Job ID = 2008163 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:30:25 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 : 16,938,647 reads read : 33,877,294 reads written : 33,877,294 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629056.sra.cache’: 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: 00:20:19 16938647 reads; of these: 16938647 (100.00%) were paired; of these: 931180 (5.50%) aligned concordantly 0 times 14095807 (83.22%) aligned concordantly exactly 1 time 1911660 (11.29%) aligned concordantly >1 times ---- 931180 pairs aligned concordantly 0 times; of these: 340018 (36.51%) aligned discordantly 1 time ---- 591162 pairs aligned 0 times concordantly or discordantly; of these: 1182324 mates make up the pairs; of these: 987469 (83.52%) aligned 0 times 93486 (7.91%) aligned exactly 1 time 101369 (8.57%) aligned >1 times 97.09% overall alignment rate Time searching: 00:20:19 Overall time: 00:20:19 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 16 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] 3829598 / 16282251 = 0.2352 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 @ Fri, 05 Jul 2019 18:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.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 @ Fri, 05 Jul 2019 18:34:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:34:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.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 @ Fri, 05 Jul 2019 18:34:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:34:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:34:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.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 @ Fri, 05 Jul 2019 18:34:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:34:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:34:48: 1000000 INFO @ Fri, 05 Jul 2019 18:34:49: 1000000 INFO @ Fri, 05 Jul 2019 18:34:50: 1000000 INFO @ Fri, 05 Jul 2019 18:34:57: 2000000 INFO @ Fri, 05 Jul 2019 18:35:01: 2000000 INFO @ Fri, 05 Jul 2019 18:35:02: 2000000 INFO @ Fri, 05 Jul 2019 18:35:06: 3000000 INFO @ Fri, 05 Jul 2019 18:35:13: 3000000 INFO @ Fri, 05 Jul 2019 18:35:14: 3000000 INFO @ Fri, 05 Jul 2019 18:35:16: 4000000 INFO @ Fri, 05 Jul 2019 18:35:25: 4000000 INFO @ Fri, 05 Jul 2019 18:35:25: 5000000 INFO @ Fri, 05 Jul 2019 18:35:27: 4000000 INFO @ Fri, 05 Jul 2019 18:35:34: 6000000 INFO @ Fri, 05 Jul 2019 18:35:36: 5000000 INFO @ Fri, 05 Jul 2019 18:35:39: 5000000 INFO @ Fri, 05 Jul 2019 18:35:43: 7000000 INFO @ Fri, 05 Jul 2019 18:35:50: 6000000 INFO @ Fri, 05 Jul 2019 18:35:52: 6000000 INFO @ Fri, 05 Jul 2019 18:35:52: 8000000 INFO @ Fri, 05 Jul 2019 18:36:01: 9000000 INFO @ Fri, 05 Jul 2019 18:36:03: 7000000 INFO @ Fri, 05 Jul 2019 18:36:05: 7000000 INFO @ Fri, 05 Jul 2019 18:36:12: 10000000 INFO @ Fri, 05 Jul 2019 18:36:16: 8000000 INFO @ Fri, 05 Jul 2019 18:36:17: 8000000 INFO @ Fri, 05 Jul 2019 18:36:21: 11000000 INFO @ Fri, 05 Jul 2019 18:36:27: 9000000 INFO @ Fri, 05 Jul 2019 18:36:28: 9000000 INFO @ Fri, 05 Jul 2019 18:36:30: 12000000 INFO @ Fri, 05 Jul 2019 18:36:39: 10000000 INFO @ Fri, 05 Jul 2019 18:36:39: 13000000 INFO @ Fri, 05 Jul 2019 18:36:40: 10000000 INFO @ Fri, 05 Jul 2019 18:36:48: 14000000 INFO @ Fri, 05 Jul 2019 18:36:50: 11000000 INFO @ Fri, 05 Jul 2019 18:36:52: 11000000 INFO @ Fri, 05 Jul 2019 18:36:57: 15000000 INFO @ Fri, 05 Jul 2019 18:37:01: 12000000 INFO @ Fri, 05 Jul 2019 18:37:04: 12000000 INFO @ Fri, 05 Jul 2019 18:37:06: 16000000 INFO @ Fri, 05 Jul 2019 18:37:13: 13000000 INFO @ Fri, 05 Jul 2019 18:37:14: 17000000 INFO @ Fri, 05 Jul 2019 18:37:15: 13000000 INFO @ Fri, 05 Jul 2019 18:37:23: 18000000 INFO @ Fri, 05 Jul 2019 18:37:24: 14000000 INFO @ Fri, 05 Jul 2019 18:37:26: 14000000 INFO @ Fri, 05 Jul 2019 18:37:31: 19000000 INFO @ Fri, 05 Jul 2019 18:37:35: 15000000 INFO @ Fri, 05 Jul 2019 18:37:37: 15000000 INFO @ Fri, 05 Jul 2019 18:37:40: 