Job ID = 2008121 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:29:41 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 ) 2019-07-05T08:35:43 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 : 12,558,241 reads read : 25,116,482 reads written : 25,116,482 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: 00:09:08 12558241 reads; of these: 12558241 (100.00%) were paired; of these: 1361464 (10.84%) aligned concordantly 0 times 9342050 (74.39%) aligned concordantly exactly 1 time 1854727 (14.77%) aligned concordantly >1 times ---- 1361464 pairs aligned concordantly 0 times; of these: 2209 (0.16%) aligned discordantly 1 time ---- 1359255 pairs aligned 0 times concordantly or discordantly; of these: 2718510 mates make up the pairs; of these: 2703243 (99.44%) aligned 0 times 10639 (0.39%) aligned exactly 1 time 4628 (0.17%) aligned >1 times 89.24% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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] 7245684 / 11197310 = 0.6471 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 17:57:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.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 BedGraph に変換中... INFO @ Fri, 05 Jul 2019 17:57:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.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 17:57:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:57:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:57:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:57:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.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 17:57:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:57:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:58:02: 1000000 INFO @ Fri, 05 Jul 2019 17:58:03: 1000000 INFO @ Fri, 05 Jul 2019 17:58:04: 1000000 INFO @ Fri, 05 Jul 2019 17:58:10: 2000000 INFO @ Fri, 05 Jul 2019 17:58:11: 2000000 INFO @ Fri, 05 Jul 2019 17:58:13: 2000000 INFO @ Fri, 05 Jul 2019 17:58:18: 3000000 INFO @ Fri, 05 Jul 2019 17:58:19: 3000000 INFO @ Fri, 05 Jul 2019 17:58:23: 3000000 INFO @ Fri, 05 Jul 2019 17:58:25: 4000000 INFO @ Fri, 05 Jul 2019 17:58:26: 4000000 INFO @ Fri, 05 Jul 2019 17:58:32: 4000000 INFO @ Fri, 05 Jul 2019 17:58:33: 5000000 INFO @ Fri, 05 Jul 2019 17:58:34: 5000000 INFO @ Fri, 05 Jul 2019 17:58:41: 6000000 INFO @ Fri, 05 Jul 2019 17:58:42: 5000000 INFO @ Fri, 05 Jul 2019 17:58:42: 6000000 INFO @ Fri, 05 Jul 2019 17:58:48: 7000000 INFO @ Fri, 05 Jul 2019 17:58:50: 7000000 INFO @ Fri, 05 Jul 2019 17:58:51: 6000000 INFO @ Fri, 05 Jul 2019 17:58:55: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 17:58:55: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 17:58:55: #1 total tags in treatment: 3951385 INFO @ Fri, 05 Jul 2019 17:58:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:58:55: #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 17:58:55: #1 tags after filtering in treatment: 3207358 INFO @ Fri, 05 Jul 2019 17:58:55: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 17:58:55: #1 finished! INFO @ Fri, 05 Jul 2019 17:58:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:58:56: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 17:58:56: Too few paired peaks (29) 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 17:58:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.05_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/ERX516013/ERX516013.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:58:56: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 17:58:56: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 17:58:56: #1 total tags in treatment: 3951385 INFO @ Fri, 05 Jul 2019 17:58:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:58:56: #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 17:58:57: #1 tags after filtering in treatment: 3207358 INFO @ Fri, 05 Jul 2019 17:58:57: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 17:58:57: #1 finished! INFO @ Fri, 05 Jul 2019 17:58:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:58:57: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 17:58:57: Too few paired peaks (29) 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 17:58:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.20_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/ERX516013/ERX516013.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:59:00: 7000000 INFO @ Fri, 05 Jul 2019 17:59:08: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 17:59:08: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 17:59:08: #1 total tags in treatment: 3951385 INFO @ Fri, 05 Jul 2019 17:59:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:59:08: #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 17:59:08: #1 tags after filtering in treatment: 3207358 INFO @ Fri, 05 Jul 2019 17:59:08: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 17:59:08: #1 finished! INFO @ Fri, 05 Jul 2019 17:59:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:59:08: #2 number of paired peaks: 29 WARNING @ Fri, 05 Jul 2019 17:59:08: Too few paired peaks (29) 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 17:59:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 590 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516013/ERX516013.10_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。