Job ID = 2640758 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T10:02:33 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 ) 2019-08-24T10:02:33 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 ) 2019-08-24T10:04:16 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 : 7,021,311 reads read : 14,042,622 reads written : 14,042,622 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: 00:02:59 7021311 reads; of these: 7021311 (100.00%) were paired; of these: 3780078 (53.84%) aligned concordantly 0 times 2590407 (36.89%) aligned concordantly exactly 1 time 650826 (9.27%) aligned concordantly >1 times ---- 3780078 pairs aligned concordantly 0 times; of these: 8793 (0.23%) aligned discordantly 1 time ---- 3771285 pairs aligned 0 times concordantly or discordantly; of these: 7542570 mates make up the pairs; of these: 7502515 (99.47%) aligned 0 times 15667 (0.21%) aligned exactly 1 time 24388 (0.32%) aligned >1 times 46.57% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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_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] 688005 / 3248753 = 0.2118 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.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 19:09:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:09:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:10:02: 1000000 INFO @ Sat, 24 Aug 2019 19:10:08: 2000000 INFO @ Sat, 24 Aug 2019 19:10:14: 3000000 INFO @ Sat, 24 Aug 2019 19:10:20: 4000000 INFO @ Sat, 24 Aug 2019 19:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.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 19:10:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:10:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:10:26: 5000000 INFO @ Sat, 24 Aug 2019 19:10:27: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:10:27: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:10:27: #1 total tags in treatment: 2553660 INFO @ Sat, 24 Aug 2019 19:10:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:10:27: #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 19:10:27: #1 tags after filtering in treatment: 2068222 INFO @ Sat, 24 Aug 2019 19:10:27: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 19:10:27: #1 finished! INFO @ Sat, 24 Aug 2019 19:10:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:10:27: #2 number of paired peaks: 72 WARNING @ Sat, 24 Aug 2019 19:10:27: Too few paired peaks (72) 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 19:10:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.05_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/ERX2732449/ERX2732449.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:10:31: 1000000 INFO @ Sat, 24 Aug 2019 19:10:37: 2000000 INFO @ Sat, 24 Aug 2019 19:10:43: 3000000 INFO @ Sat, 24 Aug 2019 19:10:50: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.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 19:10:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:10:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:10:56: 5000000 INFO @ Sat, 24 Aug 2019 19:10:57: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:10:57: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:10:57: #1 total tags in treatment: 2553660 INFO @ Sat, 24 Aug 2019 19:10:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:10:57: #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 19:10:57: #1 tags after filtering in treatment: 2068222 INFO @ Sat, 24 Aug 2019 19:10:57: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 19:10:57: #1 finished! INFO @ Sat, 24 Aug 2019 19:10:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:10:57: #2 number of paired peaks: 72 WARNING @ Sat, 24 Aug 2019 19:10:57: Too few paired peaks (72) 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 19:10:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.10_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/ERX2732449/ERX2732449.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:11:01: 1000000 INFO @ Sat, 24 Aug 2019 19:11:08: 2000000 INFO @ Sat, 24 Aug 2019 19:11:14: 3000000 INFO @ Sat, 24 Aug 2019 19:11:20: 4000000 INFO @ Sat, 24 Aug 2019 19:11:26: 5000000 INFO @ Sat, 24 Aug 2019 19:11:27: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:11:27: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:11:27: #1 total tags in treatment: 2553660 INFO @ Sat, 24 Aug 2019 19:11:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:11:27: #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 19:11:27: #1 tags after filtering in treatment: 2068222 INFO @ Sat, 24 Aug 2019 19:11:27: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 19:11:27: #1 finished! INFO @ Sat, 24 Aug 2019 19:11:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:11:27: #2 number of paired peaks: 72 WARNING @ Sat, 24 Aug 2019 19:11:27: Too few paired peaks (72) 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 19:11:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.20_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/ERX2732449/ERX2732449.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732449/ERX2732449.20_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。