Job ID = 2009745 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T10:56:07 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 : 24,421,702 reads read : 48,843,404 reads written : 48,843,404 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:56 24421702 reads; of these: 24421702 (100.00%) were paired; of these: 5179239 (21.21%) aligned concordantly 0 times 17713693 (72.53%) aligned concordantly exactly 1 time 1528770 (6.26%) aligned concordantly >1 times ---- 5179239 pairs aligned concordantly 0 times; of these: 497063 (9.60%) aligned discordantly 1 time ---- 4682176 pairs aligned 0 times concordantly or discordantly; of these: 9364352 mates make up the pairs; of these: 9030197 (96.43%) aligned 0 times 204448 (2.18%) aligned exactly 1 time 129707 (1.39%) aligned >1 times 81.51% overall alignment rate Time searching: 00:16:57 Overall time: 00:17:02 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 20 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] 12009324 / 19548026 = 0.6143 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 20:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.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 20:39:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:39:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.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 20:39:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:39:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:39:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.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 20:39:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:39:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:39:52: 1000000 INFO @ Fri, 05 Jul 2019 20:39:54: 1000000 INFO @ Fri, 05 Jul 2019 20:39:55: 1000000 INFO @ Fri, 05 Jul 2019 20:39:58: 2000000 INFO @ Fri, 05 Jul 2019 20:40:02: 2000000 INFO @ Fri, 05 Jul 2019 20:40:03: 2000000 INFO @ Fri, 05 Jul 2019 20:40:04: 3000000 INFO @ Fri, 05 Jul 2019 20:40:09: 3000000 INFO @ Fri, 05 Jul 2019 20:40:10: 4000000 INFO @ Fri, 05 Jul 2019 20:40:10: 3000000 INFO @ Fri, 05 Jul 2019 20:40:15: 5000000 INFO @ Fri, 05 Jul 2019 20:40:16: 4000000 INFO @ Fri, 05 Jul 2019 20:40:18: 4000000 INFO @ Fri, 05 Jul 2019 20:40:21: 6000000 INFO @ Fri, 05 Jul 2019 20:40:24: 5000000 INFO @ Fri, 05 Jul 2019 20:40:26: 5000000 INFO @ Fri, 05 Jul 2019 20:40:27: 7000000 INFO @ Fri, 05 Jul 2019 20:40:31: 6000000 INFO @ Fri, 05 Jul 2019 20:40:33: 8000000 INFO @ Fri, 05 Jul 2019 20:40:33: 6000000 INFO @ Fri, 05 Jul 2019 20:40:38: 7000000 INFO @ Fri, 05 Jul 2019 20:40:38: 9000000 INFO @ Fri, 05 Jul 2019 20:40:40: 7000000 INFO @ Fri, 05 Jul 2019 20:40:44: 10000000 INFO @ Fri, 05 Jul 2019 20:40:45: 8000000 INFO @ Fri, 05 Jul 2019 20:40:47: 8000000 INFO @ Fri, 05 Jul 2019 20:40:50: 11000000 INFO @ Fri, 05 Jul 2019 20:40:52: 9000000 INFO @ Fri, 05 Jul 2019 20:40:55: 9000000 INFO @ Fri, 05 Jul 2019 20:40:56: 12000000 INFO @ Fri, 05 Jul 2019 20:40:59: 10000000 INFO @ Fri, 05 Jul 2019 20:41:01: 13000000 INFO @ Fri, 05 Jul 2019 20:41:02: 10000000 INFO @ Fri, 05 Jul 2019 20:41:06: 11000000 INFO @ Fri, 05 Jul 2019 20:41:07: 14000000 INFO @ Fri, 05 Jul 2019 20:41:09: 11000000 INFO @ Fri, 05 Jul 2019 20:41:13: 15000000 INFO @ Fri, 05 Jul 2019 20:41:13: 12000000 INFO @ Fri, 05 Jul 2019 20:41:16: 12000000 INFO @ Fri, 05 Jul 2019 20:41:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:41:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:41:17: #1 total tags in treatment: 7423817 INFO @ Fri, 05 Jul 2019 20:41:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:41:17: #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 20:41:17: #1 tags after filtering in treatment: 5278844 INFO @ Fri, 05 Jul 2019 20:41:17: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 20:41:17: #1 finished! INFO @ Fri, 05 Jul 2019 20:41:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:41:18: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:41:18: 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 20:41:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1034 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:41:20: 13000000 INFO @ Fri, 05 Jul 2019 20:41:23: 13000000 INFO @ Fri, 05 Jul 2019 20:41:27: 14000000 INFO @ Fri, 05 Jul 2019 20:41:30: 14000000 INFO @ Fri, 05 Jul 2019 20:41:34: 15000000 INFO @ Fri, 05 Jul 2019 20:41:37: 15000000 INFO @ Fri, 05 Jul 2019 20:41:40: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:41:40: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:41:40: #1 total tags in treatment: 7423817 INFO @ Fri, 05 Jul 2019 20:41:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:41:40: #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 20:41:40: #1 tags after filtering in treatment: 5278844 INFO @ Fri, 05 Jul 2019 20:41:40: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 20:41:40: #1 finished! INFO @ Fri, 05 Jul 2019 20:41:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:41:41: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:41:41: 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 20:41:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.10_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 20:41:43: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 20:41:43: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 20:41:43: #1 total tags in treatment: 7423817 INFO @ Fri, 05 Jul 2019 20:41:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:41:43: #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 20:41:43: #1 tags after filtering in treatment: 5278844 INFO @ Fri, 05 Jul 2019 20:41:43: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 20:41:43: #1 finished! INFO @ Fri, 05 Jul 2019 20:41:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:41:43: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 2261 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:41:43: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 20:41:43: 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 20:41:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.20_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/SRX1462594/SRX1462594.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462594/SRX1462594.20_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。