Job ID = 2010325 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:04:34 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 ) 2019-07-05T13:06:03 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T13:06:03 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 14,379,197 reads read : 28,758,394 reads written : 28,758,394 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1009162.sra.cache’: 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: 00:18:11 14379197 reads; of these: 14379197 (100.00%) were paired; of these: 1555294 (10.82%) aligned concordantly 0 times 9946377 (69.17%) aligned concordantly exactly 1 time 2877526 (20.01%) aligned concordantly >1 times ---- 1555294 pairs aligned concordantly 0 times; of these: 119626 (7.69%) aligned discordantly 1 time ---- 1435668 pairs aligned 0 times concordantly or discordantly; of these: 2871336 mates make up the pairs; of these: 2530698 (88.14%) aligned 0 times 185407 (6.46%) aligned exactly 1 time 155231 (5.41%) aligned >1 times 91.20% overall alignment rate Time searching: 00:18:11 Overall time: 00:18:11 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] 3840681 / 12924709 = 0.2972 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 22:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.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 22:39:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:39:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.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 22:39:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:39:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.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 22:39:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:39:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:39:48: 1000000 INFO @ Fri, 05 Jul 2019 22:39:48: 1000000 INFO @ Fri, 05 Jul 2019 22:39:50: 1000000 INFO @ Fri, 05 Jul 2019 22:39:57: 2000000 INFO @ Fri, 05 Jul 2019 22:40:00: 2000000 INFO @ Fri, 05 Jul 2019 22:40:03: 2000000 INFO @ Fri, 05 Jul 2019 22:40:06: 3000000 INFO @ Fri, 05 Jul 2019 22:40:11: 3000000 INFO @ Fri, 05 Jul 2019 22:40:15: 4000000 INFO @ Fri, 05 Jul 2019 22:40:17: 3000000 INFO @ Fri, 05 Jul 2019 22:40:22: 4000000 INFO @ Fri, 05 Jul 2019 22:40:24: 5000000 INFO @ Fri, 05 Jul 2019 22:40:31: 4000000 INFO @ Fri, 05 Jul 2019 22:40:33: 6000000 INFO @ Fri, 05 Jul 2019 22:40:34: 5000000 INFO @ Fri, 05 Jul 2019 22:40:43: 7000000 INFO @ Fri, 05 Jul 2019 22:40:44: 5000000 INFO @ Fri, 05 Jul 2019 22:40:45: 6000000 INFO @ Fri, 05 Jul 2019 22:40:52: 8000000 INFO @ Fri, 05 Jul 2019 22:40:57: 6000000 INFO @ Fri, 05 Jul 2019 22:40:58: 7000000 INFO @ Fri, 05 Jul 2019 22:41:01: 9000000 INFO @ Fri, 05 Jul 2019 22:41:10: 8000000 INFO @ Fri, 05 Jul 2019 22:41:10: 7000000 INFO @ Fri, 05 Jul 2019 22:41:11: 10000000 INFO @ Fri, 05 Jul 2019 22:41:20: 11000000 INFO @ Fri, 05 Jul 2019 22:41:23: 9000000 INFO @ Fri, 05 Jul 2019 22:41:23: 8000000 INFO @ Fri, 05 Jul 2019 22:41:29: 12000000 INFO @ Fri, 05 Jul 2019 22:41:36: 10000000 INFO @ Fri, 05 Jul 2019 22:41:37: 9000000 INFO @ Fri, 05 Jul 2019 22:41:38: 13000000 INFO @ Fri, 05 Jul 2019 22:41:47: 14000000 INFO @ Fri, 05 Jul 2019 22:41:48: 11000000 INFO @ Fri, 05 Jul 2019 22:41:50: 10000000 INFO @ Fri, 05 Jul 2019 22:41:56: 15000000 INFO @ Fri, 05 Jul 2019 22:42:00: 12000000 INFO @ Fri, 05 Jul 2019 22:42:03: 11000000 INFO @ Fri, 05 Jul 2019 22:42:05: 16000000 INFO @ Fri, 05 Jul 2019 22:42:12: 13000000 INFO @ Fri, 05 Jul 2019 22:42:14: 17000000 INFO @ Fri, 05 Jul 2019 22:42:15: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 22:42:22: 18000000 INFO @ Fri, 05 Jul 2019 22:42:22: 14000000 INFO @ Fri, 05 Jul 2019 22:42:27: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 22:42:27: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 22:42:27: #1 total tags in treatment: 8993278 INFO @ Fri, 05 Jul 2019 22:42:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:42:27: #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 22:42:27: 13000000 INFO @ Fri, 05 Jul 2019 22:42:27: #1 tags after filtering in treatment: 4200624 INFO @ Fri, 05 Jul 2019 22:42:27: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 22:42:27: #1 finished! INFO @ Fri, 05 Jul 2019 22:42:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:42:28: #2 number of paired peaks: 24 WARNING @ Fri, 05 Jul 2019 22:42:28: Too few paired peaks (24) 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 22:42:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.20_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/SRX363273/SRX363273.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:42:33: 15000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 22:42:39: 14000000 INFO @ Fri, 05 Jul 2019 22:42:43: 16000000 INFO @ Fri, 05 Jul 2019 22:42:51: 15000000 INFO @ Fri, 05 Jul 2019 22:42:54: 17000000 INFO @ Fri, 05 Jul 2019 22:43:03: 16000000 INFO @ Fri, 05 Jul 2019 22:43:04: 18000000 INFO @ Fri, 05 Jul 2019 22:43:10: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 22:43:10: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 22:43:10: #1 total tags in treatment: 8993278 INFO @ Fri, 05 Jul 2019 22:43:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:43:10: #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 22:43:10: #1 tags after filtering in treatment: 4200624 INFO @ Fri, 05 Jul 2019 22:43:10: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 22:43:10: #1 finished! INFO @ Fri, 05 Jul 2019 22:43:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:43:11: #2 number of paired peaks: 24 WARNING @ Fri, 05 Jul 2019 22:43:11: Too few paired peaks (24) 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 22:43:11: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 22:43:14: 17000000 INFO @ Fri, 05 Jul 2019 22:43:26: 18000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.10_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/SRX363273/SRX363273.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:43:32: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 22:43:32: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 22:43:32: #1 total tags in treatment: 8993278 INFO @ Fri, 05 Jul 2019 22:43:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:43:32: #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 22:43:32: #1 tags after filtering in treatment: 4200624 INFO @ Fri, 05 Jul 2019 22:43:32: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 22:43:32: #1 finished! INFO @ Fri, 05 Jul 2019 22:43:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:43:33: #2 number of paired peaks: 24 WARNING @ Fri, 05 Jul 2019 22:43:33: Too few paired peaks (24) 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 22:43:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.05_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/SRX363273/SRX363273.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363273/SRX363273.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling