Job ID = 2010553 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:56:56 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 : 13,336,548 reads read : 26,673,096 reads written : 26,673,096 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: 00:10:48 13336548 reads; of these: 13336548 (100.00%) were paired; of these: 2740615 (20.55%) aligned concordantly 0 times 7133702 (53.49%) aligned concordantly exactly 1 time 3462231 (25.96%) aligned concordantly >1 times ---- 2740615 pairs aligned concordantly 0 times; of these: 299298 (10.92%) aligned discordantly 1 time ---- 2441317 pairs aligned 0 times concordantly or discordantly; of these: 4882634 mates make up the pairs; of these: 4519131 (92.56%) aligned 0 times 127490 (2.61%) aligned exactly 1 time 236013 (4.83%) aligned >1 times 83.06% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 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] 1361177 / 10884124 = 0.1251 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 23:28:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.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 23:28:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.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 23:28:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.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 23:28:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:49: 1000000 INFO @ Fri, 05 Jul 2019 23:28:51: 1000000 INFO @ Fri, 05 Jul 2019 23:28:51: 1000000 INFO @ Fri, 05 Jul 2019 23:28:56: 2000000 INFO @ Fri, 05 Jul 2019 23:29:02: 2000000 INFO @ Fri, 05 Jul 2019 23:29:03: 2000000 INFO @ Fri, 05 Jul 2019 23:29:04: 3000000 INFO @ Fri, 05 Jul 2019 23:29:11: 4000000 INFO @ Fri, 05 Jul 2019 23:29:13: 3000000 INFO @ Fri, 05 Jul 2019 23:29:14: 3000000 INFO @ Fri, 05 Jul 2019 23:29:18: 5000000 INFO @ Fri, 05 Jul 2019 23:29:23: 4000000 INFO @ Fri, 05 Jul 2019 23:29:25: 4000000 INFO @ Fri, 05 Jul 2019 23:29:25: 6000000 INFO @ Fri, 05 Jul 2019 23:29:33: 7000000 INFO @ Fri, 05 Jul 2019 23:29:33: 5000000 INFO @ Fri, 05 Jul 2019 23:29:35: 5000000 INFO @ Fri, 05 Jul 2019 23:29:40: 8000000 INFO @ Fri, 05 Jul 2019 23:29:43: 6000000 INFO @ Fri, 05 Jul 2019 23:29:46: 6000000 INFO @ Fri, 05 Jul 2019 23:29:47: 9000000 INFO @ Fri, 05 Jul 2019 23:29:53: 7000000 INFO @ Fri, 05 Jul 2019 23:29:54: 10000000 INFO @ Fri, 05 Jul 2019 23:29:57: 7000000 INFO @ Fri, 05 Jul 2019 23:30:01: 11000000 INFO @ Fri, 05 Jul 2019 23:30:03: 8000000 INFO @ Fri, 05 Jul 2019 23:30:08: 8000000 INFO @ Fri, 05 Jul 2019 23:30:08: 12000000 INFO @ Fri, 05 Jul 2019 23:30:13: 9000000 INFO @ Fri, 05 Jul 2019 23:30:16: 13000000 INFO @ Fri, 05 Jul 2019 23:30:19: 9000000 INFO @ Fri, 05 Jul 2019 23:30:23: 14000000 INFO @ Fri, 05 Jul 2019 23:30:23: 10000000 INFO @ Fri, 05 Jul 2019 23:30:30: 10000000 INFO @ Fri, 05 Jul 2019 23:30:30: 15000000 INFO @ Fri, 05 Jul 2019 23:30:34: 11000000 INFO @ Fri, 05 Jul 2019 23:30:37: 16000000 INFO @ Fri, 05 Jul 2019 23:30:40: 11000000 INFO @ Fri, 05 Jul 2019 23:30:43: 12000000 INFO @ Fri, 05 Jul 2019 23:30:44: 17000000 INFO @ Fri, 05 Jul 2019 23:30:51: 12000000 INFO @ Fri, 05 Jul 2019 23:30:52: 18000000 INFO @ Fri, 05 Jul 2019 23:30:53: 13000000 INFO @ Fri, 05 Jul 2019 23:30:59: 19000000 INFO @ Fri, 05 Jul 2019 23:31:02: 13000000 INFO @ Fri, 05 Jul 2019 23:31:02: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:31:02: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:31:02: #1 total tags in treatment: 9248907 INFO @ Fri, 05 Jul 2019 23:31:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:31:02: #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 23:31:02: #1 tags after filtering in treatment: 5972639 INFO @ Fri, 05 Jul 2019 23:31:02: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:31:02: #1 finished! INFO @ Fri, 05 Jul 2019 23:31:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:31:03: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:31:03: 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 23:31:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.20_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/SRX381254/SRX381254.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:31:03: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:31:12: 14000000 INFO @ Fri, 05 Jul 2019 23:31:13: 15000000 INFO @ Fri, 05 Jul 2019 23:31:23: 15000000 INFO @ Fri, 05 Jul 2019 23:31:23: 16000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:31:33: 17000000 INFO @ Fri, 05 Jul 2019 23:31:34: 16000000 INFO @ Fri, 05 Jul 2019 23:31:43: 18000000 INFO @ Fri, 05 Jul 2019 23:31:44: 17000000 INFO @ Fri, 05 Jul 2019 23:31:53: 19000000 INFO @ Fri, 05 Jul 2019 23:31:54: 18000000 INFO @ Fri, 05 Jul 2019 23:31:57: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:31:57: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:31:57: #1 total tags in treatment: 9248907 INFO @ Fri, 05 Jul 2019 23:31:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:31:57: #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 23:31:57: #1 tags after filtering in treatment: 5972639 INFO @ Fri, 05 Jul 2019 23:31:57: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:31:57: #1 finished! INFO @ Fri, 05 Jul 2019 23:31:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:31:58: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:31:58: 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 23:31:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.10_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/SRX381254/SRX381254.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:32:04: 19000000 INFO @ Fri, 05 Jul 2019 23:32:08: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:32:08: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:32:08: #1 total tags in treatment: 9248907 INFO @ Fri, 05 Jul 2019 23:32:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:32:08: #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 23:32:08: #1 tags after filtering in treatment: 5972639 INFO @ Fri, 05 Jul 2019 23:32:08: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:32:08: #1 finished! INFO @ Fri, 05 Jul 2019 23:32:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:32:08: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:32:08: 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 @ Fri, 05 Jul 2019 23:32:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.05_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/SRX381254/SRX381254.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381254/SRX381254.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling