Job ID = 2011740 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:19:15 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 : 12,341,645 reads read : 24,683,290 reads written : 24,683,290 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: 00:07:33 12341645 reads; of these: 12341645 (100.00%) were paired; of these: 2638311 (21.38%) aligned concordantly 0 times 8235962 (66.73%) aligned concordantly exactly 1 time 1467372 (11.89%) aligned concordantly >1 times ---- 2638311 pairs aligned concordantly 0 times; of these: 119069 (4.51%) aligned discordantly 1 time ---- 2519242 pairs aligned 0 times concordantly or discordantly; of these: 5038484 mates make up the pairs; of these: 4770711 (94.69%) aligned 0 times 160060 (3.18%) aligned exactly 1 time 107713 (2.14%) aligned >1 times 80.67% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 1243590 / 9820544 = 0.1266 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 02:35:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.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 02:35:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:35:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.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 02:35:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:35:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.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 02:35:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:35:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:35:10: 1000000 INFO @ Sat, 06 Jul 2019 02:35:11: 1000000 INFO @ Sat, 06 Jul 2019 02:35:11: 1000000 INFO @ Sat, 06 Jul 2019 02:35:19: 2000000 INFO @ Sat, 06 Jul 2019 02:35:20: 2000000 INFO @ Sat, 06 Jul 2019 02:35:20: 2000000 INFO @ Sat, 06 Jul 2019 02:35:28: 3000000 INFO @ Sat, 06 Jul 2019 02:35:28: 3000000 INFO @ Sat, 06 Jul 2019 02:35:29: 3000000 INFO @ Sat, 06 Jul 2019 02:35:36: 4000000 INFO @ Sat, 06 Jul 2019 02:35:37: 4000000 INFO @ Sat, 06 Jul 2019 02:35:39: 4000000 INFO @ Sat, 06 Jul 2019 02:35:44: 5000000 INFO @ Sat, 06 Jul 2019 02:35:45: 5000000 INFO @ Sat, 06 Jul 2019 02:35:46: 5000000 INFO @ Sat, 06 Jul 2019 02:35:51: 6000000 INFO @ Sat, 06 Jul 2019 02:35:53: 6000000 INFO @ Sat, 06 Jul 2019 02:35:53: 6000000 INFO @ Sat, 06 Jul 2019 02:35:59: 7000000 INFO @ Sat, 06 Jul 2019 02:36:00: 7000000 INFO @ Sat, 06 Jul 2019 02:36:01: 7000000 INFO @ Sat, 06 Jul 2019 02:36:06: 8000000 INFO @ Sat, 06 Jul 2019 02:36:09: 8000000 INFO @ Sat, 06 Jul 2019 02:36:10: 8000000 INFO @ Sat, 06 Jul 2019 02:36:14: 9000000 INFO @ Sat, 06 Jul 2019 02:36:18: 9000000 INFO @ Sat, 06 Jul 2019 02:36:19: 9000000 INFO @ Sat, 06 Jul 2019 02:36:21: 10000000 INFO @ Sat, 06 Jul 2019 02:36:27: 10000000 INFO @ Sat, 06 Jul 2019 02:36:28: 10000000 INFO @ Sat, 06 Jul 2019 02:36:29: 11000000 INFO @ Sat, 06 Jul 2019 02:36:36: 11000000 INFO @ Sat, 06 Jul 2019 02:36:36: 12000000 INFO @ Sat, 06 Jul 2019 02:36:37: 11000000 INFO @ Sat, 06 Jul 2019 02:36:44: 13000000 INFO @ Sat, 06 Jul 2019 02:36:44: 12000000 INFO @ Sat, 06 Jul 2019 02:36:46: 12000000 INFO @ Sat, 06 Jul 2019 02:36:51: 14000000 INFO @ Sat, 06 Jul 2019 02:36:53: 13000000 INFO @ Sat, 06 Jul 2019 02:36:55: 13000000 INFO @ Sat, 06 Jul 2019 02:36:58: 15000000 INFO @ Sat, 06 Jul 2019 02:37:02: 14000000 INFO @ Sat, 06 Jul 2019 02:37:04: 14000000 INFO @ Sat, 06 Jul 2019 02:37:06: 16000000 INFO @ Sat, 06 Jul 2019 02:37:11: 15000000 INFO @ Sat, 06 Jul 2019 02:37:13: 15000000 INFO @ Sat, 06 Jul 2019 02:37:14: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:37:17: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:37:17: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:37:17: #1 total tags in treatment: 8472262 INFO @ Sat, 06 Jul 2019 02:37:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:37:17: #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 02:37:17: #1 tags after filtering in treatment: 6184254 INFO @ Sat, 06 Jul 2019 02:37:17: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 02:37:17: #1 finished! INFO @ Sat, 06 Jul 2019 02:37:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:37:18: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:37:18: 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 @ Sat, 06 Jul 2019 02:37:18: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:37:20: 16000000 INFO @ Sat, 06 Jul 2019 02:37:22: 16000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.20_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/SRX4915180/SRX4915180.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:37:28: 17000000 INFO @ Sat, 06 Jul 2019 02:37:30: 17000000 INFO @ Sat, 06 Jul 2019 02:37:31: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:37:31: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:37:31: #1 total tags in treatment: 8472262 INFO @ Sat, 06 Jul 2019 02:37:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:37:31: #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 02:37:32: #1 tags after filtering in treatment: 6184254 INFO @ Sat, 06 Jul 2019 02:37:32: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 02:37:32: #1 finished! INFO @ Sat, 06 Jul 2019 02:37:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:37:32: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:37:32: 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 02:37:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.10_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/SRX4915180/SRX4915180.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:37:33: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:37:33: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:37:33: #1 total tags in treatment: 8472262 INFO @ Sat, 06 Jul 2019 02:37:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:37:33: #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 02:37:34: #1 tags after filtering in treatment: 6184254 INFO @ Sat, 06 Jul 2019 02:37:34: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 06 Jul 2019 02:37:34: #1 finished! INFO @ Sat, 06 Jul 2019 02:37:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:37:34: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:37:34: 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 02:37:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.05_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/SRX4915180/SRX4915180.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915180/SRX4915180.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。