Job ID = 2010720 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:13:06 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 : 11,469,031 reads read : 22,938,062 reads written : 22,938,062 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: 00:10:48 11469031 reads; of these: 11469031 (100.00%) were paired; of these: 1771533 (15.45%) aligned concordantly 0 times 8363351 (72.92%) aligned concordantly exactly 1 time 1334147 (11.63%) aligned concordantly >1 times ---- 1771533 pairs aligned concordantly 0 times; of these: 127477 (7.20%) aligned discordantly 1 time ---- 1644056 pairs aligned 0 times concordantly or discordantly; of these: 3288112 mates make up the pairs; of these: 2838845 (86.34%) aligned 0 times 321603 (9.78%) aligned exactly 1 time 127664 (3.88%) aligned >1 times 87.62% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 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] 208216 / 9798460 = 0.0212 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 00:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.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 00:49:10: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:49:10: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.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 00:49:11: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:49:11: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:49:22: 1000000 INFO @ Sat, 06 Jul 2019 00:49:23: 1000000 INFO @ Sat, 06 Jul 2019 00:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.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 00:49:25: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:49:25: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:49:33: 2000000 INFO @ Sat, 06 Jul 2019 00:49:34: 2000000 INFO @ Sat, 06 Jul 2019 00:49:35: 1000000 INFO @ Sat, 06 Jul 2019 00:49:43: 3000000 INFO @ Sat, 06 Jul 2019 00:49:44: 3000000 INFO @ Sat, 06 Jul 2019 00:49:45: 2000000 INFO @ Sat, 06 Jul 2019 00:49:53: 4000000 INFO @ Sat, 06 Jul 2019 00:49:55: 4000000 INFO @ Sat, 06 Jul 2019 00:49:55: 3000000 INFO @ Sat, 06 Jul 2019 00:50:04: 5000000 INFO @ Sat, 06 Jul 2019 00:50:05: 4000000 INFO @ Sat, 06 Jul 2019 00:50:05: 5000000 INFO @ Sat, 06 Jul 2019 00:50:14: 6000000 INFO @ Sat, 06 Jul 2019 00:50:15: 5000000 INFO @ Sat, 06 Jul 2019 00:50:15: 6000000 INFO @ Sat, 06 Jul 2019 00:50:25: 6000000 INFO @ Sat, 06 Jul 2019 00:50:25: 7000000 INFO @ Sat, 06 Jul 2019 00:50:26: 7000000 INFO @ Sat, 06 Jul 2019 00:50:34: 7000000 INFO @ Sat, 06 Jul 2019 00:50:35: 8000000 INFO @ Sat, 06 Jul 2019 00:50:36: 8000000 INFO @ Sat, 06 Jul 2019 00:50:44: 9000000 INFO @ Sat, 06 Jul 2019 00:50:46: 8000000 INFO @ Sat, 06 Jul 2019 00:50:47: 9000000 INFO @ Sat, 06 Jul 2019 00:50:53: 10000000 INFO @ Sat, 06 Jul 2019 00:50:57: 9000000 INFO @ Sat, 06 Jul 2019 00:50:58: 10000000 INFO @ Sat, 06 Jul 2019 00:51:02: 11000000 INFO @ Sat, 06 Jul 2019 00:51:08: 10000000 INFO @ Sat, 06 Jul 2019 00:51:10: 11000000 INFO @ Sat, 06 Jul 2019 00:51:11: 12000000 INFO @ Sat, 06 Jul 2019 00:51:19: 11000000 INFO @ Sat, 06 Jul 2019 00:51:20: 13000000 INFO @ Sat, 06 Jul 2019 00:51:21: 12000000 INFO @ Sat, 06 Jul 2019 00:51:29: 14000000 INFO @ Sat, 06 Jul 2019 00:51:31: 12000000 INFO @ Sat, 06 Jul 2019 00:51:32: 13000000 INFO @ Sat, 06 Jul 2019 00:51:38: 15000000 INFO @ Sat, 06 Jul 2019 00:51:42: 13000000 INFO @ Sat, 06 Jul 2019 00:51:43: 14000000 INFO @ Sat, 06 Jul 2019 00:51:47: 16000000 INFO @ Sat, 06 Jul 2019 00:51:53: 14000000 INFO @ Sat, 06 Jul 2019 00:51:55: 15000000 INFO @ Sat, 06 Jul 2019 00:51:56: 17000000 INFO @ Sat, 06 Jul 2019 00:52:04: 15000000 INFO @ Sat, 06 Jul 2019 00:52:05: 18000000 INFO @ Sat, 06 Jul 2019 00:52:06: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:52:14: 19000000 INFO @ Sat, 06 Jul 2019 00:52:16: 16000000 INFO @ Sat, 06 Jul 2019 00:52:17: 17000000 INFO @ Sat, 06 Jul 2019 00:52:21: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:52:21: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:52:21: #1 total tags in treatment: 9490215 INFO @ Sat, 06 Jul 2019 00:52:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:21: #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 00:52:21: #1 tags after filtering in treatment: 7179089 INFO @ Sat, 06 Jul 2019 00:52:21: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:52:21: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:21: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:52:21: 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 00:52:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.05_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/SRX386903/SRX386903.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:52:27: 17000000 INFO @ Sat, 06 Jul 2019 00:52:28: 18000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:52:38: 18000000 INFO @ Sat, 06 Jul 2019 00:52:39: 19000000 INFO @ Sat, 06 Jul 2019 00:52:47: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:52:47: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:52:47: #1 total tags in treatment: 9490215 INFO @ Sat, 06 Jul 2019 00:52:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:47: #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 00:52:47: #1 tags after filtering in treatment: 7179089 INFO @ Sat, 06 Jul 2019 00:52:47: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:52:47: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:52:47: 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 00:52:47: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:52:48: 19000000 INFO @ Sat, 06 Jul 2019 00:52:54: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:52:54: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:52:54: #1 total tags in treatment: 9490215 INFO @ Sat, 06 Jul 2019 00:52:54: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:52:54: #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 00:52:54: #1 tags after filtering in treatment: 7179089 INFO @ Sat, 06 Jul 2019 00:52:54: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 00:52:54: #1 finished! INFO @ Sat, 06 Jul 2019 00:52:54: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:52:54: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:52:54: 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 00:52:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.20_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/SRX386903/SRX386903.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.10_*.xls’pass1 - making usageList (0 chroms): No such file or directory: 2 millis rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386903/SRX386903.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling