Job ID = 2010706 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:58:10 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 ) 2019-07-05T14:58:10 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 ) 2019-07-05T15:06:44 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 ) 2019-07-05T15:06:44 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 : 9,042,420 reads read : 18,084,840 reads written : 18,084,840 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: 00:07:59 9042420 reads; of these: 9042420 (100.00%) were paired; of these: 1335756 (14.77%) aligned concordantly 0 times 7125610 (78.80%) aligned concordantly exactly 1 time 581054 (6.43%) aligned concordantly >1 times ---- 1335756 pairs aligned concordantly 0 times; of these: 134865 (10.10%) aligned discordantly 1 time ---- 1200891 pairs aligned 0 times concordantly or discordantly; of these: 2401782 mates make up the pairs; of these: 2120270 (88.28%) aligned 0 times 209951 (8.74%) aligned exactly 1 time 71561 (2.98%) aligned >1 times 88.28% overall alignment rate Time searching: 00:07:59 Overall time: 00:07:59 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_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] 88711 / 7814687 = 0.0114 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 @ Sat, 06 Jul 2019 00:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.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, 06 Jul 2019 00:29:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:29:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.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, 06 Jul 2019 00:29:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:29:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.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, 06 Jul 2019 00:29:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:29:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:29:48: 1000000 INFO @ Sat, 06 Jul 2019 00:29:51: 1000000 INFO @ Sat, 06 Jul 2019 00:29:58: 1000000 INFO @ Sat, 06 Jul 2019 00:29:58: 2000000 INFO @ Sat, 06 Jul 2019 00:30:05: 2000000 INFO @ Sat, 06 Jul 2019 00:30:08: 2000000 INFO @ Sat, 06 Jul 2019 00:30:09: 3000000 INFO @ Sat, 06 Jul 2019 00:30:18: 3000000 INFO @ Sat, 06 Jul 2019 00:30:18: 3000000 INFO @ Sat, 06 Jul 2019 00:30:21: 4000000 INFO @ Sat, 06 Jul 2019 00:30:27: 4000000 INFO @ Sat, 06 Jul 2019 00:30:29: 4000000 INFO @ Sat, 06 Jul 2019 00:30:33: 5000000 INFO @ Sat, 06 Jul 2019 00:30:37: 5000000 INFO @ Sat, 06 Jul 2019 00:30:40: 5000000 INFO @ Sat, 06 Jul 2019 00:30:44: 6000000 INFO @ Sat, 06 Jul 2019 00:30:47: 6000000 INFO @ Sat, 06 Jul 2019 00:30:52: 6000000 INFO @ Sat, 06 Jul 2019 00:30:56: 7000000 INFO @ Sat, 06 Jul 2019 00:30:57: 7000000 INFO @ Sat, 06 Jul 2019 00:31:04: 7000000 INFO @ Sat, 06 Jul 2019 00:31:07: 8000000 INFO @ Sat, 06 Jul 2019 00:31:08: 8000000 INFO @ Sat, 06 Jul 2019 00:31:15: 8000000 INFO @ Sat, 06 Jul 2019 00:31:17: 9000000 INFO @ Sat, 06 Jul 2019 00:31:20: 9000000 INFO @ Sat, 06 Jul 2019 00:31:27: 9000000 INFO @ Sat, 06 Jul 2019 00:31:27: 10000000 INFO @ Sat, 06 Jul 2019 00:31:32: 10000000 INFO @ Sat, 06 Jul 2019 00:31:37: 11000000 INFO @ Sat, 06 Jul 2019 00:31:38: 10000000 INFO @ Sat, 06 Jul 2019 00:31:44: 11000000 INFO @ Sat, 06 Jul 2019 00:31:47: 12000000 INFO @ Sat, 06 Jul 2019 00:31:49: 11000000 INFO @ Sat, 06 Jul 2019 00:31:55: 12000000 INFO @ Sat, 06 Jul 2019 00:31:57: 13000000 INFO @ Sat, 06 Jul 2019 00:32:01: 12000000 INFO @ Sat, 06 Jul 2019 00:32:07: 14000000 INFO @ Sat, 06 Jul 2019 00:32:07: 13000000 INFO @ Sat, 06 Jul 2019 00:32:12: 13000000 INFO @ Sat, 06 Jul 2019 00:32:17: 15000000 INFO @ Sat, 06 Jul 2019 00:32:19: 14000000 INFO @ Sat, 06 Jul 2019 00:32:24: 14000000 INFO @ Sat, 06 Jul 2019 00:32:25: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:32:25: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:32:25: #1 total tags in treatment: 7618858 INFO @ Sat, 06 Jul 2019 00:32:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:32:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:32:25: #1 tags after filtering in treatment: 5857801 INFO @ Sat, 06 Jul 2019 00:32:25: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 00:32:25: #1 finished! INFO @ Sat, 06 Jul 2019 00:32:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:32:25: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:32:25: 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, 06 Jul 2019 00:32:25: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:32:30: 15000000 BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 00:32:35: 15000000 INFO @ Sat, 06 Jul 2019 00:32:39: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:32:39: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:32:39: #1 total tags in treatment: 7618858 INFO @ Sat, 06 Jul 2019 00:32:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:32:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:32:40: #1 tags after filtering in treatment: 5857801 INFO @ Sat, 06 Jul 2019 00:32:40: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 00:32:40: #1 finished! INFO @ Sat, 06 Jul 2019 00:32:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:32:40: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:32:40: 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, 06 Jul 2019 00:32:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.05_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:32:43: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:32:43: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:32:43: #1 total tags in treatment: 7618858 INFO @ Sat, 06 Jul 2019 00:32:43: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:32:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:32:43: #1 tags after filtering in treatment: 5857801 INFO @ Sat, 06 Jul 2019 00:32:43: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 00:32:43: #1 finished! INFO @ Sat, 06 Jul 2019 00:32:43: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:32:44: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:32:44: 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, 06 Jul 2019 00:32:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.10_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/SRX386887/SRX386887.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386887/SRX386887.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。