Job ID = 2010744 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:26:49 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 ) 2019-07-05T15:26:49 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 ) 2019-07-05T15:28:00 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 : 11,129,163 reads read : 22,258,326 reads written : 22,258,326 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: 00:10:19 11129163 reads; of these: 11129163 (100.00%) were paired; of these: 1588328 (14.27%) aligned concordantly 0 times 8341838 (74.95%) aligned concordantly exactly 1 time 1198997 (10.77%) aligned concordantly >1 times ---- 1588328 pairs aligned concordantly 0 times; of these: 140665 (8.86%) aligned discordantly 1 time ---- 1447663 pairs aligned 0 times concordantly or discordantly; of these: 2895326 mates make up the pairs; of these: 2425197 (83.76%) aligned 0 times 345741 (11.94%) aligned exactly 1 time 124388 (4.30%) aligned >1 times 89.10% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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] 167467 / 9649839 = 0.0174 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 00:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.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 00:50:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:50:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.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 00:50:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:50:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:50:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.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 00:50:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:50:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:50:55: 1000000 INFO @ Sat, 06 Jul 2019 00:50:57: 1000000 INFO @ Sat, 06 Jul 2019 00:50:58: 1000000 INFO @ Sat, 06 Jul 2019 00:51:04: 2000000 INFO @ Sat, 06 Jul 2019 00:51:09: 2000000 INFO @ Sat, 06 Jul 2019 00:51:09: 2000000 INFO @ Sat, 06 Jul 2019 00:51:13: 3000000 INFO @ Sat, 06 Jul 2019 00:51:20: 3000000 INFO @ Sat, 06 Jul 2019 00:51:21: 3000000 INFO @ Sat, 06 Jul 2019 00:51:22: 4000000 INFO @ Sat, 06 Jul 2019 00:51:31: 4000000 INFO @ Sat, 06 Jul 2019 00:51:31: 5000000 INFO @ Sat, 06 Jul 2019 00:51:32: 4000000 INFO @ Sat, 06 Jul 2019 00:51:40: 6000000 INFO @ Sat, 06 Jul 2019 00:51:42: 5000000 INFO @ Sat, 06 Jul 2019 00:51:43: 5000000 INFO @ Sat, 06 Jul 2019 00:51:49: 7000000 INFO @ Sat, 06 Jul 2019 00:51:53: 6000000 INFO @ Sat, 06 Jul 2019 00:51:54: 6000000 INFO @ Sat, 06 Jul 2019 00:51:58: 8000000 INFO @ Sat, 06 Jul 2019 00:52:04: 7000000 INFO @ Sat, 06 Jul 2019 00:52:04: 7000000 INFO @ Sat, 06 Jul 2019 00:52:07: 9000000 INFO @ Sat, 06 Jul 2019 00:52:15: 8000000 INFO @ Sat, 06 Jul 2019 00:52:15: 8000000 INFO @ Sat, 06 Jul 2019 00:52:16: 10000000 INFO @ Sat, 06 Jul 2019 00:52:25: 11000000 INFO @ Sat, 06 Jul 2019 00:52:25: 9000000 INFO @ Sat, 06 Jul 2019 00:52:26: 9000000 INFO @ Sat, 06 Jul 2019 00:52:34: 12000000 INFO @ Sat, 06 Jul 2019 00:52:36: 10000000 INFO @ Sat, 06 Jul 2019 00:52:37: 10000000 INFO @ Sat, 06 Jul 2019 00:52:43: 13000000 INFO @ Sat, 06 Jul 2019 00:52:46: 11000000 INFO @ Sat, 06 Jul 2019 00:52:47: 11000000 INFO @ Sat, 06 Jul 2019 00:52:52: 14000000 INFO @ Sat, 06 Jul 2019 00:52:57: 12000000 INFO @ Sat, 06 Jul 2019 00:52:58: 12000000 INFO @ Sat, 06 Jul 2019 00:53:01: 15000000 INFO @ Sat, 06 Jul 2019 00:53:08: 13000000 INFO @ Sat, 06 Jul 2019 00:53:09: 13000000 INFO @ Sat, 06 Jul 2019 00:53:09: 16000000 INFO @ Sat, 06 Jul 2019 00:53:20: 14000000 INFO @ Sat, 06 Jul 2019 00:53:21: 17000000 INFO @ Sat, 06 Jul 2019 00:53:21: 14000000 INFO @ Sat, 06 Jul 2019 00:53:30: 18000000 INFO @ Sat, 06 Jul 2019 00:53:31: 15000000 INFO @ Sat, 06 Jul 2019 00:53:32: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:53:39: 19000000 INFO @ Sat, 06 Jul 2019 00:53:42: 16000000 INFO @ Sat, 06 Jul 2019 00:53:42: 16000000 INFO @ Sat, 06 Jul 2019 00:53:43: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:53:43: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:53:43: #1 total tags in treatment: 9374364 INFO @ Sat, 06 Jul 2019 00:53:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:53:43: #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 00:53:43: #1 tags after filtering in treatment: 7152161 INFO @ Sat, 06 Jul 2019 00:53:43: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:53:43: #1 finished! INFO @ Sat, 06 Jul 2019 00:53:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:53:44: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:53:44: 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 00:53:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.05_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/SRX386924/SRX386924.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:53:52: 17000000 INFO @ Sat, 06 Jul 2019 00:53:53: 17000000 INFO @ Sat, 06 Jul 2019 00:54:02: 18000000 INFO @ Sat, 06 Jul 2019 00:54:03: 18000000 INFO @ Sat, 06 Jul 2019 00:54:13: 19000000 INFO @ Sat, 06 Jul 2019 00:54:13: 19000000 INFO @ Sat, 06 Jul 2019 00:54:18: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:54:18: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:54:18: #1 total tags in treatment: 9374364 INFO @ Sat, 06 Jul 2019 00:54:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:54:18: #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 00:54:18: #1 tags after filtering in treatment: 7152161 INFO @ Sat, 06 Jul 2019 00:54:18: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:54:18: #1 finished! INFO @ Sat, 06 Jul 2019 00:54:18: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:54:18: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:54:18: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:54:18: #1 total tags in treatment: 9374364 INFO @ Sat, 06 Jul 2019 00:54:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:54:18: #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 00:54:19: #1 tags after filtering in treatment: 7152161 INFO @ Sat, 06 Jul 2019 00:54:19: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:54:19: #1 finished! INFO @ Sat, 06 Jul 2019 00:54:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:54:19: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:54:19: 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 00:54:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:54:19: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:54:19: 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 00:54:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.20_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/SRX386924/SRX386924.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386924/SRX386924.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling