Job ID = 2010654 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:46:44 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 ) 2019-07-05T14:48:39 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 ) 2019-07-05T14:50:22 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 ) 2019-07-05T14:52:30 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 : 9,302,899 reads read : 18,605,798 reads written : 18,605,798 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: 00:07:15 9302899 reads; of these: 9302899 (100.00%) were paired; of these: 1126824 (12.11%) aligned concordantly 0 times 7063722 (75.93%) aligned concordantly exactly 1 time 1112353 (11.96%) aligned concordantly >1 times ---- 1126824 pairs aligned concordantly 0 times; of these: 329312 (29.22%) aligned discordantly 1 time ---- 797512 pairs aligned 0 times concordantly or discordantly; of these: 1595024 mates make up the pairs; of these: 1120308 (70.24%) aligned 0 times 246874 (15.48%) aligned exactly 1 time 227842 (14.28%) aligned >1 times 93.98% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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 8 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] 633897 / 8340381 = 0.0760 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 00:09:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.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 00:09:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:09:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.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 00:09:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:09:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:09:45: 1000000 INFO @ Sat, 06 Jul 2019 00:09:48: 1000000 INFO @ Sat, 06 Jul 2019 00:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.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 00:09:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:09:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:09:53: 2000000 INFO @ Sat, 06 Jul 2019 00:09:57: 2000000 INFO @ Sat, 06 Jul 2019 00:09:57: 1000000 INFO @ Sat, 06 Jul 2019 00:10:01: 3000000 INFO @ Sat, 06 Jul 2019 00:10:05: 2000000 INFO @ Sat, 06 Jul 2019 00:10:06: 3000000 INFO @ Sat, 06 Jul 2019 00:10:08: 4000000 INFO @ Sat, 06 Jul 2019 00:10:14: 3000000 INFO @ Sat, 06 Jul 2019 00:10:15: 4000000 INFO @ Sat, 06 Jul 2019 00:10:16: 5000000 INFO @ Sat, 06 Jul 2019 00:10:22: 4000000 INFO @ Sat, 06 Jul 2019 00:10:23: 6000000 INFO @ Sat, 06 Jul 2019 00:10:24: 5000000 INFO @ Sat, 06 Jul 2019 00:10:31: 5000000 INFO @ Sat, 06 Jul 2019 00:10:31: 7000000 INFO @ Sat, 06 Jul 2019 00:10:33: 6000000 INFO @ Sat, 06 Jul 2019 00:10:39: 8000000 INFO @ Sat, 06 Jul 2019 00:10:39: 6000000 INFO @ Sat, 06 Jul 2019 00:10:43: 7000000 INFO @ Sat, 06 Jul 2019 00:10:47: 9000000 INFO @ Sat, 06 Jul 2019 00:10:48: 7000000 INFO @ Sat, 06 Jul 2019 00:10:53: 8000000 INFO @ Sat, 06 Jul 2019 00:10:54: 10000000 INFO @ Sat, 06 Jul 2019 00:10:57: 8000000 INFO @ Sat, 06 Jul 2019 00:11:02: 11000000 INFO @ Sat, 06 Jul 2019 00:11:02: 9000000 INFO @ Sat, 06 Jul 2019 00:11:05: 9000000 INFO @ Sat, 06 Jul 2019 00:11:10: 12000000 INFO @ Sat, 06 Jul 2019 00:11:12: 10000000 INFO @ Sat, 06 Jul 2019 00:11:14: 10000000 INFO @ Sat, 06 Jul 2019 00:11:17: 13000000 INFO @ Sat, 06 Jul 2019 00:11:21: 11000000 INFO @ Sat, 06 Jul 2019 00:11:23: 11000000 INFO @ Sat, 06 Jul 2019 00:11:25: 14000000 INFO @ Sat, 06 Jul 2019 00:11:30: 12000000 INFO @ Sat, 06 Jul 2019 00:11:31: 12000000 INFO @ Sat, 06 Jul 2019 00:11:33: 15000000 INFO @ Sat, 06 Jul 2019 00:11:40: 13000000 INFO @ Sat, 06 Jul 2019 00:11:40: 13000000 INFO @ Sat, 06 Jul 2019 00:11:40: 16000000 INFO @ Sat, 06 Jul 2019 00:11:42: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:11:42: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:11:42: #1 total tags in treatment: 7554612 INFO @ Sat, 06 Jul 2019 00:11:42: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:11:42: #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 00:11:42: #1 tags after filtering in treatment: 4556510 INFO @ Sat, 06 Jul 2019 00:11:42: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 00:11:42: #1 finished! INFO @ Sat, 06 Jul 2019 00:11:42: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:11:43: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 00:11:43: Too few paired peaks (30) 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 00:11:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.05_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/SRX3865845/SRX3865845.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:11:49: 14000000 INFO @ Sat, 06 Jul 2019 00:11:49: 14000000 INFO @ Sat, 06 Jul 2019 00:11:57: 15000000 INFO @ Sat, 06 Jul 2019 00:11:58: 15000000 INFO @ Sat, 06 Jul 2019 00:12:05: 16000000 INFO @ Sat, 06 Jul 2019 00:12:07: 16000000 INFO @ Sat, 06 Jul 2019 00:12:07: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:12:07: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:12:07: #1 total tags in treatment: 7554612 INFO @ Sat, 06 Jul 2019 00:12:07: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:12:07: #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 00:12:08: #1 tags after filtering in treatment: 4556510 INFO @ Sat, 06 Jul 2019 00:12:08: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 00:12:08: #1 finished! INFO @ Sat, 06 Jul 2019 00:12:08: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:12:08: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 00:12:08: Too few paired peaks (30) 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 00:12:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.20_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/SRX3865845/SRX3865845.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:12:09: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:12:09: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:12:09: #1 total tags in treatment: 7554612 INFO @ Sat, 06 Jul 2019 00:12:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:12:09: #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 00:12:09: #1 tags after filtering in treatment: 4556510 INFO @ Sat, 06 Jul 2019 00:12:09: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 06 Jul 2019 00:12:09: #1 finished! INFO @ Sat, 06 Jul 2019 00:12:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:12:09: #2 number of paired peaks: 30 WARNING @ Sat, 06 Jul 2019 00:12:09: Too few paired peaks (30) 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 00:12:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.10_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/SRX3865845/SRX3865845.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865845/SRX3865845.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。