Job ID = 2011739 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:19:08 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 ) 2019-07-05T17:19:15 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 : 9,956,244 reads read : 19,912,488 reads written : 19,912,488 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: 00:05:09 9956244 reads; of these: 9956244 (100.00%) were paired; of these: 3412257 (34.27%) aligned concordantly 0 times 5586806 (56.11%) aligned concordantly exactly 1 time 957181 (9.61%) aligned concordantly >1 times ---- 3412257 pairs aligned concordantly 0 times; of these: 96433 (2.83%) aligned discordantly 1 time ---- 3315824 pairs aligned 0 times concordantly or discordantly; of these: 6631648 mates make up the pairs; of these: 6465694 (97.50%) aligned 0 times 88335 (1.33%) aligned exactly 1 time 77619 (1.17%) aligned >1 times 67.53% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 1142482 / 6638826 = 0.1721 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 @ Sat, 06 Jul 2019 02:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.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, 06 Jul 2019 02:29:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:29:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.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, 06 Jul 2019 02:29:49: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:29:49: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:29:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.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, 06 Jul 2019 02:29:50: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:29:50: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:29:54: 1000000 INFO @ Sat, 06 Jul 2019 02:29:57: 1000000 INFO @ Sat, 06 Jul 2019 02:29:58: 1000000 INFO @ Sat, 06 Jul 2019 02:30:01: 2000000 INFO @ Sat, 06 Jul 2019 02:30:05: 2000000 INFO @ Sat, 06 Jul 2019 02:30:07: 2000000 INFO @ Sat, 06 Jul 2019 02:30:08: 3000000 INFO @ Sat, 06 Jul 2019 02:30:12: 3000000 INFO @ Sat, 06 Jul 2019 02:30:14: 4000000 INFO @ Sat, 06 Jul 2019 02:30:15: 3000000 INFO @ Sat, 06 Jul 2019 02:30:20: 4000000 INFO @ Sat, 06 Jul 2019 02:30:21: 5000000 INFO @ Sat, 06 Jul 2019 02:30:24: 4000000 INFO @ Sat, 06 Jul 2019 02:30:27: 5000000 INFO @ Sat, 06 Jul 2019 02:30:27: 6000000 INFO @ Sat, 06 Jul 2019 02:30:32: 5000000 INFO @ Sat, 06 Jul 2019 02:30:34: 7000000 INFO @ Sat, 06 Jul 2019 02:30:34: 6000000 INFO @ Sat, 06 Jul 2019 02:30:40: 8000000 INFO @ Sat, 06 Jul 2019 02:30:40: 6000000 INFO @ Sat, 06 Jul 2019 02:30:41: 7000000 INFO @ Sat, 06 Jul 2019 02:30:47: 9000000 INFO @ Sat, 06 Jul 2019 02:30:48: 8000000 INFO @ Sat, 06 Jul 2019 02:30:49: 7000000 INFO @ Sat, 06 Jul 2019 02:30:53: 10000000 INFO @ Sat, 06 Jul 2019 02:30:56: 9000000 INFO @ Sat, 06 Jul 2019 02:30:57: 8000000 INFO @ Sat, 06 Jul 2019 02:30:59: 11000000 INFO @ Sat, 06 Jul 2019 02:31:00: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:31:00: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:31:00: #1 total tags in treatment: 5414631 INFO @ Sat, 06 Jul 2019 02:31:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:31:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:31:01: #1 tags after filtering in treatment: 4296083 INFO @ Sat, 06 Jul 2019 02:31:01: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 02:31:01: #1 finished! INFO @ Sat, 06 Jul 2019 02:31:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:31:01: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:31:01: Too few paired peaks (28) 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, 06 Jul 2019 02:31:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.05_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 02:31:03: 10000000 INFO @ Sat, 06 Jul 2019 02:31:06: 9000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:31:10: 11000000 INFO @ Sat, 06 Jul 2019 02:31:11: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:31:11: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:31:11: #1 total tags in treatment: 5414631 INFO @ Sat, 06 Jul 2019 02:31:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:31:11: #1 tags after filtering in treatment: 4296083 INFO @ Sat, 06 Jul 2019 02:31:11: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 02:31:11: #1 finished! INFO @ Sat, 06 Jul 2019 02:31:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:31:12: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:31:12: Too few paired peaks (28) 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, 06 Jul 2019 02:31:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.20_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/SRX4915178/SRX4915178.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:31:14: 10000000 INFO @ Sat, 06 Jul 2019 02:31:22: 11000000 INFO @ Sat, 06 Jul 2019 02:31:24: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:31:24: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:31:24: #1 total tags in treatment: 5414631 INFO @ Sat, 06 Jul 2019 02:31:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:31:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:31:24: #1 tags after filtering in treatment: 4296083 INFO @ Sat, 06 Jul 2019 02:31:24: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 02:31:24: #1 finished! INFO @ Sat, 06 Jul 2019 02:31:24: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:31:24: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:31:24: Too few paired peaks (28) 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, 06 Jul 2019 02:31:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.10_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/SRX4915178/SRX4915178.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915178/SRX4915178.10_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。