Job ID = 2641117 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T12:32:37 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 ) 2019-08-24T12:32:37 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 : 8,485,111 reads read : 16,970,222 reads written : 16,970,222 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: 00:00:01 Multiseed full-index search: 00:13:06 8485111 reads; of these: 8485111 (100.00%) were paired; of these: 6682792 (78.76%) aligned concordantly 0 times 1608945 (18.96%) aligned concordantly exactly 1 time 193374 (2.28%) aligned concordantly >1 times ---- 6682792 pairs aligned concordantly 0 times; of these: 4917226 (73.58%) aligned discordantly 1 time ---- 1765566 pairs aligned 0 times concordantly or discordantly; of these: 3531132 mates make up the pairs; of these: 2168841 (61.42%) aligned 0 times 196779 (5.57%) aligned exactly 1 time 1165512 (33.01%) aligned >1 times 87.22% overall alignment rate Time searching: 00:13:07 Overall time: 00:13:07 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] 252223 / 6716206 = 0.0376 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.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 22:01:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:01:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:01:20: 1000000 INFO @ Sat, 24 Aug 2019 22:01:30: 2000000 INFO @ Sat, 24 Aug 2019 22:01:38: 3000000 INFO @ Sat, 24 Aug 2019 22:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.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 22:01:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:01:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:01:47: 4000000 INFO @ Sat, 24 Aug 2019 22:01:51: 1000000 INFO @ Sat, 24 Aug 2019 22:01:56: 5000000 INFO @ Sat, 24 Aug 2019 22:01:59: 2000000 INFO @ Sat, 24 Aug 2019 22:02:05: 6000000 INFO @ Sat, 24 Aug 2019 22:02:08: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:02:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.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 22:02:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:02:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:02:13: 7000000 INFO @ Sat, 24 Aug 2019 22:02:16: 4000000 INFO @ Sat, 24 Aug 2019 22:02:22: 1000000 INFO @ Sat, 24 Aug 2019 22:02:22: 8000000 INFO @ Sat, 24 Aug 2019 22:02:25: 5000000 INFO @ Sat, 24 Aug 2019 22:02:31: 9000000 INFO @ Sat, 24 Aug 2019 22:02:33: 2000000 INFO @ Sat, 24 Aug 2019 22:02:34: 6000000 INFO @ Sat, 24 Aug 2019 22:02:40: 10000000 INFO @ Sat, 24 Aug 2019 22:02:43: 7000000 INFO @ Sat, 24 Aug 2019 22:02:44: 3000000 INFO @ Sat, 24 Aug 2019 22:02:48: 11000000 INFO @ Sat, 24 Aug 2019 22:02:52: 8000000 INFO @ Sat, 24 Aug 2019 22:02:54: 4000000 INFO @ Sat, 24 Aug 2019 22:02:57: 12000000 INFO @ Sat, 24 Aug 2019 22:03:00: 9000000 INFO @ Sat, 24 Aug 2019 22:03:05: 5000000 INFO @ Sat, 24 Aug 2019 22:03:06: 13000000 INFO @ Sat, 24 Aug 2019 22:03:09: 10000000 INFO @ Sat, 24 Aug 2019 22:03:15: 14000000 INFO @ Sat, 24 Aug 2019 22:03:16: 6000000 INFO @ Sat, 24 Aug 2019 22:03:18: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:03:18: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:03:18: #1 total tags in treatment: 1743351 INFO @ Sat, 24 Aug 2019 22:03:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:03:18: #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 22:03:18: #1 tags after filtering in treatment: 1644358 INFO @ Sat, 24 Aug 2019 22:03:18: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 24 Aug 2019 22:03:18: #1 finished! INFO @ Sat, 24 Aug 2019 22:03:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:03:18: #2 number of paired peaks: 45 WARNING @ Sat, 24 Aug 2019 22:03:18: Too few paired peaks (45) 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 22:03:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.05_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/SRX5546556/SRX5546556.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:03:18: 11000000 INFO @ Sat, 24 Aug 2019 22:03:26: 12000000 INFO @ Sat, 24 Aug 2019 22:03:27: 7000000 INFO @ Sat, 24 Aug 2019 22:03:35: 13000000 INFO @ Sat, 24 Aug 2019 22:03:37: 8000000 INFO @ Sat, 24 Aug 2019 22:03:43: 14000000 INFO @ Sat, 24 Aug 2019 22:03:46: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:03:46: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:03:46: #1 total tags in treatment: 1743351 INFO @ Sat, 24 Aug 2019 22:03:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:03:46: #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 22:03:46: #1 tags after filtering in treatment: 1644358 INFO @ Sat, 24 Aug 2019 22:03:46: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 24 Aug 2019 22:03:46: #1 finished! INFO @ Sat, 24 Aug 2019 22:03:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:03:46: #2 number of paired peaks: 45 WARNING @ Sat, 24 Aug 2019 22:03:46: Too few paired peaks (45) 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 22:03:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.10_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/SRX5546556/SRX5546556.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:03:47: 9000000 INFO @ Sat, 24 Aug 2019 22:03:57: 10000000 INFO @ Sat, 24 Aug 2019 22:04:07: 11000000 INFO @ Sat, 24 Aug 2019 22:04:17: 12000000 INFO @ Sat, 24 Aug 2019 22:04:26: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:04:36: 14000000 INFO @ Sat, 24 Aug 2019 22:04:39: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:04:39: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:04:39: #1 total tags in treatment: 1743351 INFO @ Sat, 24 Aug 2019 22:04:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:04:39: #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 22:04:39: #1 tags after filtering in treatment: 1644358 INFO @ Sat, 24 Aug 2019 22:04:39: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 24 Aug 2019 22:04:39: #1 finished! INFO @ Sat, 24 Aug 2019 22:04:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:04:39: #2 number of paired peaks: 45 WARNING @ Sat, 24 Aug 2019 22:04:39: Too few paired peaks (45) 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 22:04:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.20_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/SRX5546556/SRX5546556.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546556/SRX5546556.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。