Job ID = 2008300 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T09:29:01 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 ) 2019-07-05T09:38:42 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 : 21,316,863 reads read : 42,633,726 reads written : 42,633,726 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: 00:24:21 21316863 reads; of these: 21316863 (100.00%) were paired; of these: 4986843 (23.39%) aligned concordantly 0 times 13405716 (62.89%) aligned concordantly exactly 1 time 2924304 (13.72%) aligned concordantly >1 times ---- 4986843 pairs aligned concordantly 0 times; of these: 445006 (8.92%) aligned discordantly 1 time ---- 4541837 pairs aligned 0 times concordantly or discordantly; of these: 9083674 mates make up the pairs; of these: 8370403 (92.15%) aligned 0 times 227481 (2.50%) aligned exactly 1 time 485790 (5.35%) aligned >1 times 80.37% overall alignment rate Time searching: 00:24:21 Overall time: 00:24:21 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 16 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] 5194805 / 16725300 = 0.3106 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 20:04:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.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 20:04:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:04:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:04:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.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 20:04:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:04:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.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 20:04:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:04:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:04:33: 1000000 INFO @ Fri, 05 Jul 2019 20:04:34: 1000000 INFO @ Fri, 05 Jul 2019 20:04:36: 1000000 INFO @ Fri, 05 Jul 2019 20:04:42: 2000000 INFO @ Fri, 05 Jul 2019 20:04:43: 2000000 INFO @ Fri, 05 Jul 2019 20:04:45: 2000000 INFO @ Fri, 05 Jul 2019 20:04:51: 3000000 INFO @ Fri, 05 Jul 2019 20:04:52: 3000000 INFO @ Fri, 05 Jul 2019 20:04:55: 3000000 INFO @ Fri, 05 Jul 2019 20:05:00: 4000000 INFO @ Fri, 05 Jul 2019 20:05:02: 4000000 INFO @ Fri, 05 Jul 2019 20:05:05: 4000000 INFO @ Fri, 05 Jul 2019 20:05:09: 5000000 INFO @ Fri, 05 Jul 2019 20:05:11: 5000000 INFO @ Fri, 05 Jul 2019 20:05:15: 5000000 INFO @ Fri, 05 Jul 2019 20:05:19: 6000000 INFO @ Fri, 05 Jul 2019 20:05:20: 6000000 INFO @ Fri, 05 Jul 2019 20:05:25: 6000000 INFO @ Fri, 05 Jul 2019 20:05:28: 7000000 INFO @ Fri, 05 Jul 2019 20:05:30: 7000000 INFO @ Fri, 05 Jul 2019 20:05:34: 7000000 INFO @ Fri, 05 Jul 2019 20:05:37: 8000000 INFO @ Fri, 05 Jul 2019 20:05:39: 8000000 INFO @ Fri, 05 Jul 2019 20:05:43: 8000000 INFO @ Fri, 05 Jul 2019 20:05:47: 9000000 INFO @ Fri, 05 Jul 2019 20:05:48: 9000000 INFO @ Fri, 05 Jul 2019 20:05:53: 9000000 INFO @ Fri, 05 Jul 2019 20:05:56: 10000000 INFO @ Fri, 05 Jul 2019 20:05:58: 10000000 INFO @ Fri, 05 Jul 2019 20:06:02: 10000000 INFO @ Fri, 05 Jul 2019 20:06:05: 11000000 INFO @ Fri, 05 Jul 2019 20:06:07: 11000000 INFO @ Fri, 05 Jul 2019 20:06:11: 11000000 INFO @ Fri, 05 Jul 2019 20:06:15: 12000000 INFO @ Fri, 05 Jul 2019 20:06:16: 12000000 INFO @ Fri, 05 Jul 2019 20:06:20: 12000000 INFO @ Fri, 05 Jul 2019 20:06:24: 13000000 INFO @ Fri, 05 Jul 2019 20:06:25: 13000000 INFO @ Fri, 05 Jul 2019 20:06:29: 13000000 INFO @ Fri, 05 Jul 2019 20:06:33: 14000000 INFO @ Fri, 05 Jul 2019 20:06:35: 14000000 INFO @ Fri, 05 Jul 2019 20:06:39: 14000000 INFO @ Fri, 05 Jul 2019 20:06:42: 15000000 INFO @ Fri, 05 Jul 2019 20:06:44: 15000000 INFO @ Fri, 05 Jul 2019 20:06:48: 15000000 INFO @ Fri, 05 Jul 2019 20:06:51: 16000000 INFO @ Fri, 05 Jul 2019 20:06:52: 16000000 INFO @ Fri, 05 Jul 2019 20:06:57: 16000000 INFO @ Fri, 05 Jul 2019 20:07:00: 17000000 INFO @ Fri, 05 Jul 2019 20:07:01: 17000000 INFO @ Fri, 05 Jul 2019 20:07:05: 17000000 INFO @ Fri, 05 Jul 2019 20:07:08: 18000000 INFO @ Fri, 05 Jul 2019 20:07:10: 18000000 INFO @ Fri, 05 Jul 2019 20:07:14: 18000000 INFO @ Fri, 05 Jul 2019 20:07:17: 19000000 INFO @ Fri, 05 Jul 2019 20:07:19: 19000000 INFO @ Fri, 05 Jul 2019 20:07:23: 19000000 INFO @ Fri, 05 Jul 2019 20:07:26: 20000000 INFO @ Fri, 05 Jul 2019 20:07:28: 20000000 INFO @ Fri, 05 Jul 2019 20:07:32: 20000000 INFO @ Fri, 05 Jul 2019 20:07:35: 21000000 INFO @ Fri, 05 Jul 2019 20:07:37: 21000000 INFO @ Fri, 05 Jul 2019 20:07:41: 21000000 INFO @ Fri, 05 Jul 2019 20:07:44: 22000000 INFO @ Fri, 05 Jul 2019 20:07:45: 22000000 INFO @ Fri, 05 Jul 2019 20:07:50: 22000000 INFO @ Fri, 05 Jul 2019 20:07:53: 23000000 INFO @ Fri, 05 Jul 2019 20:07:54: 23000000 INFO @ Fri, 05 Jul 2019 20:07:58: 23000000 INFO @ Fri, 05 Jul 2019 20:08:00: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 20:08:00: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 20:08:00: #1 total tags in treatment: 11200339 INFO @ Fri, 05 Jul 2019 20:08:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:08:00: #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 20:08:01: #1 tags after filtering in treatment: 5240952 INFO @ Fri, 05 Jul 2019 20:08:01: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 20:08:01: #1 finished! INFO @ Fri, 05 Jul 2019 20:08:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:08:01: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:08:01: 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 20:08:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.05_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/ERX585810/ERX585810.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:08:02: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 20:08:02: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 20:08:02: #1 total tags in treatment: 11200339 INFO @ Fri, 05 Jul 2019 20:08:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:08:02: #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 20:08:02: #1 tags after filtering in treatment: 5240952 INFO @ Fri, 05 Jul 2019 20:08:02: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 20:08:02: #1 finished! INFO @ Fri, 05 Jul 2019 20:08:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:08:03: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:08:03: 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 20:08:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.10_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/ERX585810/ERX585810.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:08:06: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 20:08:06: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 20:08:06: #1 total tags in treatment: 11200339 INFO @ Fri, 05 Jul 2019 20:08:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:08:06: #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 20:08:06: #1 tags after filtering in treatment: 5240952 INFO @ Fri, 05 Jul 2019 20:08:06: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 20:08:06: #1 finished! INFO @ Fri, 05 Jul 2019 20:08:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:08:07: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:08:07: 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 20:08:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.20_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/ERX585810/ERX585810.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585810/ERX585810.20_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。