Job ID = 2008120 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:39:34 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 ) 2019-07-05T08:39:34 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 : 12,183,811 reads read : 24,367,622 reads written : 24,367,622 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: 00:08:18 12183811 reads; of these: 12183811 (100.00%) were paired; of these: 355514 (2.92%) aligned concordantly 0 times 11111368 (91.20%) aligned concordantly exactly 1 time 716929 (5.88%) aligned concordantly >1 times ---- 355514 pairs aligned concordantly 0 times; of these: 5696 (1.60%) aligned discordantly 1 time ---- 349818 pairs aligned 0 times concordantly or discordantly; of these: 699636 mates make up the pairs; of these: 686569 (98.13%) aligned 0 times 10952 (1.57%) aligned exactly 1 time 2115 (0.30%) aligned >1 times 97.18% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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] 2456170 / 11829151 = 0.2076 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 @ Fri, 05 Jul 2019 18:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.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 @ Fri, 05 Jul 2019 18:15:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:15:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.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 @ Fri, 05 Jul 2019 18:15:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:15:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.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 @ Fri, 05 Jul 2019 18:15:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:15:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:15:25: 1000000 INFO @ Fri, 05 Jul 2019 18:15:26: 1000000 INFO @ Fri, 05 Jul 2019 18:15:29: 1000000 INFO @ Fri, 05 Jul 2019 18:15:32: 2000000 INFO @ Fri, 05 Jul 2019 18:15:33: 2000000 INFO @ Fri, 05 Jul 2019 18:15:36: 2000000 INFO @ Fri, 05 Jul 2019 18:15:39: 3000000 INFO @ Fri, 05 Jul 2019 18:15:40: 3000000 INFO @ Fri, 05 Jul 2019 18:15:44: 3000000 INFO @ Fri, 05 Jul 2019 18:15:45: 4000000 INFO @ Fri, 05 Jul 2019 18:15:46: 4000000 INFO @ Fri, 05 Jul 2019 18:15:52: 4000000 INFO @ Fri, 05 Jul 2019 18:15:52: 5000000 INFO @ Fri, 05 Jul 2019 18:15:53: 5000000 INFO @ Fri, 05 Jul 2019 18:15:58: 6000000 INFO @ Fri, 05 Jul 2019 18:15:59: 5000000 INFO @ Fri, 05 Jul 2019 18:16:00: 6000000 INFO @ Fri, 05 Jul 2019 18:16:05: 7000000 INFO @ Fri, 05 Jul 2019 18:16:06: 7000000 INFO @ Fri, 05 Jul 2019 18:16:07: 6000000 INFO @ Fri, 05 Jul 2019 18:16:12: 8000000 INFO @ Fri, 05 Jul 2019 18:16:13: 8000000 INFO @ Fri, 05 Jul 2019 18:16:14: 7000000 INFO @ Fri, 05 Jul 2019 18:16:18: 9000000 INFO @ Fri, 05 Jul 2019 18:16:20: 9000000 INFO @ Fri, 05 Jul 2019 18:16:22: 8000000 INFO @ Fri, 05 Jul 2019 18:16:25: 10000000 INFO @ Fri, 05 Jul 2019 18:16:26: 10000000 INFO @ Fri, 05 Jul 2019 18:16:30: 9000000 INFO @ Fri, 05 Jul 2019 18:16:31: 11000000 INFO @ Fri, 05 Jul 2019 18:16:33: 11000000 INFO @ Fri, 05 Jul 2019 18:16:37: 10000000 INFO @ Fri, 05 Jul 2019 18:16:38: 12000000 INFO @ Fri, 05 Jul 2019 18:16:39: 12000000 INFO @ Fri, 05 Jul 2019 18:16:44: 13000000 INFO @ Fri, 05 Jul 2019 18:16:45: 11000000 INFO @ Fri, 05 Jul 2019 18:16:46: 13000000 INFO @ Fri, 05 Jul 2019 18:16:51: 14000000 INFO @ Fri, 05 Jul 2019 18:16:52: 12000000 INFO @ Fri, 05 Jul 2019 18:16:52: 14000000 INFO @ Fri, 05 Jul 2019 18:16:57: 15000000 INFO @ Fri, 05 Jul 2019 18:16:59: 15000000 INFO @ Fri, 05 Jul 2019 18:17:00: 13000000 INFO @ Fri, 05 Jul 2019 18:17:04: 16000000 INFO @ Fri, 05 Jul 2019 18:17:06: 16000000 INFO @ Fri, 05 Jul 2019 18:17:07: 14000000 INFO @ Fri, 05 Jul 2019 18:17:11: 17000000 INFO @ Fri, 05 Jul 2019 18:17:12: 17000000 INFO @ Fri, 05 Jul 2019 18:17:15: 15000000 INFO @ Fri, 05 Jul 2019 18:17:18: 18000000 INFO @ Fri, 05 Jul 2019 18:17:19: 18000000 INFO @ Fri, 05 Jul 2019 18:17:22: 16000000 INFO @ Fri, 05 Jul 2019 18:17:23: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:17:23: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:17:23: #1 total tags in treatment: 9372195 INFO @ Fri, 05 Jul 2019 18:17:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:17:23: #1 tags after filtering in treatment: 5719460 INFO @ Fri, 05 Jul 2019 18:17:23: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 18:17:23: #1 finished! INFO @ Fri, 05 Jul 2019 18:17:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:17:24: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:17:24: 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 @ Fri, 05 Jul 2019 18:17:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.05_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/ERX516012/ERX516012.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:17:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:17:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:17:25: #1 total tags in treatment: 9372195 INFO @ Fri, 05 Jul 2019 18:17:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:17:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:17:25: #1 tags after filtering in treatment: 5719460 INFO @ Fri, 05 Jul 2019 18:17:25: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 18:17:25: #1 finished! INFO @ Fri, 05 Jul 2019 18:17:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:17:25: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:17:25: 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 @ Fri, 05 Jul 2019 18:17:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.10_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/ERX516012/ERX516012.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:17:30: 17000000 INFO @ Fri, 05 Jul 2019 18:17:37: 18000000 INFO @ Fri, 05 Jul 2019 18:17:43: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 18:17:43: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 18:17:43: #1 total tags in treatment: 9372195 INFO @ Fri, 05 Jul 2019 18:17:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:17:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:17:43: #1 tags after filtering in treatment: 5719460 INFO @ Fri, 05 Jul 2019 18:17:43: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 18:17:43: #1 finished! INFO @ Fri, 05 Jul 2019 18:17:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:17:43: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:17:43: 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 @ Fri, 05 Jul 2019 18:17:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.20_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/ERX516012/ERX516012.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX516012/ERX516012.20_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。