Job ID = 2010990 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T16:32:40 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 ) 2019-07-05T16:35:41 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 ) 2019-07-05T16:35:41 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 : 9,085,329 reads read : 18,170,658 reads written : 18,170,658 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: 00:05:28 9085329 reads; of these: 9085329 (100.00%) were paired; of these: 4394892 (48.37%) aligned concordantly 0 times 4169973 (45.90%) aligned concordantly exactly 1 time 520464 (5.73%) aligned concordantly >1 times ---- 4394892 pairs aligned concordantly 0 times; of these: 36780 (0.84%) aligned discordantly 1 time ---- 4358112 pairs aligned 0 times concordantly or discordantly; of these: 8716224 mates make up the pairs; of these: 4764333 (54.66%) aligned 0 times 3491195 (40.05%) aligned exactly 1 time 460696 (5.29%) aligned >1 times 73.78% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 183624 / 4724890 = 0.0389 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 01:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.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 01:46:53: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:46:53: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.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 01:46:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:46:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:46:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.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 01:46:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:46:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:47:00: 1000000 INFO @ Sat, 06 Jul 2019 01:47:03: 1000000 INFO @ Sat, 06 Jul 2019 01:47:04: 1000000 INFO @ Sat, 06 Jul 2019 01:47:08: 2000000 INFO @ Sat, 06 Jul 2019 01:47:13: 2000000 INFO @ Sat, 06 Jul 2019 01:47:14: 2000000 INFO @ Sat, 06 Jul 2019 01:47:15: 3000000 INFO @ Sat, 06 Jul 2019 01:47:23: 4000000 INFO @ Sat, 06 Jul 2019 01:47:23: 3000000 INFO @ Sat, 06 Jul 2019 01:47:24: 3000000 INFO @ Sat, 06 Jul 2019 01:47:30: 5000000 INFO @ Sat, 06 Jul 2019 01:47:32: 4000000 INFO @ Sat, 06 Jul 2019 01:47:33: 4000000 INFO @ Sat, 06 Jul 2019 01:47:38: 6000000 INFO @ Sat, 06 Jul 2019 01:47:41: 5000000 INFO @ Sat, 06 Jul 2019 01:47:43: 5000000 INFO @ Sat, 06 Jul 2019 01:47:46: 7000000 INFO @ Sat, 06 Jul 2019 01:47:50: 6000000 INFO @ Sat, 06 Jul 2019 01:47:52: 6000000 INFO @ Sat, 06 Jul 2019 01:47:54: 8000000 INFO @ Sat, 06 Jul 2019 01:47:57: 7000000 INFO @ Sat, 06 Jul 2019 01:48:01: 9000000 INFO @ Sat, 06 Jul 2019 01:48:01: 7000000 INFO @ Sat, 06 Jul 2019 01:48:05: 8000000 INFO @ Sat, 06 Jul 2019 01:48:08: 10000000 INFO @ Sat, 06 Jul 2019 01:48:10: 8000000 INFO @ Sat, 06 Jul 2019 01:48:12: 9000000 INFO @ Sat, 06 Jul 2019 01:48:16: 11000000 INFO @ Sat, 06 Jul 2019 01:48:19: 9000000 INFO @ Sat, 06 Jul 2019 01:48:19: 10000000 INFO @ Sat, 06 Jul 2019 01:48:24: 12000000 INFO @ Sat, 06 Jul 2019 01:48:27: 11000000 INFO @ Sat, 06 Jul 2019 01:48:29: 10000000 INFO @ Sat, 06 Jul 2019 01:48:31: 13000000 INFO @ Sat, 06 Jul 2019 01:48:31: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:48:31: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:48:31: #1 total tags in treatment: 4507120 INFO @ Sat, 06 Jul 2019 01:48:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:48:31: #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 01:48:31: #1 tags after filtering in treatment: 3078556 INFO @ Sat, 06 Jul 2019 01:48:31: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 01:48:31: #1 finished! INFO @ Sat, 06 Jul 2019 01:48:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:48:32: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 01:48:32: Too few paired peaks (1) 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 01:48:32: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:48:34: 12000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.05_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/SRX4342936/SRX4342936.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:48:38: 11000000 INFO @ Sat, 06 Jul 2019 01:48:41: 13000000 INFO @ Sat, 06 Jul 2019 01:48:42: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:48:42: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:48:42: #1 total tags in treatment: 4507120 INFO @ Sat, 06 Jul 2019 01:48:42: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:48:42: #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 01:48:42: #1 tags after filtering in treatment: 3078556 INFO @ Sat, 06 Jul 2019 01:48:42: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 01:48:42: #1 finished! INFO @ Sat, 06 Jul 2019 01:48:42: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:48:42: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 01:48:42: Too few paired peaks (1) 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 01:48:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.20_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/SRX4342936/SRX4342936.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:48:47: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:48:55: 13000000 INFO @ Sat, 06 Jul 2019 01:48:55: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 01:48:55: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 01:48:55: #1 total tags in treatment: 4507120 INFO @ Sat, 06 Jul 2019 01:48:55: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:48:55: #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 01:48:55: #1 tags after filtering in treatment: 3078556 INFO @ Sat, 06 Jul 2019 01:48:55: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 01:48:55: #1 finished! INFO @ Sat, 06 Jul 2019 01:48:55: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:48:56: #2 number of paired peaks: 1 WARNING @ Sat, 06 Jul 2019 01:48:56: Too few paired peaks (1) 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 01:48:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.10_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/SRX4342936/SRX4342936.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4342936/SRX4342936.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。