Job ID = 2641004 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:34:11 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 : 12,446,675 reads read : 24,893,350 reads written : 24,893,350 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: 00:17:24 12446675 reads; of these: 12446675 (100.00%) were paired; of these: 2045907 (16.44%) aligned concordantly 0 times 8312486 (66.78%) aligned concordantly exactly 1 time 2088282 (16.78%) aligned concordantly >1 times ---- 2045907 pairs aligned concordantly 0 times; of these: 1086089 (53.09%) aligned discordantly 1 time ---- 959818 pairs aligned 0 times concordantly or discordantly; of these: 1919636 mates make up the pairs; of these: 1245201 (64.87%) aligned 0 times 215863 (11.24%) aligned exactly 1 time 458572 (23.89%) aligned >1 times 95.00% overall alignment rate Time searching: 00:17:24 Overall time: 00:17:24 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 12 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] 1035376 / 11483229 = 0.0902 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.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 21:07:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:07:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:07:37: 1000000 INFO @ Sat, 24 Aug 2019 21:07:48: 2000000 INFO @ Sat, 24 Aug 2019 21:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.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 21:07:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:07:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:07:58: 3000000 INFO @ Sat, 24 Aug 2019 21:08:06: 1000000 INFO @ Sat, 24 Aug 2019 21:08:09: 4000000 INFO @ Sat, 24 Aug 2019 21:08:15: 2000000 INFO @ Sat, 24 Aug 2019 21:08:21: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:08:25: 3000000 INFO @ Sat, 24 Aug 2019 21:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.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 21:08:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:08:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:08:32: 6000000 INFO @ Sat, 24 Aug 2019 21:08:35: 4000000 INFO @ Sat, 24 Aug 2019 21:08:38: 1000000 INFO @ Sat, 24 Aug 2019 21:08:43: 7000000 INFO @ Sat, 24 Aug 2019 21:08:44: 5000000 INFO @ Sat, 24 Aug 2019 21:08:49: 2000000 INFO @ Sat, 24 Aug 2019 21:08:54: 6000000 INFO @ Sat, 24 Aug 2019 21:08:54: 8000000 INFO @ Sat, 24 Aug 2019 21:09:00: 3000000 INFO @ Sat, 24 Aug 2019 21:09:04: 7000000 INFO @ Sat, 24 Aug 2019 21:09:05: 9000000 INFO @ Sat, 24 Aug 2019 21:09:12: 4000000 INFO @ Sat, 24 Aug 2019 21:09:13: 8000000 INFO @ Sat, 24 Aug 2019 21:09:17: 10000000 INFO @ Sat, 24 Aug 2019 21:09:23: 9000000 INFO @ Sat, 24 Aug 2019 21:09:23: 5000000 INFO @ Sat, 24 Aug 2019 21:09:28: 11000000 INFO @ Sat, 24 Aug 2019 21:09:33: 10000000 INFO @ Sat, 24 Aug 2019 21:09:35: 6000000 INFO @ Sat, 24 Aug 2019 21:09:40: 12000000 INFO @ Sat, 24 Aug 2019 21:09:42: 11000000 INFO @ Sat, 24 Aug 2019 21:09:46: 7000000 INFO @ Sat, 24 Aug 2019 21:09:51: 13000000 INFO @ Sat, 24 Aug 2019 21:09:52: 12000000 INFO @ Sat, 24 Aug 2019 21:09:57: 8000000 INFO @ Sat, 24 Aug 2019 21:10:02: 13000000 INFO @ Sat, 24 Aug 2019 21:10:02: 14000000 INFO @ Sat, 24 Aug 2019 21:10:09: 9000000 INFO @ Sat, 24 Aug 2019 21:10:12: 14000000 INFO @ Sat, 24 Aug 2019 21:10:13: 15000000 INFO @ Sat, 24 Aug 2019 21:10:20: 10000000 INFO @ Sat, 24 Aug 2019 21:10:21: 15000000 INFO @ Sat, 24 Aug 2019 21:10:25: 16000000 INFO @ Sat, 24 Aug 2019 21:10:31: 16000000 INFO @ Sat, 24 Aug 2019 21:10:32: 11000000 INFO @ Sat, 24 Aug 2019 21:10:36: 17000000 INFO @ Sat, 24 Aug 2019 21:10:40: 17000000 INFO @ Sat, 24 Aug 2019 21:10:43: 12000000 INFO @ Sat, 24 Aug 2019 21:10:47: 18000000 INFO @ Sat, 24 Aug 2019 21:10:50: 18000000 INFO @ Sat, 24 Aug 2019 21:10:54: 13000000 INFO @ Sat, 24 Aug 2019 21:10:58: 19000000 INFO @ Sat, 24 Aug 2019 21:11:00: 19000000 INFO @ Sat, 24 Aug 2019 21:11:06: 14000000 INFO @ Sat, 24 Aug 2019 21:11:10: 20000000 INFO @ Sat, 24 Aug 2019 21:11:10: 20000000 INFO @ Sat, 24 Aug 2019 21:11:17: 15000000 INFO @ Sat, 24 Aug 2019 21:11:20: 21000000 INFO @ Sat, 24 Aug 2019 21:11:22: 21000000 INFO @ Sat, 24 Aug 2019 21:11:25: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:11:25: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:11:25: #1 total tags in treatment: 9408938 INFO @ Sat, 24 Aug 2019 21:11:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:25: #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 21:11:25: #1 tags after filtering in treatment: 6681917 INFO @ Sat, 24 Aug 2019 21:11:25: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:11:25: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:26: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:11:26: 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, 24 Aug 2019 21:11:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.10_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/SRX4936110/SRX4936110.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:11:28: 16000000 INFO @ Sat, 24 Aug 2019 21:11:29: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:11:29: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:11:29: #1 total tags in treatment: 9408938 INFO @ Sat, 24 Aug 2019 21:11:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:29: #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 21:11:29: #1 tags after filtering in treatment: 6681917 INFO @ Sat, 24 Aug 2019 21:11:29: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:11:29: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:30: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:11:30: 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, 24 Aug 2019 21:11:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.05_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/SRX4936110/SRX4936110.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:11:39: 17000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:11:50: 18000000 INFO @ Sat, 24 Aug 2019 21:12:01: 19000000 INFO @ Sat, 24 Aug 2019 21:12:12: 20000000 INFO @ Sat, 24 Aug 2019 21:12:23: 21000000 INFO @ Sat, 24 Aug 2019 21:12:29: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:12:29: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:12:29: #1 total tags in treatment: 9408938 INFO @ Sat, 24 Aug 2019 21:12:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:12:29: #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 21:12:29: #1 tags after filtering in treatment: 6681917 INFO @ Sat, 24 Aug 2019 21:12:29: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:12:29: #1 finished! INFO @ Sat, 24 Aug 2019 21:12:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:12:29: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:12:29: 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, 24 Aug 2019 21:12:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.20_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/SRX4936110/SRX4936110.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936110/SRX4936110.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling