Job ID = 2010750 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:17:51 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 ) 2019-07-05T15:21:37 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 ) 2019-07-05T15:21:37 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 : 14,495,345 reads read : 28,990,690 reads written : 28,990,690 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: 00:13:19 14495345 reads; of these: 14495345 (100.00%) were paired; of these: 2069899 (14.28%) aligned concordantly 0 times 10974838 (75.71%) aligned concordantly exactly 1 time 1450608 (10.01%) aligned concordantly >1 times ---- 2069899 pairs aligned concordantly 0 times; of these: 186513 (9.01%) aligned discordantly 1 time ---- 1883386 pairs aligned 0 times concordantly or discordantly; of these: 3766772 mates make up the pairs; of these: 3159488 (83.88%) aligned 0 times 452741 (12.02%) aligned exactly 1 time 154543 (4.10%) aligned >1 times 89.10% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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] 245197 / 12574323 = 0.0195 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 01:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.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 01:06:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:06:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.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 01:06:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:06:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:06:08: 1000000 INFO @ Sat, 06 Jul 2019 01:06:10: 1000000 INFO @ Sat, 06 Jul 2019 01:06:16: 2000000 INFO @ Sat, 06 Jul 2019 01:06:19: 2000000 INFO @ Sat, 06 Jul 2019 01:06:23: 3000000 INFO @ Sat, 06 Jul 2019 01:06:28: 3000000 INFO @ Sat, 06 Jul 2019 01:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.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 01:06:29: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:06:29: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:06:31: 4000000 INFO @ Sat, 06 Jul 2019 01:06:37: 4000000 INFO @ Sat, 06 Jul 2019 01:06:37: 1000000 INFO @ Sat, 06 Jul 2019 01:06:39: 5000000 INFO @ Sat, 06 Jul 2019 01:06:45: 2000000 INFO @ Sat, 06 Jul 2019 01:06:46: 5000000 INFO @ Sat, 06 Jul 2019 01:06:47: 6000000 INFO @ Sat, 06 Jul 2019 01:06:53: 3000000 INFO @ Sat, 06 Jul 2019 01:06:55: 7000000 INFO @ Sat, 06 Jul 2019 01:06:56: 6000000 INFO @ Sat, 06 Jul 2019 01:07:01: 4000000 INFO @ Sat, 06 Jul 2019 01:07:02: 8000000 INFO @ Sat, 06 Jul 2019 01:07:05: 7000000 INFO @ Sat, 06 Jul 2019 01:07:09: 5000000 INFO @ Sat, 06 Jul 2019 01:07:10: 9000000 INFO @ Sat, 06 Jul 2019 01:07:14: 8000000 INFO @ Sat, 06 Jul 2019 01:07:17: 6000000 INFO @ Sat, 06 Jul 2019 01:07:18: 10000000 INFO @ Sat, 06 Jul 2019 01:07:23: 9000000 INFO @ Sat, 06 Jul 2019 01:07:24: 7000000 INFO @ Sat, 06 Jul 2019 01:07:26: 11000000 INFO @ Sat, 06 Jul 2019 01:07:32: 10000000 INFO @ Sat, 06 Jul 2019 01:07:32: 8000000 INFO @ Sat, 06 Jul 2019 01:07:33: 12000000 INFO @ Sat, 06 Jul 2019 01:07:40: 9000000 INFO @ Sat, 06 Jul 2019 01:07:41: 11000000 INFO @ Sat, 06 Jul 2019 01:07:41: 13000000 INFO @ Sat, 06 Jul 2019 01:07:48: 10000000 INFO @ Sat, 06 Jul 2019 01:07:49: 14000000 INFO @ Sat, 06 Jul 2019 01:07:50: 12000000 INFO @ Sat, 06 Jul 2019 01:07:55: 11000000 INFO @ Sat, 06 Jul 2019 01:07:57: 15000000 INFO @ Sat, 06 Jul 2019 01:07:59: 13000000 INFO @ Sat, 06 Jul 2019 01:08:03: 12000000 INFO @ Sat, 06 Jul 2019 01:08:04: 16000000 INFO @ Sat, 06 Jul 2019 01:08:07: 14000000 INFO @ Sat, 06 Jul 2019 01:08:11: 13000000 INFO @ Sat, 06 Jul 2019 01:08:12: 17000000 INFO @ Sat, 06 Jul 2019 01:08:16: 15000000 INFO @ Sat, 06 Jul 2019 01:08:18: 14000000 INFO @ Sat, 06 Jul 2019 01:08:20: 18000000 INFO @ Sat, 06 Jul 2019 01:08:25: 16000000 INFO @ Sat, 06 Jul 2019 01:08:26: 15000000 INFO @ Sat, 06 Jul 2019 01:08:27: 19000000 INFO @ Sat, 06 Jul 2019 01:08:34: 16000000 INFO @ Sat, 06 Jul 2019 01:08:34: 17000000 INFO @ Sat, 06 Jul 2019 01:08:35: 20000000 INFO @ Sat, 06 Jul 2019 01:08:42: 17000000 INFO @ Sat, 06 Jul 2019 01:08:43: 21000000 INFO @ Sat, 06 Jul 2019 01:08:43: 18000000 INFO @ Sat, 06 Jul 2019 01:08:49: 18000000 INFO @ Sat, 06 Jul 2019 01:08:51: 22000000 INFO @ Sat, 06 Jul 2019 01:08:52: 19000000 INFO @ Sat, 06 Jul 2019 01:08:57: 19000000 INFO @ Sat, 06 Jul 2019 01:08:59: 23000000 INFO @ Sat, 06 Jul 2019 01:09:01: 20000000 INFO @ Sat, 06 Jul 2019 01:09:05: 20000000 INFO @ Sat, 06 Jul 2019 01:09:06: 24000000 INFO @ Sat, 06 Jul 2019 01:09:10: 21000000 INFO @ Sat, 06 Jul 2019 01:09:13: 21000000 INFO @ Sat, 06 Jul 2019 01:09:14: 25000000 INFO @ Sat, 06 Jul 2019 01:09:17: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 01:09:17: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 01:09:17: #1 total tags in treatment: 12181924 INFO @ Sat, 06 Jul 2019 01:09:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:09:17: #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 01:09:17: #1 tags after filtering in treatment: 8833617 INFO @ Sat, 06 Jul 2019 01:09:17: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 01:09:17: #1 finished! INFO @ Sat, 06 Jul 2019 01:09:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:09:18: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:09:18: 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 @ Sat, 06 Jul 2019 01:09:18: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:09:19: 22000000 INFO @ Sat, 06 Jul 2019 01:09:20: 22000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.05_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/SRX386930/SRX386930.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:09:27: 23000000 INFO @ Sat, 06 Jul 2019 01:09:28: 23000000 INFO @ Sat, 06 Jul 2019 01:09:35: 24000000 INFO @ Sat, 06 Jul 2019 01:09:36: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:09:43: 25000000 INFO @ Sat, 06 Jul 2019 01:09:43: 25000000 INFO @ Sat, 06 Jul 2019 01:09:46: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 01:09:46: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 01:09:46: #1 total tags in treatment: 12181924 INFO @ Sat, 06 Jul 2019 01:09:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:09:46: #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 01:09:46: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 01:09:46: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 01:09:46: #1 total tags in treatment: 12181924 INFO @ Sat, 06 Jul 2019 01:09:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:09:46: #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 01:09:46: #1 tags after filtering in treatment: 8833617 INFO @ Sat, 06 Jul 2019 01:09:46: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 01:09:46: #1 finished! INFO @ Sat, 06 Jul 2019 01:09:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:09:46: #1 tags after filtering in treatment: 8833617 INFO @ Sat, 06 Jul 2019 01:09:46: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 01:09:46: #1 finished! INFO @ Sat, 06 Jul 2019 01:09:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:09:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:09:47: 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 @ Sat, 06 Jul 2019 01:09:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.10_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/SRX386930/SRX386930.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:09:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 01:09:47: 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 @ Sat, 06 Jul 2019 01:09:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.20_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/SRX386930/SRX386930.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386930/SRX386930.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。