Job ID = 2010319 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:07:03 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 ) 2019-07-05T13:08:59 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 : 9,983,787 reads read : 19,967,574 reads written : 19,967,574 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: 00:07:31 9983787 reads; of these: 9983787 (100.00%) were paired; of these: 1126445 (11.28%) aligned concordantly 0 times 6566116 (65.77%) aligned concordantly exactly 1 time 2291226 (22.95%) aligned concordantly >1 times ---- 1126445 pairs aligned concordantly 0 times; of these: 9492 (0.84%) aligned discordantly 1 time ---- 1116953 pairs aligned 0 times concordantly or discordantly; of these: 2233906 mates make up the pairs; of these: 2000267 (89.54%) aligned 0 times 119389 (5.34%) aligned exactly 1 time 114250 (5.11%) aligned >1 times 89.98% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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_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] 501467 / 8862658 = 0.0566 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 22:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.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 22:33:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:33:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.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 22:33:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:33:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.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 22:33:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:33:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:33:51: 1000000 INFO @ Fri, 05 Jul 2019 22:33:53: 1000000 INFO @ Fri, 05 Jul 2019 22:33:53: 1000000 INFO @ Fri, 05 Jul 2019 22:34:00: 2000000 INFO @ Fri, 05 Jul 2019 22:34:02: 2000000 INFO @ Fri, 05 Jul 2019 22:34:03: 2000000 INFO @ Fri, 05 Jul 2019 22:34:09: 3000000 INFO @ Fri, 05 Jul 2019 22:34:12: 3000000 INFO @ Fri, 05 Jul 2019 22:34:14: 3000000 INFO @ Fri, 05 Jul 2019 22:34:18: 4000000 INFO @ Fri, 05 Jul 2019 22:34:21: 4000000 INFO @ Fri, 05 Jul 2019 22:34:24: 4000000 INFO @ Fri, 05 Jul 2019 22:34:27: 5000000 INFO @ Fri, 05 Jul 2019 22:34:30: 5000000 INFO @ Fri, 05 Jul 2019 22:34:35: 5000000 INFO @ Fri, 05 Jul 2019 22:34:36: 6000000 INFO @ Fri, 05 Jul 2019 22:34:39: 6000000 INFO @ Fri, 05 Jul 2019 22:34:45: 7000000 INFO @ Fri, 05 Jul 2019 22:34:45: 6000000 INFO @ Fri, 05 Jul 2019 22:34:48: 7000000 INFO @ Fri, 05 Jul 2019 22:34:55: 8000000 INFO @ Fri, 05 Jul 2019 22:34:56: 7000000 INFO @ Fri, 05 Jul 2019 22:34:59: 8000000 INFO @ Fri, 05 Jul 2019 22:35:04: 9000000 INFO @ Fri, 05 Jul 2019 22:35:07: 8000000 INFO @ Fri, 05 Jul 2019 22:35:09: 9000000 INFO @ Fri, 05 Jul 2019 22:35:13: 10000000 INFO @ Fri, 05 Jul 2019 22:35:16: 9000000 INFO @ Fri, 05 Jul 2019 22:35:18: 10000000 INFO @ Fri, 05 Jul 2019 22:35:22: 11000000 INFO @ Fri, 05 Jul 2019 22:35:27: 11000000 INFO @ Fri, 05 Jul 2019 22:35:27: 10000000 INFO @ Fri, 05 Jul 2019 22:35:31: 12000000 INFO @ Fri, 05 Jul 2019 22:35:36: 12000000 INFO @ Fri, 05 Jul 2019 22:35:37: 11000000 INFO @ Fri, 05 Jul 2019 22:35:40: 13000000 INFO @ Fri, 05 Jul 2019 22:35:45: 13000000 INFO @ Fri, 05 Jul 2019 22:35:47: 12000000 INFO @ Fri, 05 Jul 2019 22:35:50: 14000000 INFO @ Fri, 05 Jul 2019 22:35:55: 14000000 INFO @ Fri, 05 Jul 2019 22:35:58: 13000000 INFO @ Fri, 05 Jul 2019 22:36:00: 15000000 INFO @ Fri, 05 Jul 2019 22:36:05: 15000000 INFO @ Fri, 05 Jul 2019 22:36:08: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 22:36:10: 16000000 INFO @ Fri, 05 Jul 2019 22:36:15: 16000000 INFO @ Fri, 05 Jul 2019 22:36:19: 15000000 INFO @ Fri, 05 Jul 2019 22:36:20: #1 tag size is determined as 45 bps INFO @ Fri, 05 Jul 2019 22:36:20: #1 tag size = 45 INFO @ Fri, 05 Jul 2019 22:36:20: #1 total tags in treatment: 8355998 INFO @ Fri, 05 Jul 2019 22:36:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:36:20: #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 22:36:20: #1 tags after filtering in treatment: 5506284 INFO @ Fri, 05 Jul 2019 22:36:20: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 22:36:20: #1 finished! INFO @ Fri, 05 Jul 2019 22:36:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:36:20: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:36:20: 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 22:36:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.05_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/SRX363260/SRX363260.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:36:24: #1 tag size is determined as 45 bps INFO @ Fri, 05 Jul 2019 22:36:24: #1 tag size = 45 INFO @ Fri, 05 Jul 2019 22:36:24: #1 total tags in treatment: 8355998 INFO @ Fri, 05 Jul 2019 22:36:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:36:24: #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 22:36:24: #1 tags after filtering in treatment: 5506284 INFO @ Fri, 05 Jul 2019 22:36:24: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 22:36:24: #1 finished! INFO @ Fri, 05 Jul 2019 22:36:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:36:24: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:36:24: 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 22:36:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 19 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 22:36:29: 16000000 INFO @ Fri, 05 Jul 2019 22:36:39: #1 tag size is determined as 45 bps INFO @ Fri, 05 Jul 2019 22:36:39: #1 tag size = 45 INFO @ Fri, 05 Jul 2019 22:36:39: #1 total tags in treatment: 8355998 INFO @ Fri, 05 Jul 2019 22:36:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:36:39: #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 22:36:39: #1 tags after filtering in treatment: 5506284 INFO @ Fri, 05 Jul 2019 22:36:39: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 22:36:39: #1 finished! INFO @ Fri, 05 Jul 2019 22:36:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:36:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:36:39: 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 22:36:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363260/SRX363260.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling