times 96.06% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 507580 / 10999554 = 0.0461 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.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 19:12:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:12:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:12:39: 1000000 INFO @ Sat, 24 Aug 2019 19:12:45: 2000000 INFO @ Sat, 24 Aug 2019 19:12:51: 3000000 INFO @ Sat, 24 Aug 2019 19:12:57: 4000000 INFO @ Sat, 24 Aug 2019 19:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.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 19:13:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:13:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:13:03: 5000000 INFO @ Sat, 24 Aug 2019 19:13:09: 1000000 INFO @ Sat, 24 Aug 2019 19:13:09: 6000000 INFO @ Sat, 24 Aug 2019 19:13:15: 7000000 INFO @ Sat, 24 Aug 2019 19:13:15: 2000000 INFO @ Sat, 24 Aug 2019 19:13:21: 8000000 INFO @ Sat, 24 Aug 2019 19:13:21: 3000000 INFO @ Sat, 24 Aug 2019 19:13:27: 9000000 INFO @ Sat, 24 Aug 2019 19:13:28: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.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 19:13:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:13:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:13:33: 10000000 INFO @ Sat, 24 Aug 2019 19:13:34: 5000000 INFO @ Sat, 24 Aug 2019 19:13:39: 1000000 INFO @ Sat, 24 Aug 2019 19:13:39: 11000000 INFO @ Sat, 24 Aug 2019 19:13:40: 6000000 INFO @ Sat, 24 Aug 2019 19:13:45: 12000000 INFO @ Sat, 24 Aug 2019 19:13:45: 2000000 INFO @ Sat, 24 Aug 2019 19:13:46: 7000000 INFO @ Sat, 24 Aug 2019 19:13:51: 13000000 INFO @ Sat, 24 Aug 2019 19:13:52: 3000000 INFO @ Sat, 24 Aug 2019 19:13:52: 8000000 INFO @ Sat, 24 Aug 2019 19:13:58: 14000000 INFO @ Sat, 24 Aug 2019 19:13:58: 4000000 INFO @ Sat, 24 Aug 2019 19:13:58: 9000000 INFO @ Sat, 24 Aug 2019 19:14:04: 15000000 INFO @ Sat, 24 Aug 2019 19:14:04: 5000000 INFO @ Sat, 24 Aug 2019 19:14:04: 10000000 INFO @ Sat, 24 Aug 2019 19:14:10: 16000000 INFO @ Sat, 24 Aug 2019 19:14:10: 6000000 INFO @ Sat, 24 Aug 2019 19:14:10: 11000000 INFO @ Sat, 24 Aug 2019 19:14:16: 17000000 INFO @ Sat, 24 Aug 2019 19:14:16: 7000000 INFO @ Sat, 24 Aug 2019 19:14:17: 12000000 INFO @ Sat, 24 Aug 2019 19:14:22: 18000000 INFO @ Sat, 24 Aug 2019 19:14:22: 8000000 INFO @ Sat, 24 Aug 2019 19:14:23: 13000000 INFO @ Sat, 24 Aug 2019 19:14:28: 19000000 INFO @ Sat, 24 Aug 2019 19:14:28: 9000000 INFO @ Sat, 24 Aug 2019 19:14:29: 14000000 INFO @ Sat, 24 Aug 2019 19:14:34: 20000000 INFO @ Sat, 24 Aug 2019 19:14:35: 10000000 INFO @ Sat, 24 Aug 2019 19:14:35: 15000000 INFO @ Sat, 24 Aug 2019 19:14:40: 21000000 INFO @ Sat, 24 Aug 2019 19:14:41: 11000000 INFO @ Sat, 24 Aug 2019 19:14:41: 16000000 INFO @ Sat, 24 Aug 2019 19:14:42: #1 tag size is determined as 32 bps INFO @ Sat, 24 Aug 2019 19:14:42: #1 tag size = 32 INFO @ Sat, 24 Aug 2019 19:14:42: #1 total tags in treatment: 10471832 INFO @ Sat, 24 Aug 2019 19:14:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:14:42: #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 19:14:42: #1 tags after filtering in treatment: 7907303 INFO @ Sat, 24 Aug 2019 19:14:42: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:14:42: #1 finished! INFO @ Sat, 24 Aug 2019 19:14:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:14:43: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:14:43: 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, 24 Aug 2019 19:14:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.05_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/ERX2732440/ERX2732440.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:14:47: 12000000 INFO @ Sat, 24 Aug 2019 19:14:47: 17000000 INFO @ Sat, 24 Aug 2019 19:14:53: 13000000 INFO @ Sat, 24 Aug 2019 19:14:53: 18000000 INFO @ Sat, 24 Aug 2019 19:14:59: 14000000 INFO @ Sat, 24 Aug 2019 19:14:59: 19000000 INFO @ Sat, 24 Aug 2019 19:15:05: 15000000 INFO @ Sat, 24 Aug 2019 19:15:05: 20000000 INFO @ Sat, 24 Aug 2019 19:15:11: 16000000 INFO @ Sat, 24 Aug 2019 19:15:11: 21000000 INFO @ Sat, 24 Aug 2019 19:15:13: #1 tag size is determined as 32 bps INFO @ Sat, 24 Aug 2019 19:15:13: #1 tag size = 32 INFO @ Sat, 24 Aug 2019 19:15:13: #1 total tags in treatment: 10471832 INFO @ Sat, 24 Aug 2019 19:15:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:15:13: #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 19:15:14: #1 tags after filtering in treatment: 7907303 INFO @ Sat, 24 Aug 2019 19:15:14: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:15:14: #1 finished! INFO @ Sat, 24 Aug 2019 19:15:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:15:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:15:14: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:15:14: 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 @ Sat, 24 Aug 2019 19:15:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.10_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/ERX2732440/ERX2732440.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:15:17: 17000000 INFO @ Sat, 24 Aug 2019 19:15:23: 18000000 INFO @ Sat, 24 Aug 2019 19:15:29: 19000000 INFO @ Sat, 24 Aug 2019 19:15:35: 20000000 INFO @ Sat, 24 Aug 2019 19:15:41: 21000000 INFO @ Sat, 24 Aug 2019 19:15:43: #1 tag size is determined as 32 bps INFO @ Sat, 24 Aug 2019 19:15:43: #1 tag size = 32 INFO @ Sat, 24 Aug 2019 19:15:43: #1 total tags in treatment: 10471832 INFO @ Sat, 24 Aug 2019 19:15:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:15:43: #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 19:15:43: #1 tags after filtering in treatment: 7907303 INFO @ Sat, 24 Aug 2019 19:15:43: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 24 Aug 2019 19:15:43: #1 finished! INFO @ Sat, 24 Aug 2019 19:15:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:15:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:15:43: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:15:43: 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, 24 Aug 2019 19:15:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.20_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/ERX2732440/ERX2732440.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732440/ERX2732440.20_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。