Job ID = 2640770 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T10:04:16 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 : 11,195,184 reads read : 22,390,368 reads written : 22,390,368 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: 00:06:51 11195184 reads; of these: 11195184 (100.00%) were paired; of these: 1960826 (17.51%) aligned concordantly 0 times 7279388 (65.02%) aligned concordantly exactly 1 time 1954970 (17.46%) aligned concordantly >1 times ---- 1960826 pairs aligned concordantly 0 times; of these: 21279 (1.09%) aligned discordantly 1 time ---- 1939547 pairs aligned 0 times concordantly or discordantly; of these: 3879094 mates make up the pairs; of these: 3797943 (97.91%) aligned 0 times 35214 (0.91%) aligned exactly 1 time 45937 (1.18%) aligned >1 times 83.04% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 8 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] 1451824 / 9249425 = 0.1570 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:21:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.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 19:21:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:31: 1000000 INFO @ Sat, 24 Aug 2019 19:21:37: 2000000 INFO @ Sat, 24 Aug 2019 19:21:43: 3000000 INFO @ Sat, 24 Aug 2019 19:21:49: 4000000 INFO @ Sat, 24 Aug 2019 19:21:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.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 19:21:54: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:54: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:55: 5000000 INFO @ Sat, 24 Aug 2019 19:22:00: 1000000 INFO @ Sat, 24 Aug 2019 19:22:01: 6000000 INFO @ Sat, 24 Aug 2019 19:22:06: 2000000 INFO @ Sat, 24 Aug 2019 19:22:08: 7000000 INFO @ Sat, 24 Aug 2019 19:22:13: 3000000 INFO @ Sat, 24 Aug 2019 19:22:14: 8000000 INFO @ Sat, 24 Aug 2019 19:22:19: 4000000 INFO @ Sat, 24 Aug 2019 19:22:20: 9000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.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 19:22:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:22:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:22:25: 5000000 INFO @ Sat, 24 Aug 2019 19:22:26: 10000000 INFO @ Sat, 24 Aug 2019 19:22:32: 6000000 INFO @ Sat, 24 Aug 2019 19:22:32: 1000000 INFO @ Sat, 24 Aug 2019 19:22:33: 11000000 INFO @ Sat, 24 Aug 2019 19:22:38: 7000000 INFO @ Sat, 24 Aug 2019 19:22:39: 12000000 INFO @ Sat, 24 Aug 2019 19:22:40: 2000000 INFO @ Sat, 24 Aug 2019 19:22:44: 8000000 INFO @ Sat, 24 Aug 2019 19:22:45: 13000000 INFO @ Sat, 24 Aug 2019 19:22:47: 3000000 INFO @ Sat, 24 Aug 2019 19:22:51: 9000000 INFO @ Sat, 24 Aug 2019 19:22:51: 14000000 INFO @ Sat, 24 Aug 2019 19:22:55: 4000000 INFO @ Sat, 24 Aug 2019 19:22:57: 10000000 INFO @ Sat, 24 Aug 2019 19:22:58: 15000000 INFO @ Sat, 24 Aug 2019 19:23:02: #1 tag size is determined as 33 bps INFO @ Sat, 24 Aug 2019 19:23:02: #1 tag size = 33 INFO @ Sat, 24 Aug 2019 19:23:02: #1 total tags in treatment: 7783150 INFO @ Sat, 24 Aug 2019 19:23:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:02: #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 19:23:03: #1 tags after filtering in treatment: 5658269 INFO @ Sat, 24 Aug 2019 19:23:03: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:23:03: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:23:03: 5000000 INFO @ Sat, 24 Aug 2019 19:23:03: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:23:03: 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 @ Sat, 24 Aug 2019 19:23:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.05_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/ERX2732455/ERX2732455.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:23:04: 11000000 INFO @ Sat, 24 Aug 2019 19:23:10: 12000000 INFO @ Sat, 24 Aug 2019 19:23:10: 6000000 INFO @ Sat, 24 Aug 2019 19:23:16: 13000000 INFO @ Sat, 24 Aug 2019 19:23:18: 7000000 INFO @ Sat, 24 Aug 2019 19:23:23: 14000000 INFO @ Sat, 24 Aug 2019 19:23:25: 8000000 INFO @ Sat, 24 Aug 2019 19:23:29: 15000000 INFO @ Sat, 24 Aug 2019 19:23:33: 9000000 INFO @ Sat, 24 Aug 2019 19:23:33: #1 tag size is determined as 33 bps INFO @ Sat, 24 Aug 2019 19:23:33: #1 tag size = 33 INFO @ Sat, 24 Aug 2019 19:23:33: #1 total tags in treatment: 7783150 INFO @ Sat, 24 Aug 2019 19:23:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:33: #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 19:23:33: #1 tags after filtering in treatment: 5658269 INFO @ Sat, 24 Aug 2019 19:23:33: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:23:33: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:23:34: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:23:34: 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 19:23:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.10_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/ERX2732455/ERX2732455.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:23:40: 10000000 INFO @ Sat, 24 Aug 2019 19:23:48: 11000000 INFO @ Sat, 24 Aug 2019 19:23:55: 12000000 INFO @ Sat, 24 Aug 2019 19:24:02: 13000000 INFO @ Sat, 24 Aug 2019 19:24:10: 14000000 INFO @ Sat, 24 Aug 2019 19:24:17: 15000000 INFO @ Sat, 24 Aug 2019 19:24:22: #1 tag size is determined as 33 bps INFO @ Sat, 24 Aug 2019 19:24:22: #1 tag size = 33 INFO @ Sat, 24 Aug 2019 19:24:22: #1 total tags in treatment: 7783150 INFO @ Sat, 24 Aug 2019 19:24:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:24:22: #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 19:24:22: #1 tags after filtering in treatment: 5658269 INFO @ Sat, 24 Aug 2019 19:24:22: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:24:22: #1 finished! INFO @ Sat, 24 Aug 2019 19:24:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:24:23: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:24:23: 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 19:24:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.20_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/ERX2732455/ERX2732455.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732455/ERX2732455.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。