Job ID = 2010658 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:47:56 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 ) 2019-07-05T14:47:56 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 : 6,129,143 reads read : 12,258,286 reads written : 12,258,286 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: 00:03:41 6129143 reads; of these: 6129143 (100.00%) were paired; of these: 856001 (13.97%) aligned concordantly 0 times 4107086 (67.01%) aligned concordantly exactly 1 time 1166056 (19.02%) aligned concordantly >1 times ---- 856001 pairs aligned concordantly 0 times; of these: 20988 (2.45%) aligned discordantly 1 time ---- 835013 pairs aligned 0 times concordantly or discordantly; of these: 1670026 mates make up the pairs; of these: 1408325 (84.33%) aligned 0 times 188978 (11.32%) aligned exactly 1 time 72723 (4.35%) aligned >1 times 88.51% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 599034 / 5289642 = 0.1132 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 23:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.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 23:57:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.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 23:57:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:15: 1000000 INFO @ Fri, 05 Jul 2019 23:57:17: 1000000 INFO @ Fri, 05 Jul 2019 23:57:21: 2000000 INFO @ Fri, 05 Jul 2019 23:57:24: 2000000 INFO @ Fri, 05 Jul 2019 23:57:27: 3000000 INFO @ Fri, 05 Jul 2019 23:57:30: 3000000 INFO @ Fri, 05 Jul 2019 23:57:33: 4000000 INFO @ Fri, 05 Jul 2019 23:57:37: 4000000 INFO @ Fri, 05 Jul 2019 23:57:38: 5000000 INFO @ Fri, 05 Jul 2019 23:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.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 23:57:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:43: 5000000 INFO @ Fri, 05 Jul 2019 23:57:44: 6000000 INFO @ Fri, 05 Jul 2019 23:57:47: 1000000 INFO @ Fri, 05 Jul 2019 23:57:50: 6000000 INFO @ Fri, 05 Jul 2019 23:57:50: 7000000 INFO @ Fri, 05 Jul 2019 23:57:53: 2000000 INFO @ Fri, 05 Jul 2019 23:57:56: 8000000 INFO @ Fri, 05 Jul 2019 23:57:56: 7000000 INFO @ Fri, 05 Jul 2019 23:57:59: 3000000 INFO @ Fri, 05 Jul 2019 23:58:02: 9000000 INFO @ Fri, 05 Jul 2019 23:58:02: 8000000 INFO @ Fri, 05 Jul 2019 23:58:05: 4000000 INFO @ Fri, 05 Jul 2019 23:58:06: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:58:06: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:58:06: #1 total tags in treatment: 4674496 INFO @ Fri, 05 Jul 2019 23:58:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:58:06: #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 23:58:06: #1 tags after filtering in treatment: 2970178 INFO @ Fri, 05 Jul 2019 23:58:06: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:58:06: #1 finished! INFO @ Fri, 05 Jul 2019 23:58:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:58:06: #2 number of paired peaks: 34 WARNING @ Fri, 05 Jul 2019 23:58:06: Too few paired peaks (34) 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 23:58:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.05_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/SRX3865856/SRX3865856.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:58:09: 9000000 INFO @ Fri, 05 Jul 2019 23:58:10: 5000000 INFO @ Fri, 05 Jul 2019 23:58:13: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:58:13: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:58:13: #1 total tags in treatment: 4674496 INFO @ Fri, 05 Jul 2019 23:58:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:58:13: #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 23:58:13: #1 tags after filtering in treatment: 2970178 INFO @ Fri, 05 Jul 2019 23:58:13: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:58:13: #1 finished! INFO @ Fri, 05 Jul 2019 23:58:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:58:13: #2 number of paired peaks: 34 WARNING @ Fri, 05 Jul 2019 23:58:13: Too few paired peaks (34) 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 23:58:13: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:58:16: 6000000 INFO @ Fri, 05 Jul 2019 23:58:22: 7000000 INFO @ Fri, 05 Jul 2019 23:58:28: 8000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.10_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/SRX3865856/SRX3865856.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:58:33: 9000000 INFO @ Fri, 05 Jul 2019 23:58:37: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 23:58:37: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 23:58:37: #1 total tags in treatment: 4674496 INFO @ Fri, 05 Jul 2019 23:58:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:58:37: #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 23:58:37: #1 tags after filtering in treatment: 2970178 INFO @ Fri, 05 Jul 2019 23:58:37: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:58:37: #1 finished! INFO @ Fri, 05 Jul 2019 23:58:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:58:37: #2 number of paired peaks: 34 WARNING @ Fri, 05 Jul 2019 23:58:37: Too few paired peaks (34) 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 23:58:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.20_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/SRX3865856/SRX3865856.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865856/SRX3865856.20_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。