Job ID = 2010709 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:11:51 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 : NET - Reading information from the socket failed ) 2019-07-05T15:11:51 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 : NET - Reading information from the socket failed ) spots read : 8,156,947 reads read : 16,313,894 reads written : 16,313,894 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: 00:07:32 8156947 reads; of these: 8156947 (100.00%) were paired; of these: 1200112 (14.71%) aligned concordantly 0 times 6261849 (76.77%) aligned concordantly exactly 1 time 694986 (8.52%) aligned concordantly >1 times ---- 1200112 pairs aligned concordantly 0 times; of these: 102826 (8.57%) aligned discordantly 1 time ---- 1097286 pairs aligned 0 times concordantly or discordantly; of these: 2194572 mates make up the pairs; of these: 1946633 (88.70%) aligned 0 times 171873 (7.83%) aligned exactly 1 time 76066 (3.47%) aligned >1 times 88.07% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 87681 / 7040679 = 0.0125 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 00:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.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 00:29:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:29:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.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 00:29:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:29:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.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 00:29:57: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:29:57: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:30:03: 1000000 INFO @ Sat, 06 Jul 2019 00:30:04: 1000000 INFO @ Sat, 06 Jul 2019 00:30:07: 1000000 INFO @ Sat, 06 Jul 2019 00:30:11: 2000000 INFO @ Sat, 06 Jul 2019 00:30:12: 2000000 INFO @ Sat, 06 Jul 2019 00:30:16: 2000000 INFO @ Sat, 06 Jul 2019 00:30:19: 3000000 INFO @ Sat, 06 Jul 2019 00:30:20: 3000000 INFO @ Sat, 06 Jul 2019 00:30:25: 3000000 INFO @ Sat, 06 Jul 2019 00:30:27: 4000000 INFO @ Sat, 06 Jul 2019 00:30:28: 4000000 INFO @ Sat, 06 Jul 2019 00:30:34: 4000000 INFO @ Sat, 06 Jul 2019 00:30:34: 5000000 INFO @ Sat, 06 Jul 2019 00:30:35: 5000000 INFO @ Sat, 06 Jul 2019 00:30:42: 6000000 INFO @ Sat, 06 Jul 2019 00:30:43: 5000000 INFO @ Sat, 06 Jul 2019 00:30:43: 6000000 INFO @ Sat, 06 Jul 2019 00:30:50: 7000000 INFO @ Sat, 06 Jul 2019 00:30:51: 7000000 INFO @ Sat, 06 Jul 2019 00:30:52: 6000000 INFO @ Sat, 06 Jul 2019 00:30:58: 8000000 INFO @ Sat, 06 Jul 2019 00:30:58: 8000000 INFO @ Sat, 06 Jul 2019 00:31:01: 7000000 INFO @ Sat, 06 Jul 2019 00:31:06: 9000000 INFO @ Sat, 06 Jul 2019 00:31:06: 9000000 INFO @ Sat, 06 Jul 2019 00:31:10: 8000000 INFO @ Sat, 06 Jul 2019 00:31:13: 10000000 INFO @ Sat, 06 Jul 2019 00:31:14: 10000000 INFO @ Sat, 06 Jul 2019 00:31:19: 9000000 INFO @ Sat, 06 Jul 2019 00:31:21: 11000000 INFO @ Sat, 06 Jul 2019 00:31:22: 11000000 INFO @ Sat, 06 Jul 2019 00:31:28: 10000000 INFO @ Sat, 06 Jul 2019 00:31:29: 12000000 INFO @ Sat, 06 Jul 2019 00:31:29: 12000000 INFO @ Sat, 06 Jul 2019 00:31:37: 11000000 INFO @ Sat, 06 Jul 2019 00:31:37: 13000000 INFO @ Sat, 06 Jul 2019 00:31:37: 13000000 INFO @ Sat, 06 Jul 2019 00:31:45: 14000000 INFO @ Sat, 06 Jul 2019 00:31:45: 14000000 INFO @ Sat, 06 Jul 2019 00:31:46: 12000000 INFO @ Sat, 06 Jul 2019 00:31:46: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:31:46: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:31:46: #1 total tags in treatment: 6869789 INFO @ Sat, 06 Jul 2019 00:31:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:31:46: #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 00:31:46: #1 tags after filtering in treatment: 5478950 INFO @ Sat, 06 Jul 2019 00:31:46: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:31:46: #1 finished! INFO @ Sat, 06 Jul 2019 00:31:46: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:31:46: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:31:46: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:31:46: #1 total tags in treatment: 6869789 INFO @ Sat, 06 Jul 2019 00:31:46: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:31:46: #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 00:31:47: #1 tags after filtering in treatment: 5478950 INFO @ Sat, 06 Jul 2019 00:31:47: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:31:47: #1 finished! INFO @ Sat, 06 Jul 2019 00:31:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:31:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:31:47: 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 00:31:47: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:31:47: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:31:47: 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 00:31:47: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:31:54: 13000000 INFO @ Sat, 06 Jul 2019 00:32:03: 14000000 INFO @ Sat, 06 Jul 2019 00:32:05: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:32:05: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:32:05: #1 total tags in treatment: 6869789 INFO @ Sat, 06 Jul 2019 00:32:05: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:32:05: #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 00:32:05: #1 tags after filtering in treatment: 5478950 INFO @ Sat, 06 Jul 2019 00:32:05: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:32:05: #1 finished! INFO @ Sat, 06 Jul 2019 00:32:05: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:32:05: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:32:05: 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 00:32:05: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.20_peaks.narrowPeak : No such file or directoryBigWig に変換中... pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386890/SRX386890.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。