20000000 INFO @ Fri, 05 Jul 2019 18:37:46: 16000000 INFO @ Fri, 05 Jul 2019 18:37:48: 16000000 INFO @ Fri, 05 Jul 2019 18:37:49: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:37:57: 17000000 INFO @ Fri, 05 Jul 2019 18:37:57: 22000000 INFO @ Fri, 05 Jul 2019 18:37:59: 17000000 INFO @ Fri, 05 Jul 2019 18:38:06: 23000000 INFO @ Fri, 05 Jul 2019 18:38:08: 18000000 INFO @ Fri, 05 Jul 2019 18:38:10: 18000000 INFO @ Fri, 05 Jul 2019 18:38:14: 24000000 INFO @ Fri, 05 Jul 2019 18:38:20: 19000000 INFO @ Fri, 05 Jul 2019 18:38:22: 19000000 INFO @ Fri, 05 Jul 2019 18:38:22: 25000000 INFO @ Fri, 05 Jul 2019 18:38:25: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:38:25: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:38:25: #1 total tags in treatment: 12194320 INFO @ Fri, 05 Jul 2019 18:38:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:38:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:38:25: #1 tags after filtering in treatment: 5740038 INFO @ Fri, 05 Jul 2019 18:38:25: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 18:38:25: #1 finished! INFO @ Fri, 05 Jul 2019 18:38:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:38:25: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:38:25: 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 @ Fri, 05 Jul 2019 18:38:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.10_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/ERX585700/ERX585700.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:38:32: 20000000 INFO @ Fri, 05 Jul 2019 18:38:33: 20000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:38:43: 21000000 INFO @ Fri, 05 Jul 2019 18:38:44: 21000000 INFO @ Fri, 05 Jul 2019 18:38:54: 22000000 INFO @ Fri, 05 Jul 2019 18:38:55: 22000000 INFO @ Fri, 05 Jul 2019 18:39:05: 23000000 INFO @ Fri, 05 Jul 2019 18:39:06: 23000000 INFO @ Fri, 05 Jul 2019 18:39:16: 24000000 INFO @ Fri, 05 Jul 2019 18:39:16: 24000000 INFO @ Fri, 05 Jul 2019 18:39:27: 25000000 INFO @ Fri, 05 Jul 2019 18:39:27: 25000000 INFO @ Fri, 05 Jul 2019 18:39:29: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:39:29: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:39:29: #1 total tags in treatment: 12194320 INFO @ Fri, 05 Jul 2019 18:39:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:39:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:39:29: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:39:29: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:39:29: #1 total tags in treatment: 12194320 INFO @ Fri, 05 Jul 2019 18:39:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:39:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 18:39:30: #1 tags after filtering in treatment: 5740038 INFO @ Fri, 05 Jul 2019 18:39:30: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 18:39:30: #1 finished! INFO @ Fri, 05 Jul 2019 18:39:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:39:30: #1 tags after filtering in treatment: 5740038 INFO @ Fri, 05 Jul 2019 18:39:30: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 05 Jul 2019 18:39:30: #1 finished! INFO @ Fri, 05 Jul 2019 18:39:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:39:30: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:39:30: 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 @ Fri, 05 Jul 2019 18:39:30: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:39:30: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:39:30: 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 @ Fri, 05 Jul 2019 18:39:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.20_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/ERX585700/ERX585700.05_model.r’: No such file or directory pass1 - making usageList (0 chroms)rm: : 2 millis cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.05_peaks.narrowPeak’: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585700/ERX585700.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling