Job ID = 2008317 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T09:32:12 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 ) 2019-07-05T09:32:12 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 : 12,583,627 reads read : 25,167,254 reads written : 25,167,254 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: 00:23:21 12583627 reads; of these: 12583627 (100.00%) were paired; of these: 917914 (7.29%) aligned concordantly 0 times 10670038 (84.79%) aligned concordantly exactly 1 time 995675 (7.91%) aligned concordantly >1 times ---- 917914 pairs aligned concordantly 0 times; of these: 269985 (29.41%) aligned discordantly 1 time ---- 647929 pairs aligned 0 times concordantly or discordantly; of these: 1295858 mates make up the pairs; of these: 1196690 (92.35%) aligned 0 times 48590 (3.75%) aligned exactly 1 time 50578 (3.90%) aligned >1 times 95.25% overall alignment rate Time searching: 00:23:21 Overall time: 00:23:21 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 12 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] 2566407 / 11889146 = 0.2159 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 19:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.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 19:34:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.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 19:34:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:34: 1000000 INFO @ Fri, 05 Jul 2019 19:34:34: 1000000 INFO @ Fri, 05 Jul 2019 19:34:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.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 19:34:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:42: 1000000 INFO @ Fri, 05 Jul 2019 19:34:43: 2000000 INFO @ Fri, 05 Jul 2019 19:34:43: 2000000 INFO @ Fri, 05 Jul 2019 19:34:50: 2000000 INFO @ Fri, 05 Jul 2019 19:34:53: 3000000 INFO @ Fri, 05 Jul 2019 19:34:53: 3000000 INFO @ Fri, 05 Jul 2019 19:34:57: 3000000 INFO @ Fri, 05 Jul 2019 19:35:01: 4000000 INFO @ Fri, 05 Jul 2019 19:35:03: 4000000 INFO @ Fri, 05 Jul 2019 19:35:05: 4000000 INFO @ Fri, 05 Jul 2019 19:35:09: 5000000 INFO @ Fri, 05 Jul 2019 19:35:13: 5000000 INFO @ Fri, 05 Jul 2019 19:35:13: 5000000 INFO @ Fri, 05 Jul 2019 19:35:18: 6000000 INFO @ Fri, 05 Jul 2019 19:35:20: 6000000 INFO @ Fri, 05 Jul 2019 19:35:23: 6000000 INFO @ Fri, 05 Jul 2019 19:35:26: 7000000 INFO @ Fri, 05 Jul 2019 19:35:28: 7000000 INFO @ Fri, 05 Jul 2019 19:35:34: 7000000 INFO @ Fri, 05 Jul 2019 19:35:35: 8000000 INFO @ Fri, 05 Jul 2019 19:35:36: 8000000 INFO @ Fri, 05 Jul 2019 19:35:43: 9000000 INFO @ Fri, 05 Jul 2019 19:35:43: 9000000 INFO @ Fri, 05 Jul 2019 19:35:44: 8000000 INFO @ Fri, 05 Jul 2019 19:35:51: 10000000 INFO @ Fri, 05 Jul 2019 19:35:52: 10000000 INFO @ Fri, 05 Jul 2019 19:35:54: 9000000 INFO @ Fri, 05 Jul 2019 19:35:58: 11000000 INFO @ Fri, 05 Jul 2019 19:36:00: 11000000 INFO @ Fri, 05 Jul 2019 19:36:04: 10000000 INFO @ Fri, 05 Jul 2019 19:36:07: 12000000 INFO @ Fri, 05 Jul 2019 19:36:09: 12000000 INFO @ Fri, 05 Jul 2019 19:36:14: 11000000 INFO @ Fri, 05 Jul 2019 19:36:15: 13000000 INFO @ Fri, 05 Jul 2019 19:36:18: 13000000 INFO @ Fri, 05 Jul 2019 19:36:22: 14000000 INFO @ Fri, 05 Jul 2019 19:36:24: 12000000 INFO @ Fri, 05 Jul 2019 19:36:26: 14000000 INFO @ Fri, 05 Jul 2019 19:36:30: 15000000 INFO @ Fri, 05 Jul 2019 19:36:34: 13000000 INFO @ Fri, 05 Jul 2019 19:36:35: 15000000 INFO @ Fri, 05 Jul 2019 19:36:37: 16000000 INFO @ Fri, 05 Jul 2019 19:36:43: 16000000 INFO @ Fri, 05 Jul 2019 19:36:44: 14000000 INFO @ Fri, 05 Jul 2019 19:36:46: 17000000 INFO @ Fri, 05 Jul 2019 19:36:51: 17000000 INFO @ Fri, 05 Jul 2019 19:36:53: 18000000 INFO @ Fri, 05 Jul 2019 19:36:54: 15000000 INFO @ Fri, 05 Jul 2019 19:36:59: 18000000 INFO @ Fri, 05 Jul 2019 19:37:00: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:37:00: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:37:00: #1 total tags in treatment: 9114272 INFO @ Fri, 05 Jul 2019 19:37:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:37:00: #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 19:37:00: #1 tags after filtering in treatment: 4596536 INFO @ Fri, 05 Jul 2019 19:37:00: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 05 Jul 2019 19:37:00: #1 finished! INFO @ Fri, 05 Jul 2019 19:37:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:37:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:37:00: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:37:00: 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 19:37:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.20_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/ERX585826/ERX585826.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:37:04: 16000000 INFO @ Fri, 05 Jul 2019 19:37:06: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:37:06: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:37:06: #1 total tags in treatment: 9114272 INFO @ Fri, 05 Jul 2019 19:37:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:37:06: #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 19:37:06: #1 tags after filtering in treatment: 4596536 INFO @ Fri, 05 Jul 2019 19:37:06: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 05 Jul 2019 19:37:06: #1 finished! INFO @ Fri, 05 Jul 2019 19:37:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:37:07: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:37:07: 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 19:37:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.10_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/ERX585826/ERX585826.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:37:13: 17000000 INFO @ Fri, 05 Jul 2019 19:37:23: 18000000 INFO @ Fri, 05 Jul 2019 19:37:31: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:37:31: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:37:31: #1 total tags in treatment: 9114272 INFO @ Fri, 05 Jul 2019 19:37:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:37:31: #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 19:37:31: #1 tags after filtering in treatment: 4596536 INFO @ Fri, 05 Jul 2019 19:37:31: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 05 Jul 2019 19:37:31: #1 finished! INFO @ Fri, 05 Jul 2019 19:37:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:37:31: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 19:37:31: 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 19:37:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.05_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/ERX585826/ERX585826.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585826/ERX585826.05_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。