Job ID = 2010323 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 ) spots read : 28,837,258 reads read : 57,674,516 reads written : 57,674,516 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1009160.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: 00:17:50 28837258 reads; of these: 28837258 (100.00%) were paired; of these: 2958831 (10.26%) aligned concordantly 0 times 19037193 (66.02%) aligned concordantly exactly 1 time 6841234 (23.72%) aligned concordantly >1 times ---- 2958831 pairs aligned concordantly 0 times; of these: 18324 (0.62%) aligned discordantly 1 time ---- 2940507 pairs aligned 0 times concordantly or discordantly; of these: 5881014 mates make up the pairs; of these: 5407812 (91.95%) aligned 0 times 316033 (5.37%) aligned exactly 1 time 157169 (2.67%) aligned >1 times 90.62% overall alignment rate Time searching: 00:17:50 Overall time: 00:17:50 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] 12639929 / 25888336 = 0.4882 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 22:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.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 22:40:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:40:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.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 22:40:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:40:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:40:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.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 22:40:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:40:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:40:48: 1000000 INFO @ Fri, 05 Jul 2019 22:40:51: 1000000 INFO @ Fri, 05 Jul 2019 22:40:53: 1000000 INFO @ Fri, 05 Jul 2019 22:40:55: 2000000 INFO @ Fri, 05 Jul 2019 22:40:58: 2000000 INFO @ Fri, 05 Jul 2019 22:41:01: 2000000 INFO @ Fri, 05 Jul 2019 22:41:01: 3000000 INFO @ Fri, 05 Jul 2019 22:41:06: 3000000 INFO @ Fri, 05 Jul 2019 22:41:08: 4000000 INFO @ Fri, 05 Jul 2019 22:41:09: 3000000 INFO @ Fri, 05 Jul 2019 22:41:14: 4000000 INFO @ Fri, 05 Jul 2019 22:41:14: 5000000 INFO @ Fri, 05 Jul 2019 22:41:18: 4000000 INFO @ Fri, 05 Jul 2019 22:41:21: 6000000 INFO @ Fri, 05 Jul 2019 22:41:22: 5000000 INFO @ Fri, 05 Jul 2019 22:41:26: 5000000 INFO @ Fri, 05 Jul 2019 22:41:27: 7000000 INFO @ Fri, 05 Jul 2019 22:41:29: 6000000 INFO @ Fri, 05 Jul 2019 22:41:33: 8000000 INFO @ Fri, 05 Jul 2019 22:41:34: 6000000 INFO @ Fri, 05 Jul 2019 22:41:36: 7000000 INFO @ Fri, 05 Jul 2019 22:41:39: 9000000 INFO @ Fri, 05 Jul 2019 22:41:42: 7000000 INFO @ Fri, 05 Jul 2019 22:41:44: 8000000 INFO @ Fri, 05 Jul 2019 22:41:46: 10000000 INFO @ Fri, 05 Jul 2019 22:41:50: 8000000 INFO @ Fri, 05 Jul 2019 22:41:51: 9000000 INFO @ Fri, 05 Jul 2019 22:41:52: 11000000 INFO @ Fri, 05 Jul 2019 22:41:58: 12000000 INFO @ Fri, 05 Jul 2019 22:41:58: 10000000 INFO @ Fri, 05 Jul 2019 22:41:59: 9000000 INFO @ Fri, 05 Jul 2019 22:42:04: 13000000 INFO @ Fri, 05 Jul 2019 22:42:06: 11000000 INFO @ Fri, 05 Jul 2019 22:42:07: 10000000 INFO @ Fri, 05 Jul 2019 22:42:10: 14000000 INFO @ Fri, 05 Jul 2019 22:42:13: 12000000 INFO @ Fri, 05 Jul 2019 22:42:15: 11000000 INFO @ Fri, 05 Jul 2019 22:42:17: 15000000 INFO @ Fri, 05 Jul 2019 22:42:21: 13000000 INFO @ Fri, 05 Jul 2019 22:42:22: 12000000 INFO @ Fri, 05 Jul 2019 22:42:23: 16000000 INFO @ Fri, 05 Jul 2019 22:42:28: 14000000 INFO @ Fri, 05 Jul 2019 22:42:29: 17000000 INFO @ Fri, 05 Jul 2019 22:42:30: 13000000 INFO @ Fri, 05 Jul 2019 22:42:35: 15000000 INFO @ Fri, 05 Jul 2019 22:42:35: 18000000 INFO @ Fri, 05 Jul 2019 22:42:37: 14000000 INFO @ Fri, 05 Jul 2019 22:42:41: 19000000 INFO @ Fri, 05 Jul 2019 22:42:42: 16000000 INFO @ Fri, 05 Jul 2019 22:42:44: 15000000 INFO @ Fri, 05 Jul 2019 22:42:47: 20000000 INFO @ Fri, 05 Jul 2019 22:42:49: 17000000 INFO @ Fri, 05 Jul 2019 22:42:50: 16000000 INFO @ Fri, 05 Jul 2019 22:42:54: 21000000 INFO @ Fri, 05 Jul 2019 22:42:56: 18000000 INFO @ Fri, 05 Jul 2019 22:42:57: 17000000 INFO @ Fri, 05 Jul 2019 22:43:00: 22000000 INFO @ Fri, 05 Jul 2019 22:43:03: 19000000 INFO @ Fri, 05 Jul 2019 22:43:04: 18000000 INFO @ Fri, 05 Jul 2019 22:43:06: 23000000 INFO @ Fri, 05 Jul 2019 22:43:11: 20000000 INFO @ Fri, 05 Jul 2019 22:43:11: 19000000 INFO @ Fri, 05 Jul 2019 22:43:12: 24000000 INFO @ Fri, 05 Jul 2019 22:43:18: 20000000 INFO @ Fri, 05 Jul 2019 22:43:18: 21000000 INFO @ Fri, 05 Jul 2019 22:43:18: 25000000 INFO @ Fri, 05 Jul 2019 22:43:24: 26000000 INFO @ Fri, 05 Jul 2019 22:43:24: 21000000 INFO @ Fri, 05 Jul 2019 22:43:25: 22000000 INFO @ Fri, 05 Jul 2019 22:43:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 22:43:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 22:43:30: #1 total tags in treatment: 13243097 INFO @ Fri, 05 Jul 2019 22:43:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:43:30: #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 22:43:31: #1 tags after filtering in treatment: 8211221 INFO @ Fri, 05 Jul 2019 22:43:31: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 22:43:31: #1 finished! INFO @ Fri, 05 Jul 2019 22:43:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:43:31: 22000000 INFO @ Fri, 05 Jul 2019 22:43:31: #2 number of paired peaks: 0 INFO @ Fri, 05 Jul 2019 22:43:32: 23000000 WARNING @ Fri, 05 Jul 2019 22:43:34: 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 22:43:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.05_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/SRX363263/SRX363263.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:43:41: 23000000 INFO @ Fri, 05 Jul 2019 22:43:41: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 22:43:48: 24000000 INFO @ Fri, 05 Jul 2019 22:43:48: 25000000 INFO @ Fri, 05 Jul 2019 22:43:54: 25000000 INFO @ Fri, 05 Jul 2019 22:43:55: 26000000 INFO @ Fri, 05 Jul 2019 22:44:01: 26000000 INFO @ Fri, 05 Jul 2019 22:44:02: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 22:44:02: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 22:44:02: #1 total tags in treatment: 13243097 INFO @ Fri, 05 Jul 2019 22:44:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:44:02: #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 22:44:03: #1 tags after filtering in treatment: 8211221 INFO @ Fri, 05 Jul 2019 22:44:03: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 22:44:03: #1 finished! INFO @ Fri, 05 Jul 2019 22:44:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:44:03: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 22:44:03: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:44:03: 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 22:44:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.10_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/SRX363263/SRX363263.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:44:07: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 22:44:07: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 22:44:07: #1 total tags in treatment: 13243097 INFO @ Fri, 05 Jul 2019 22:44:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:44:07: #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 22:44:08: #1 tags after filtering in treatment: 8211221 INFO @ Fri, 05 Jul 2019 22:44:08: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 22:44:08: #1 finished! INFO @ Fri, 05 Jul 2019 22:44:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:44:08: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 22:44:08: 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 22:44:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.20_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/SRX363263/SRX363263.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363263/SRX363263.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling