Job ID = 2011857 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:50:10 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 ) 2019-07-05T17:50:10 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 ) 2019-07-05T17:56:45 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 : 19,027,595 reads read : 38,055,190 reads written : 38,055,190 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: 00:14:19 19027595 reads; of these: 19027595 (100.00%) were paired; of these: 944494 (4.96%) aligned concordantly 0 times 15657685 (82.29%) aligned concordantly exactly 1 time 2425416 (12.75%) aligned concordantly >1 times ---- 944494 pairs aligned concordantly 0 times; of these: 95318 (10.09%) aligned discordantly 1 time ---- 849176 pairs aligned 0 times concordantly or discordantly; of these: 1698352 mates make up the pairs; of these: 1455422 (85.70%) aligned 0 times 177789 (10.47%) aligned exactly 1 time 65141 (3.84%) aligned >1 times 96.18% overall alignment rate Time searching: 00:14:19 Overall time: 00:14:19 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 16 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] 3276622 / 18137436 = 0.1807 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 03:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.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 03:25:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:25:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.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 03:25:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:25:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.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 03:25:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:25:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:25:10: 1000000 INFO @ Sat, 06 Jul 2019 03:25:11: 1000000 INFO @ Sat, 06 Jul 2019 03:25:12: 1000000 INFO @ Sat, 06 Jul 2019 03:25:17: 2000000 INFO @ Sat, 06 Jul 2019 03:25:18: 2000000 INFO @ Sat, 06 Jul 2019 03:25:19: 2000000 INFO @ Sat, 06 Jul 2019 03:25:24: 3000000 INFO @ Sat, 06 Jul 2019 03:25:26: 3000000 INFO @ Sat, 06 Jul 2019 03:25:26: 3000000 INFO @ Sat, 06 Jul 2019 03:25:30: 4000000 INFO @ Sat, 06 Jul 2019 03:25:33: 4000000 INFO @ Sat, 06 Jul 2019 03:25:34: 4000000 INFO @ Sat, 06 Jul 2019 03:25:37: 5000000 INFO @ Sat, 06 Jul 2019 03:25:40: 5000000 INFO @ Sat, 06 Jul 2019 03:25:41: 5000000 INFO @ Sat, 06 Jul 2019 03:25:43: 6000000 INFO @ Sat, 06 Jul 2019 03:25:48: 6000000 INFO @ Sat, 06 Jul 2019 03:25:48: 6000000 INFO @ Sat, 06 Jul 2019 03:25:50: 7000000 INFO @ Sat, 06 Jul 2019 03:25:55: 7000000 INFO @ Sat, 06 Jul 2019 03:25:56: 7000000 INFO @ Sat, 06 Jul 2019 03:25:57: 8000000 INFO @ Sat, 06 Jul 2019 03:26:02: 8000000 INFO @ Sat, 06 Jul 2019 03:26:03: 8000000 INFO @ Sat, 06 Jul 2019 03:26:03: 9000000 INFO @ Sat, 06 Jul 2019 03:26:09: 9000000 INFO @ Sat, 06 Jul 2019 03:26:10: 10000000 INFO @ Sat, 06 Jul 2019 03:26:10: 9000000 INFO @ Sat, 06 Jul 2019 03:26:16: 10000000 INFO @ Sat, 06 Jul 2019 03:26:16: 11000000 INFO @ Sat, 06 Jul 2019 03:26:17: 10000000 INFO @ Sat, 06 Jul 2019 03:26:22: 11000000 INFO @ Sat, 06 Jul 2019 03:26:23: 12000000 INFO @ Sat, 06 Jul 2019 03:26:25: 11000000 INFO @ Sat, 06 Jul 2019 03:26:29: 13000000 INFO @ Sat, 06 Jul 2019 03:26:29: 12000000 INFO @ Sat, 06 Jul 2019 03:26:32: 12000000 INFO @ Sat, 06 Jul 2019 03:26:36: 14000000 INFO @ Sat, 06 Jul 2019 03:26:36: 13000000 INFO @ Sat, 06 Jul 2019 03:26:39: 13000000 INFO @ Sat, 06 Jul 2019 03:26:42: 15000000 INFO @ Sat, 06 Jul 2019 03:26:43: 14000000 INFO @ Sat, 06 Jul 2019 03:26:46: 14000000 INFO @ Sat, 06 Jul 2019 03:26:49: 16000000 INFO @ Sat, 06 Jul 2019 03:26:50: 15000000 INFO @ Sat, 06 Jul 2019 03:26:53: 15000000 INFO @ Sat, 06 Jul 2019 03:26:55: 17000000 INFO @ Sat, 06 Jul 2019 03:26:57: 16000000 INFO @ Sat, 06 Jul 2019 03:27:01: 16000000 INFO @ Sat, 06 Jul 2019 03:27:02: 18000000 INFO @ Sat, 06 Jul 2019 03:27:04: 17000000 INFO @ Sat, 06 Jul 2019 03:27:08: 17000000 INFO @ Sat, 06 Jul 2019 03:27:08: 19000000 INFO @ Sat, 06 Jul 2019 03:27:11: 18000000 INFO @ Sat, 06 Jul 2019 03:27:15: 20000000 INFO @ Sat, 06 Jul 2019 03:27:15: 18000000 INFO @ Sat, 06 Jul 2019 03:27:18: 19000000 INFO @ Sat, 06 Jul 2019 03:27:21: 21000000 INFO @ Sat, 06 Jul 2019 03:27:22: 19000000 INFO @ Sat, 06 Jul 2019 03:27:24: 20000000 INFO @ Sat, 06 Jul 2019 03:27:28: 22000000 INFO @ Sat, 06 Jul 2019 03:27:29: 20000000 INFO @ Sat, 06 Jul 2019 03:27:31: 21000000 INFO @ Sat, 06 Jul 2019 03:27:34: 23000000 INFO @ Sat, 06 Jul 2019 03:27:36: 21000000 INFO @ Sat, 06 Jul 2019 03:27:38: 22000000 INFO @ Sat, 06 Jul 2019 03:27:41: 24000000 INFO @ Sat, 06 Jul 2019 03:27:43: 22000000 INFO @ Sat, 06 Jul 2019 03:27:45: 23000000 INFO @ Sat, 06 Jul 2019 03:27:47: 25000000 INFO @ Sat, 06 Jul 2019 03:27:50: 23000000 INFO @ Sat, 06 Jul 2019 03:27:52: 24000000 INFO @ Sat, 06 Jul 2019 03:27:53: 26000000 INFO @ Sat, 06 Jul 2019 03:27:57: 24000000 INFO @ Sat, 06 Jul 2019 03:27:58: 25000000 INFO @ Sat, 06 Jul 2019 03:28:00: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:28:04: 25000000 INFO @ Sat, 06 Jul 2019 03:28:05: 26000000 INFO @ Sat, 06 Jul 2019 03:28:06: 28000000 INFO @ Sat, 06 Jul 2019 03:28:10: 26000000 INFO @ Sat, 06 Jul 2019 03:28:12: 27000000 INFO @ Sat, 06 Jul 2019 03:28:12: 29000000 INFO @ Sat, 06 Jul 2019 03:28:17: 27000000 INFO @ Sat, 06 Jul 2019 03:28:18: 28000000 INFO @ Sat, 06 Jul 2019 03:28:19: 30000000 INFO @ Sat, 06 Jul 2019 03:28:19: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:28:19: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:28:19: #1 total tags in treatment: 14813304 INFO @ Sat, 06 Jul 2019 03:28:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:28:19: #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 03:28:19: #1 tags after filtering in treatment: 7990847 INFO @ Sat, 06 Jul 2019 03:28:19: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 06 Jul 2019 03:28:19: #1 finished! INFO @ Sat, 06 Jul 2019 03:28:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:28:20: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:28:20: 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 03:28:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.05_peaks.narrowPeak: No such file or directory BigWig に変換しました。 pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:28:24: 28000000 INFO @ Sat, 06 Jul 2019 03:28:25: 29000000 INFO @ Sat, 06 Jul 2019 03:28:31: 29000000 INFO @ Sat, 06 Jul 2019 03:28:31: 30000000 INFO @ Sat, 06 Jul 2019 03:28:32: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:28:32: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:28:32: #1 total tags in treatment: 14813304 INFO @ Sat, 06 Jul 2019 03:28:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:28:32: #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 03:28:32: #1 tags after filtering in treatment: 7990847 INFO @ Sat, 06 Jul 2019 03:28:32: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 06 Jul 2019 03:28:32: #1 finished! INFO @ Sat, 06 Jul 2019 03:28:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:28:33: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:28:33: 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 03:28:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.20_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/SRX5170654/SRX5170654.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:28:37: 30000000 INFO @ Sat, 06 Jul 2019 03:28:38: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:28:38: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:28:38: #1 total tags in treatment: 14813304 INFO @ Sat, 06 Jul 2019 03:28:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:28:38: #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 03:28:38: #1 tags after filtering in treatment: 7990847 INFO @ Sat, 06 Jul 2019 03:28:38: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 06 Jul 2019 03:28:38: #1 finished! INFO @ Sat, 06 Jul 2019 03:28:38: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:28:39: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:28:39: 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 03:28:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.10_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/SRX5170654/SRX5170654.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170654/SRX5170654.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling