Job ID = 2009850 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T11:11:59 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 : 15,371,473 reads read : 30,742,946 reads written : 30,742,946 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR583975.sra.cache’: 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: 00:17:29 15371473 reads; of these: 15371473 (100.00%) were paired; of these: 5355938 (34.84%) aligned concordantly 0 times 9121346 (59.34%) aligned concordantly exactly 1 time 894189 (5.82%) aligned concordantly >1 times ---- 5355938 pairs aligned concordantly 0 times; of these: 2083477 (38.90%) aligned discordantly 1 time ---- 3272461 pairs aligned 0 times concordantly or discordantly; of these: 6544922 mates make up the pairs; of these: 4753635 (72.63%) aligned 0 times 1344522 (20.54%) aligned exactly 1 time 446765 (6.83%) aligned >1 times 84.54% overall alignment rate Time searching: 00:17:29 Overall time: 00:17:29 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] 2295395 / 11846218 = 0.1938 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 20:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.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 20:53:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.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 20:53:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.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 20:53:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:09: 1000000 INFO @ Fri, 05 Jul 2019 20:53:11: 1000000 INFO @ Fri, 05 Jul 2019 20:53:12: 1000000 INFO @ Fri, 05 Jul 2019 20:53:19: 2000000 INFO @ Fri, 05 Jul 2019 20:53:21: 2000000 INFO @ Fri, 05 Jul 2019 20:53:23: 2000000 INFO @ Fri, 05 Jul 2019 20:53:27: 3000000 INFO @ Fri, 05 Jul 2019 20:53:31: 3000000 INFO @ Fri, 05 Jul 2019 20:53:34: 3000000 INFO @ Fri, 05 Jul 2019 20:53:36: 4000000 INFO @ Fri, 05 Jul 2019 20:53:40: 4000000 INFO @ Fri, 05 Jul 2019 20:53:45: 5000000 INFO @ Fri, 05 Jul 2019 20:53:45: 4000000 INFO @ Fri, 05 Jul 2019 20:53:50: 5000000 INFO @ Fri, 05 Jul 2019 20:53:53: 6000000 INFO @ Fri, 05 Jul 2019 20:53:56: 5000000 INFO @ Fri, 05 Jul 2019 20:54:00: 6000000 INFO @ Fri, 05 Jul 2019 20:54:02: 7000000 INFO @ Fri, 05 Jul 2019 20:54:06: 6000000 INFO @ Fri, 05 Jul 2019 20:54:09: 7000000 INFO @ Fri, 05 Jul 2019 20:54:10: 8000000 INFO @ Fri, 05 Jul 2019 20:54:17: 7000000 INFO @ Fri, 05 Jul 2019 20:54:19: 9000000 INFO @ Fri, 05 Jul 2019 20:54:19: 8000000 INFO @ Fri, 05 Jul 2019 20:54:27: 10000000 INFO @ Fri, 05 Jul 2019 20:54:28: 8000000 INFO @ Fri, 05 Jul 2019 20:54:29: 9000000 INFO @ Fri, 05 Jul 2019 20:54:36: 11000000 INFO @ Fri, 05 Jul 2019 20:54:38: 10000000 INFO @ Fri, 05 Jul 2019 20:54:39: 9000000 INFO @ Fri, 05 Jul 2019 20:54:44: 12000000 INFO @ Fri, 05 Jul 2019 20:54:48: 11000000 INFO @ Fri, 05 Jul 2019 20:54:49: 10000000 INFO @ Fri, 05 Jul 2019 20:54:53: 13000000 INFO @ Fri, 05 Jul 2019 20:54:57: 12000000 INFO @ Fri, 05 Jul 2019 20:55:00: 11000000 INFO @ Fri, 05 Jul 2019 20:55:02: 14000000 INFO @ Fri, 05 Jul 2019 20:55:07: 13000000 INFO @ Fri, 05 Jul 2019 20:55:09: 12000000 INFO @ Fri, 05 Jul 2019 20:55:12: 15000000 INFO @ Fri, 05 Jul 2019 20:55:17: 14000000 INFO @ Fri, 05 Jul 2019 20:55:19: 13000000 INFO @ Fri, 05 Jul 2019 20:55:21: 16000000 INFO @ Fri, 05 Jul 2019 20:55:27: 15000000 INFO @ Fri, 05 Jul 2019 20:55:29: 14000000 INFO @ Fri, 05 Jul 2019 20:55:30: 17000000 INFO @ Fri, 05 Jul 2019 20:55:37: 16000000 INFO @ Fri, 05 Jul 2019 20:55:39: 15000000 INFO @ Fri, 05 Jul 2019 20:55:40: 18000000 INFO @ Fri, 05 Jul 2019 20:55:46: 17000000 INFO @ Fri, 05 Jul 2019 20:55:49: 19000000 INFO @ Fri, 05 Jul 2019 20:55:50: 16000000 INFO @ Fri, 05 Jul 2019 20:55:56: 18000000 INFO @ Fri, 05 Jul 2019 20:55:58: 20000000 INFO @ Fri, 05 Jul 2019 20:56:01: 17000000 INFO @ Fri, 05 Jul 2019 20:56:06: 19000000 INFO @ Fri, 05 Jul 2019 20:56:06: 21000000 INFO @ Fri, 05 Jul 2019 20:56:10: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 20:56:10: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 20:56:10: #1 total tags in treatment: 8041729 INFO @ Fri, 05 Jul 2019 20:56:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:10: #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 20:56:10: #1 tags after filtering in treatment: 3896664 INFO @ Fri, 05 Jul 2019 20:56:10: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 20:56:10: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:10: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:56:10: 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 20:56:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.05_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/SRX193167/SRX193167.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:56:12: 18000000 INFO @ Fri, 05 Jul 2019 20:56:15: 20000000 INFO @ Fri, 05 Jul 2019 20:56:23: 19000000 INFO @ Fri, 05 Jul 2019 20:56:25: 21000000 INFO @ Fri, 05 Jul 2019 20:56:29: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 20:56:29: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 20:56:29: #1 total tags in treatment: 8041729 INFO @ Fri, 05 Jul 2019 20:56:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:29: #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 20:56:29: #1 tags after filtering in treatment: 3896664 INFO @ Fri, 05 Jul 2019 20:56:29: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 20:56:29: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:29: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:56:29: 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 20:56:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.20_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/SRX193167/SRX193167.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:56:33: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 20:56:44: 21000000 INFO @ Fri, 05 Jul 2019 20:56:48: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 20:56:48: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 20:56:48: #1 total tags in treatment: 8041729 INFO @ Fri, 05 Jul 2019 20:56:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:48: #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 20:56:48: #1 tags after filtering in treatment: 3896664 INFO @ Fri, 05 Jul 2019 20:56:48: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 20:56:48: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:49: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:56:49: 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 20:56:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.10_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/SRX193167/SRX193167.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX193167/SRX193167.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling