Job ID = 2641008 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:18:36 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 ) 2019-08-24T11:33:00 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 : 14,961,751 reads read : 29,923,502 reads written : 29,923,502 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: 00:17:41 14961751 reads; of these: 14961751 (100.00%) were paired; of these: 3225161 (21.56%) aligned concordantly 0 times 9138380 (61.08%) aligned concordantly exactly 1 time 2598210 (17.37%) aligned concordantly >1 times ---- 3225161 pairs aligned concordantly 0 times; of these: 943952 (29.27%) aligned discordantly 1 time ---- 2281209 pairs aligned 0 times concordantly or discordantly; of these: 4562418 mates make up the pairs; of these: 3919539 (85.91%) aligned 0 times 185800 (4.07%) aligned exactly 1 time 457079 (10.02%) aligned >1 times 86.90% overall alignment rate Time searching: 00:17:41 Overall time: 00:17:41 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] 1931963 / 12677470 = 0.1524 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:16:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.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 21:16:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:10: 1000000 INFO @ Sat, 24 Aug 2019 21:16:18: 2000000 INFO @ Sat, 24 Aug 2019 21:16:27: 3000000 INFO @ Sat, 24 Aug 2019 21:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.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 21:16:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:16:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:16:35: 4000000 INFO @ Sat, 24 Aug 2019 21:16:41: 1000000 INFO @ Sat, 24 Aug 2019 21:16:44: 5000000 INFO @ Sat, 24 Aug 2019 21:16:51: 2000000 INFO @ Sat, 24 Aug 2019 21:16:52: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:17:00: 3000000 INFO @ Sat, 24 Aug 2019 21:17:01: 7000000 INFO @ Sat, 24 Aug 2019 21:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.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 21:17:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:17:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:17:09: 8000000 INFO @ Sat, 24 Aug 2019 21:17:10: 1000000 INFO @ Sat, 24 Aug 2019 21:17:10: 4000000 INFO @ Sat, 24 Aug 2019 21:17:18: 9000000 INFO @ Sat, 24 Aug 2019 21:17:18: 2000000 INFO @ Sat, 24 Aug 2019 21:17:20: 5000000 INFO @ Sat, 24 Aug 2019 21:17:27: 10000000 INFO @ Sat, 24 Aug 2019 21:17:27: 3000000 INFO @ Sat, 24 Aug 2019 21:17:30: 6000000 INFO @ Sat, 24 Aug 2019 21:17:36: 11000000 INFO @ Sat, 24 Aug 2019 21:17:36: 4000000 INFO @ Sat, 24 Aug 2019 21:17:40: 7000000 INFO @ Sat, 24 Aug 2019 21:17:45: 12000000 INFO @ Sat, 24 Aug 2019 21:17:45: 5000000 INFO @ Sat, 24 Aug 2019 21:17:49: 8000000 INFO @ Sat, 24 Aug 2019 21:17:53: 13000000 INFO @ Sat, 24 Aug 2019 21:17:53: 6000000 INFO @ Sat, 24 Aug 2019 21:17:59: 9000000 INFO @ Sat, 24 Aug 2019 21:18:02: 14000000 INFO @ Sat, 24 Aug 2019 21:18:02: 7000000 INFO @ Sat, 24 Aug 2019 21:18:09: 10000000 INFO @ Sat, 24 Aug 2019 21:18:10: 15000000 INFO @ Sat, 24 Aug 2019 21:18:11: 8000000 INFO @ Sat, 24 Aug 2019 21:18:19: 11000000 INFO @ Sat, 24 Aug 2019 21:18:20: 9000000 INFO @ Sat, 24 Aug 2019 21:18:20: 16000000 INFO @ Sat, 24 Aug 2019 21:18:29: 12000000 INFO @ Sat, 24 Aug 2019 21:18:29: 10000000 INFO @ Sat, 24 Aug 2019 21:18:29: 17000000 INFO @ Sat, 24 Aug 2019 21:18:37: 11000000 INFO @ Sat, 24 Aug 2019 21:18:38: 18000000 INFO @ Sat, 24 Aug 2019 21:18:38: 13000000 INFO @ Sat, 24 Aug 2019 21:18:46: 12000000 INFO @ Sat, 24 Aug 2019 21:18:47: 19000000 INFO @ Sat, 24 Aug 2019 21:18:48: 14000000 INFO @ Sat, 24 Aug 2019 21:18:55: 13000000 INFO @ Sat, 24 Aug 2019 21:18:55: 20000000 INFO @ Sat, 24 Aug 2019 21:18:58: 15000000 INFO @ Sat, 24 Aug 2019 21:19:03: 14000000 INFO @ Sat, 24 Aug 2019 21:19:04: 21000000 INFO @ Sat, 24 Aug 2019 21:19:08: 16000000 INFO @ Sat, 24 Aug 2019 21:19:12: 15000000 INFO @ Sat, 24 Aug 2019 21:19:13: 22000000 INFO @ Sat, 24 Aug 2019 21:19:14: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:19:14: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:19:14: #1 total tags in treatment: 9872637 INFO @ Sat, 24 Aug 2019 21:19:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:19:14: #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 21:19:15: #1 tags after filtering in treatment: 6966105 INFO @ Sat, 24 Aug 2019 21:19:15: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:19:15: #1 finished! INFO @ Sat, 24 Aug 2019 21:19:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:19:15: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:19:15: 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 21:19:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.05_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/SRX4936114/SRX4936114.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:19:18: 17000000 INFO @ Sat, 24 Aug 2019 21:19:21: 16000000 INFO @ Sat, 24 Aug 2019 21:19:27: 18000000 INFO @ Sat, 24 Aug 2019 21:19:29: 17000000 INFO @ Sat, 24 Aug 2019 21:19:37: 19000000 INFO @ Sat, 24 Aug 2019 21:19:38: 18000000 INFO @ Sat, 24 Aug 2019 21:19:46: 19000000 INFO @ Sat, 24 Aug 2019 21:19:47: 20000000 INFO @ Sat, 24 Aug 2019 21:19:55: 20000000 INFO @ Sat, 24 Aug 2019 21:19:56: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:20:03: 21000000 INFO @ Sat, 24 Aug 2019 21:20:06: 22000000 INFO @ Sat, 24 Aug 2019 21:20:07: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:20:07: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:20:07: #1 total tags in treatment: 9872637 INFO @ Sat, 24 Aug 2019 21:20:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:20:07: #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 21:20:08: #1 tags after filtering in treatment: 6966105 INFO @ Sat, 24 Aug 2019 21:20:08: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:20:08: #1 finished! INFO @ Sat, 24 Aug 2019 21:20:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:20:08: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:20:08: 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 21:20:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.10_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/SRX4936114/SRX4936114.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:20:12: 22000000 INFO @ Sat, 24 Aug 2019 21:20:13: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:20:13: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:20:13: #1 total tags in treatment: 9872637 INFO @ Sat, 24 Aug 2019 21:20:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:20:13: #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 21:20:13: #1 tags after filtering in treatment: 6966105 INFO @ Sat, 24 Aug 2019 21:20:13: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:20:13: #1 finished! INFO @ Sat, 24 Aug 2019 21:20:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:20:14: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:20:14: 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 21:20:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.20_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/SRX4936114/SRX4936114.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936114/SRX4936114.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。