Job ID = 2010697 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:58:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 9,020,189 reads read : 18,040,378 reads written : 18,040,378 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: 00:06:28 9020189 reads; of these: 9020189 (100.00%) were paired; of these: 4582857 (50.81%) aligned concordantly 0 times 3510923 (38.92%) aligned concordantly exactly 1 time 926409 (10.27%) aligned concordantly >1 times ---- 4582857 pairs aligned concordantly 0 times; of these: 121639 (2.65%) aligned discordantly 1 time ---- 4461218 pairs aligned 0 times concordantly or discordantly; of these: 8922436 mates make up the pairs; of these: 5124251 (57.43%) aligned 0 times 2995187 (33.57%) aligned exactly 1 time 802998 (9.00%) aligned >1 times 71.60% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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_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] 706853 / 4557238 = 0.1551 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 00:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.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 00:09:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:09:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.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 00:09:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:09:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:09:47: 1000000 INFO @ Sat, 06 Jul 2019 00:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.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 00:09:50: 1000000 INFO @ Sat, 06 Jul 2019 00:09:52: 2000000 INFO @ Sat, 06 Jul 2019 00:09:56: 1000000 INFO @ Sat, 06 Jul 2019 00:09:58: 2000000 INFO @ Sat, 06 Jul 2019 00:09:58: 3000000 INFO @ Sat, 06 Jul 2019 00:10:03: 4000000 INFO @ Sat, 06 Jul 2019 00:10:05: 2000000 INFO @ Sat, 06 Jul 2019 00:10:06: 3000000 INFO @ Sat, 06 Jul 2019 00:10:09: 5000000 INFO @ Sat, 06 Jul 2019 00:10:13: 3000000 INFO @ Sat, 06 Jul 2019 00:10:14: 6000000 INFO @ Sat, 06 Jul 2019 00:10:15: 4000000 INFO @ Sat, 06 Jul 2019 00:10:19: 7000000 INFO @ Sat, 06 Jul 2019 00:10:22: 4000000 INFO @ Sat, 06 Jul 2019 00:10:23: 5000000 INFO @ Sat, 06 Jul 2019 00:10:24: 8000000 INFO @ Sat, 06 Jul 2019 00:10:30: 9000000 INFO @ Sat, 06 Jul 2019 00:10:30: 5000000 INFO @ Sat, 06 Jul 2019 00:10:31: 6000000 INFO @ Sat, 06 Jul 2019 00:10:35: 10000000 INFO @ Sat, 06 Jul 2019 00:10:38: 6000000 INFO @ Sat, 06 Jul 2019 00:10:39: 7000000 INFO @ Sat, 06 Jul 2019 00:10:41: 11000000 INFO @ Sat, 06 Jul 2019 00:10:43: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:10:43: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:10:43: #1 total tags in treatment: 3738800 INFO @ Sat, 06 Jul 2019 00:10:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:10:43: #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 00:10:43: #1 tags after filtering in treatment: 2485250 INFO @ Sat, 06 Jul 2019 00:10:43: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 00:10:43: #1 finished! INFO @ Sat, 06 Jul 2019 00:10:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:10:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:10:44: #2 number of paired peaks: 13 WARNING @ Sat, 06 Jul 2019 00:10:44: Too few paired peaks (13) 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 00:10:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.05_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/SRX3865929/SRX3865929.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:10:46: 7000000 INFO @ Sat, 06 Jul 2019 00:10:47: 8000000 INFO @ Sat, 06 Jul 2019 00:10:54: 8000000 INFO @ Sat, 06 Jul 2019 00:10:55: 9000000 INFO @ Sat, 06 Jul 2019 00:11:02: 9000000 INFO @ Sat, 06 Jul 2019 00:11:03: 10000000 INFO @ Sat, 06 Jul 2019 00:11:10: 10000000 INFO @ Sat, 06 Jul 2019 00:11:12: 11000000 INFO @ Sat, 06 Jul 2019 00:11:16: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:11:16: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:11:16: #1 total tags in treatment: 3738800 INFO @ Sat, 06 Jul 2019 00:11:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:11:16: #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 00:11:16: #1 tags after filtering in treatment: 2485250 INFO @ Sat, 06 Jul 2019 00:11:16: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 00:11:16: #1 finished! INFO @ Sat, 06 Jul 2019 00:11:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:11:16: #2 number of paired peaks: 13 WARNING @ Sat, 06 Jul 2019 00:11:16: Too few paired peaks (13) 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 00:11:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.10_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/SRX3865929/SRX3865929.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:11:18: 11000000 INFO @ Sat, 06 Jul 2019 00:11:22: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:11:22: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:11:22: #1 total tags in treatment: 3738800 INFO @ Sat, 06 Jul 2019 00:11:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:11:22: #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 00:11:22: #1 tags after filtering in treatment: 2485250 INFO @ Sat, 06 Jul 2019 00:11:22: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 06 Jul 2019 00:11:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:11:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:11:22: #2 number of paired peaks: 13 WARNING @ Sat, 06 Jul 2019 00:11:22: Too few paired peaks (13) 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 00:11:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.20_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/SRX3865929/SRX3865929.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865929/SRX3865929.20_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。