Job ID = 2641000 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:34:11 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 ) 2019-08-24T11:34:56 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 ) 2019-08-24T11:34:56 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 : 14,348,020 reads read : 28,696,040 reads written : 28,696,040 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: 00:16:21 14348020 reads; of these: 14348020 (100.00%) were paired; of these: 3062044 (21.34%) aligned concordantly 0 times 9260610 (64.54%) aligned concordantly exactly 1 time 2025366 (14.12%) aligned concordantly >1 times ---- 3062044 pairs aligned concordantly 0 times; of these: 671378 (21.93%) aligned discordantly 1 time ---- 2390666 pairs aligned 0 times concordantly or discordantly; of these: 4781332 mates make up the pairs; of these: 4370233 (91.40%) aligned 0 times 124171 (2.60%) aligned exactly 1 time 286928 (6.00%) aligned >1 times 84.77% overall alignment rate Time searching: 00:16:21 Overall time: 00:16:21 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 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] 1322727 / 11954651 = 0.1106 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:08:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.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, 24 Aug 2019 21:08:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:08:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:08:48: 1000000 INFO @ Sat, 24 Aug 2019 21:08:59: 2000000 INFO @ Sat, 24 Aug 2019 21:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.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, 24 Aug 2019 21:09:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:09:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:09:09: 3000000 INFO @ Sat, 24 Aug 2019 21:09:17: 1000000 INFO @ Sat, 24 Aug 2019 21:09:19: 4000000 INFO @ Sat, 24 Aug 2019 21:09:27: 2000000 INFO @ Sat, 24 Aug 2019 21:09:28: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.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, 24 Aug 2019 21:09:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:09:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:09:38: 3000000 INFO @ Sat, 24 Aug 2019 21:09:38: 6000000 INFO @ Sat, 24 Aug 2019 21:09:47: 1000000 INFO @ Sat, 24 Aug 2019 21:09:48: 7000000 INFO @ Sat, 24 Aug 2019 21:09:49: 4000000 INFO @ Sat, 24 Aug 2019 21:09:56: 2000000 INFO @ Sat, 24 Aug 2019 21:09:58: 8000000 INFO @ Sat, 24 Aug 2019 21:10:00: 5000000 INFO @ Sat, 24 Aug 2019 21:10:07: 3000000 INFO @ Sat, 24 Aug 2019 21:10:08: 9000000 INFO @ Sat, 24 Aug 2019 21:10:11: 6000000 INFO @ Sat, 24 Aug 2019 21:10:18: 10000000 INFO @ Sat, 24 Aug 2019 21:10:19: 4000000 INFO @ Sat, 24 Aug 2019 21:10:22: 7000000 INFO @ Sat, 24 Aug 2019 21:10:28: 11000000 INFO @ Sat, 24 Aug 2019 21:10:30: 5000000 INFO @ Sat, 24 Aug 2019 21:10:33: 8000000 INFO @ Sat, 24 Aug 2019 21:10:39: 12000000 INFO @ Sat, 24 Aug 2019 21:10:42: 6000000 INFO @ Sat, 24 Aug 2019 21:10:44: 9000000 INFO @ Sat, 24 Aug 2019 21:10:51: 13000000 INFO @ Sat, 24 Aug 2019 21:10:53: 7000000 INFO @ Sat, 24 Aug 2019 21:10:55: 10000000 INFO @ Sat, 24 Aug 2019 21:11:03: 8000000 INFO @ Sat, 24 Aug 2019 21:11:04: 14000000 INFO @ Sat, 24 Aug 2019 21:11:06: 11000000 INFO @ Sat, 24 Aug 2019 21:11:13: 9000000 INFO @ Sat, 24 Aug 2019 21:11:16: 15000000 INFO @ Sat, 24 Aug 2019 21:11:16: 12000000 INFO @ Sat, 24 Aug 2019 21:11:24: 10000000 INFO @ Sat, 24 Aug 2019 21:11:27: 13000000 INFO @ Sat, 24 Aug 2019 21:11:28: 16000000 INFO @ Sat, 24 Aug 2019 21:11:34: 11000000 INFO @ Sat, 24 Aug 2019 21:11:37: 14000000 INFO @ Sat, 24 Aug 2019 21:11:41: 17000000 INFO @ Sat, 24 Aug 2019 21:11:45: 12000000 INFO @ Sat, 24 Aug 2019 21:11:48: 15000000 INFO @ Sat, 24 Aug 2019 21:11:54: 18000000 INFO @ Sat, 24 Aug 2019 21:11:55: 13000000 INFO @ Sat, 24 Aug 2019 21:11:58: 16000000 INFO @ Sat, 24 Aug 2019 21:12:05: 14000000 INFO @ Sat, 24 Aug 2019 21:12:07: 19000000 INFO @ Sat, 24 Aug 2019 21:12:09: 17000000 INFO @ Sat, 24 Aug 2019 21:12:14: 15000000 INFO @ Sat, 24 Aug 2019 21:12:19: 18000000 INFO @ Sat, 24 Aug 2019 21:12:20: 20000000 INFO @ Sat, 24 Aug 2019 21:12:24: 16000000 INFO @ Sat, 24 Aug 2019 21:12:30: 19000000 INFO @ Sat, 24 Aug 2019 21:12:33: 21000000 INFO @ Sat, 24 Aug 2019 21:12:33: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:12:40: 20000000 INFO @ Sat, 24 Aug 2019 21:12:41: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:12:41: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:12:41: #1 total tags in treatment: 9997913 INFO @ Sat, 24 Aug 2019 21:12:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:12:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:12:41: #1 tags after filtering in treatment: 7231844 INFO @ Sat, 24 Aug 2019 21:12:41: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:12:41: #1 finished! INFO @ Sat, 24 Aug 2019 21:12:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:12:42: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:12:42: 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, 24 Aug 2019 21:12:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.05_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/SRX4936106/SRX4936106.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:12:43: 18000000 INFO @ Sat, 24 Aug 2019 21:12:51: 21000000 INFO @ Sat, 24 Aug 2019 21:12:52: 19000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:12:57: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:12:57: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:12:57: #1 total tags in treatment: 9997913 INFO @ Sat, 24 Aug 2019 21:12:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:12:58: #1 tags after filtering in treatment: 7231844 INFO @ Sat, 24 Aug 2019 21:12:58: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:12:58: #1 finished! INFO @ Sat, 24 Aug 2019 21:12:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:12:58: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:12:58: 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, 24 Aug 2019 21:12:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.10_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/SRX4936106/SRX4936106.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:13:01: 20000000 INFO @ Sat, 24 Aug 2019 21:13:11: 21000000 INFO @ Sat, 24 Aug 2019 21:13:18: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:13:18: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:13:18: #1 total tags in treatment: 9997913 INFO @ Sat, 24 Aug 2019 21:13:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:13:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:13:18: #1 tags after filtering in treatment: 7231844 INFO @ Sat, 24 Aug 2019 21:13:18: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 24 Aug 2019 21:13:18: #1 finished! INFO @ Sat, 24 Aug 2019 21:13:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:13:18: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:13:18: 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, 24 Aug 2019 21:13:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.20_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/SRX4936106/SRX4936106.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936106/SRX4936106.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling