Job ID = 2641007 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:31:57 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 ) 2019-08-24T11:31:57 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 : 14,883,305 reads read : 29,766,610 reads written : 29,766,610 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: 00:18:05 14883305 reads; of these: 14883305 (100.00%) were paired; of these: 2845624 (19.12%) aligned concordantly 0 times 10483183 (70.44%) aligned concordantly exactly 1 time 1554498 (10.44%) aligned concordantly >1 times ---- 2845624 pairs aligned concordantly 0 times; of these: 1087433 (38.21%) aligned discordantly 1 time ---- 1758191 pairs aligned 0 times concordantly or discordantly; of these: 3516382 mates make up the pairs; of these: 2984363 (84.87%) aligned 0 times 195619 (5.56%) aligned exactly 1 time 336400 (9.57%) aligned >1 times 89.97% overall alignment rate Time searching: 00:18:05 Overall time: 00:18:05 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] 1331624 / 13122689 = 0.1015 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.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, 24 Aug 2019 21:14:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:14:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:15:00: 1000000 INFO @ Sat, 24 Aug 2019 21:15:09: 2000000 INFO @ Sat, 24 Aug 2019 21:15:18: 3000000 INFO @ Sat, 24 Aug 2019 21:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.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, 24 Aug 2019 21:15:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:15:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:15:27: 4000000 INFO @ Sat, 24 Aug 2019 21:15:30: 1000000 INFO @ Sat, 24 Aug 2019 21:15:36: 5000000 INFO @ Sat, 24 Aug 2019 21:15:39: 2000000 INFO @ Sat, 24 Aug 2019 21:15:46: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:15:49: 3000000 INFO @ Sat, 24 Aug 2019 21:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.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, 24 Aug 2019 21:15:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:15:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:15:55: 7000000 INFO @ Sat, 24 Aug 2019 21:15:58: 4000000 INFO @ Sat, 24 Aug 2019 21:16:00: 1000000 INFO @ Sat, 24 Aug 2019 21:16:04: 8000000 INFO @ Sat, 24 Aug 2019 21:16:07: 5000000 INFO @ Sat, 24 Aug 2019 21:16:09: 2000000 INFO @ Sat, 24 Aug 2019 21:16:14: 9000000 INFO @ Sat, 24 Aug 2019 21:16:17: 6000000 INFO @ Sat, 24 Aug 2019 21:16:18: 3000000 INFO @ Sat, 24 Aug 2019 21:16:23: 10000000 INFO @ Sat, 24 Aug 2019 21:16:26: 7000000 INFO @ Sat, 24 Aug 2019 21:16:28: 4000000 INFO @ Sat, 24 Aug 2019 21:16:33: 11000000 INFO @ Sat, 24 Aug 2019 21:16:36: 8000000 INFO @ Sat, 24 Aug 2019 21:16:37: 5000000 INFO @ Sat, 24 Aug 2019 21:16:42: 12000000 INFO @ Sat, 24 Aug 2019 21:16:45: 9000000 INFO @ Sat, 24 Aug 2019 21:16:46: 6000000 INFO @ Sat, 24 Aug 2019 21:16:51: 13000000 INFO @ Sat, 24 Aug 2019 21:16:54: 10000000 INFO @ Sat, 24 Aug 2019 21:16:56: 7000000 INFO @ Sat, 24 Aug 2019 21:17:01: 14000000 INFO @ Sat, 24 Aug 2019 21:17:04: 11000000 INFO @ Sat, 24 Aug 2019 21:17:05: 8000000 INFO @ Sat, 24 Aug 2019 21:17:10: 15000000 INFO @ Sat, 24 Aug 2019 21:17:13: 12000000 INFO @ Sat, 24 Aug 2019 21:17:14: 9000000 INFO @ Sat, 24 Aug 2019 21:17:19: 16000000 INFO @ Sat, 24 Aug 2019 21:17:23: 13000000 INFO @ Sat, 24 Aug 2019 21:17:24: 10000000 INFO @ Sat, 24 Aug 2019 21:17:29: 17000000 INFO @ Sat, 24 Aug 2019 21:17:32: 14000000 INFO @ Sat, 24 Aug 2019 21:17:33: 11000000 INFO @ Sat, 24 Aug 2019 21:17:38: 18000000 INFO @ Sat, 24 Aug 2019 21:17:41: 15000000 INFO @ Sat, 24 Aug 2019 21:17:42: 12000000 INFO @ Sat, 24 Aug 2019 21:17:47: 19000000 INFO @ Sat, 24 Aug 2019 21:17:51: 16000000 INFO @ Sat, 24 Aug 2019 21:17:51: 13000000 INFO @ Sat, 24 Aug 2019 21:17:57: 20000000 INFO @ Sat, 24 Aug 2019 21:18:00: 17000000 INFO @ Sat, 24 Aug 2019 21:18:01: 14000000 INFO @ Sat, 24 Aug 2019 21:18:06: 21000000 INFO @ Sat, 24 Aug 2019 21:18:10: 18000000 INFO @ Sat, 24 Aug 2019 21:18:10: 15000000 INFO @ Sat, 24 Aug 2019 21:18:15: 22000000 INFO @ Sat, 24 Aug 2019 21:18:19: 19000000 INFO @ Sat, 24 Aug 2019 21:18:19: 16000000 INFO @ Sat, 24 Aug 2019 21:18:25: 23000000 INFO @ Sat, 24 Aug 2019 21:18:28: 20000000 INFO @ Sat, 24 Aug 2019 21:18:28: 17000000 INFO @ Sat, 24 Aug 2019 21:18:34: 24000000 INFO @ Sat, 24 Aug 2019 21:18:35: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:18:35: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:18:35: #1 total tags in treatment: 10766153 INFO @ Sat, 24 Aug 2019 21:18:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:18:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:18:35: #1 tags after filtering in treatment: 7871909 INFO @ Sat, 24 Aug 2019 21:18:35: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:18:35: #1 finished! INFO @ Sat, 24 Aug 2019 21:18:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:18:36: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:18:36: 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, 24 Aug 2019 21:18:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.05_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/SRX4936113/SRX4936113.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:18:38: 21000000 INFO @ Sat, 24 Aug 2019 21:18:38: 18000000 INFO @ Sat, 24 Aug 2019 21:18:47: 22000000 INFO @ Sat, 24 Aug 2019 21:18:47: 19000000 INFO @ Sat, 24 Aug 2019 21:18:56: 23000000 INFO @ Sat, 24 Aug 2019 21:18:56: 20000000 INFO @ Sat, 24 Aug 2019 21:19:05: 24000000 INFO @ Sat, 24 Aug 2019 21:19:05: 21000000 INFO @ Sat, 24 Aug 2019 21:19:06: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:19:06: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:19:06: #1 total tags in treatment: 10766153 INFO @ Sat, 24 Aug 2019 21:19:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:19:07: #1 tags after filtering in treatment: 7871909 INFO @ Sat, 24 Aug 2019 21:19:07: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:19:07: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:07: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:07: 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, 24 Aug 2019 21:19:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.10_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/SRX4936113/SRX4936113.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:19:14: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:19:23: 23000000 INFO @ Sat, 24 Aug 2019 21:19:32: 24000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:19:33: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:19:33: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:19:33: #1 total tags in treatment: 10766153 INFO @ Sat, 24 Aug 2019 21:19:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:19:33: #1 tags after filtering in treatment: 7871909 INFO @ Sat, 24 Aug 2019 21:19:33: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 21:19:33: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:34: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:34: 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, 24 Aug 2019 21:19:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.20_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/SRX4936113/SRX4936113.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936113/SRX4936113.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling