Job ID = 2010324 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:06:54 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 ) 2019-07-05T13:08:59 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 ) 2019-07-05T13:15:59 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 : 29,177,780 reads read : 58,355,560 reads written : 58,355,560 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: 00:39:23 29177780 reads; of these: 29177780 (100.00%) were paired; of these: 1952218 (6.69%) aligned concordantly 0 times 22561660 (77.32%) aligned concordantly exactly 1 time 4663902 (15.98%) aligned concordantly >1 times ---- 1952218 pairs aligned concordantly 0 times; of these: 291887 (14.95%) aligned discordantly 1 time ---- 1660331 pairs aligned 0 times concordantly or discordantly; of these: 3320662 mates make up the pairs; of these: 2796214 (84.21%) aligned 0 times 304990 (9.18%) aligned exactly 1 time 219458 (6.61%) aligned >1 times 95.21% overall alignment rate Time searching: 00:39:23 Overall time: 00:39:23 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] 1780257 / 27478108 = 0.0648 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 23:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.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 23:23:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.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 23:23:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.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 23:23:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:55: 1000000 INFO @ Fri, 05 Jul 2019 23:23:55: 1000000 INFO @ Fri, 05 Jul 2019 23:23:57: 1000000 INFO @ Fri, 05 Jul 2019 23:24:01: 2000000 INFO @ Fri, 05 Jul 2019 23:24:03: 2000000 INFO @ Fri, 05 Jul 2019 23:24:05: 2000000 INFO @ Fri, 05 Jul 2019 23:24:07: 3000000 INFO @ Fri, 05 Jul 2019 23:24:11: 3000000 INFO @ Fri, 05 Jul 2019 23:24:13: 3000000 INFO @ Fri, 05 Jul 2019 23:24:14: 4000000 INFO @ Fri, 05 Jul 2019 23:24:18: 4000000 INFO @ Fri, 05 Jul 2019 23:24:21: 4000000 INFO @ Fri, 05 Jul 2019 23:24:21: 5000000 INFO @ Fri, 05 Jul 2019 23:24:26: 5000000 INFO @ Fri, 05 Jul 2019 23:24:27: 6000000 INFO @ Fri, 05 Jul 2019 23:24:29: 5000000 INFO @ Fri, 05 Jul 2019 23:24:34: 7000000 INFO @ Fri, 05 Jul 2019 23:24:34: 6000000 INFO @ Fri, 05 Jul 2019 23:24:36: 6000000 INFO @ Fri, 05 Jul 2019 23:24:40: 8000000 INFO @ Fri, 05 Jul 2019 23:24:42: 7000000 INFO @ Fri, 05 Jul 2019 23:24:44: 7000000 INFO @ Fri, 05 Jul 2019 23:24:46: 9000000 INFO @ Fri, 05 Jul 2019 23:24:50: 8000000 INFO @ Fri, 05 Jul 2019 23:24:52: 8000000 INFO @ Fri, 05 Jul 2019 23:24:53: 10000000 INFO @ Fri, 05 Jul 2019 23:24:57: 9000000 INFO @ Fri, 05 Jul 2019 23:24:59: 11000000 INFO @ Fri, 05 Jul 2019 23:25:00: 9000000 INFO @ Fri, 05 Jul 2019 23:25:05: 12000000 INFO @ Fri, 05 Jul 2019 23:25:05: 10000000 INFO @ Fri, 05 Jul 2019 23:25:07: 10000000 INFO @ Fri, 05 Jul 2019 23:25:12: 13000000 INFO @ Fri, 05 Jul 2019 23:25:13: 11000000 INFO @ Fri, 05 Jul 2019 23:25:15: 11000000 INFO @ Fri, 05 Jul 2019 23:25:18: 14000000 INFO @ Fri, 05 Jul 2019 23:25:21: 12000000 INFO @ Fri, 05 Jul 2019 23:25:23: 12000000 INFO @ Fri, 05 Jul 2019 23:25:24: 15000000 INFO @ Fri, 05 Jul 2019 23:25:28: 13000000 INFO @ Fri, 05 Jul 2019 23:25:30: 16000000 INFO @ Fri, 05 Jul 2019 23:25:31: 13000000 INFO @ Fri, 05 Jul 2019 23:25:36: 14000000 INFO @ Fri, 05 Jul 2019 23:25:37: 17000000 INFO @ Fri, 05 Jul 2019 23:25:38: 14000000 INFO @ Fri, 05 Jul 2019 23:25:43: 18000000 INFO @ Fri, 05 Jul 2019 23:25:44: 15000000 INFO @ Fri, 05 Jul 2019 23:25:46: 15000000 INFO @ Fri, 05 Jul 2019 23:25:49: 19000000 INFO @ Fri, 05 Jul 2019 23:25:52: 16000000 INFO @ Fri, 05 Jul 2019 23:25:54: 16000000 INFO @ Fri, 05 Jul 2019 23:25:56: 20000000 INFO @ Fri, 05 Jul 2019 23:25:59: 17000000 INFO @ Fri, 05 Jul 2019 23:26:01: 17000000 INFO @ Fri, 05 Jul 2019 23:26:02: 21000000 INFO @ Fri, 05 Jul 2019 23:26:07: 18000000 INFO @ Fri, 05 Jul 2019 23:26:08: 22000000 INFO @ Fri, 05 Jul 2019 23:26:09: 18000000 INFO @ Fri, 05 Jul 2019 23:26:15: 23000000 INFO @ Fri, 05 Jul 2019 23:26:15: 19000000 INFO @ Fri, 05 Jul 2019 23:26:17: 19000000 INFO @ Fri, 05 Jul 2019 23:26:21: 24000000 INFO @ Fri, 05 Jul 2019 23:26:23: 20000000 INFO @ Fri, 05 Jul 2019 23:26:25: 20000000 INFO @ Fri, 05 Jul 2019 23:26:28: 25000000 INFO @ Fri, 05 Jul 2019 23:26:31: 21000000 INFO @ Fri, 05 Jul 2019 23:26:33: 21000000 INFO @ Fri, 05 Jul 2019 23:26:34: 26000000 INFO @ Fri, 05 Jul 2019 23:26:38: 22000000 INFO @ Fri, 05 Jul 2019 23:26:41: 22000000 INFO @ Fri, 05 Jul 2019 23:26:41: 27000000 INFO @ Fri, 05 Jul 2019 23:26:47: 23000000 INFO @ Fri, 05 Jul 2019 23:26:47: 28000000 INFO @ Fri, 05 Jul 2019 23:26:49: 23000000 INFO @ Fri, 05 Jul 2019 23:26:53: 29000000 INFO @ Fri, 05 Jul 2019 23:26:55: 24000000 INFO @ Fri, 05 Jul 2019 23:26:57: 24000000 INFO @ Fri, 05 Jul 2019 23:27:00: 30000000 INFO @ Fri, 05 Jul 2019 23:27:03: 25000000 INFO @ Fri, 05 Jul 2019 23:27:05: 25000000 INFO @ Fri, 05 Jul 2019 23:27:06: 31000000 INFO @ Fri, 05 Jul 2019 23:27:11: 26000000 INFO @ Fri, 05 Jul 2019 23:27:13: 32000000 INFO @ Fri, 05 Jul 2019 23:27:13: 26000000 INFO @ Fri, 05 Jul 2019 23:27:19: 33000000 INFO @ Fri, 05 Jul 2019 23:27:19: 27000000 INFO @ Fri, 05 Jul 2019 23:27:21: 27000000 INFO @ Fri, 05 Jul 2019 23:27:25: 34000000 INFO @ Fri, 05 Jul 2019 23:27:27: 28000000 INFO @ Fri, 05 Jul 2019 23:27:29: 28000000 INFO @ Fri, 05 Jul 2019 23:27:32: 35000000 INFO @ Fri, 05 Jul 2019 23:27:35: 29000000 INFO @ Fri, 05 Jul 2019 23:27:37: 29000000 INFO @ Fri, 05 Jul 2019 23:27:38: 36000000 INFO @ Fri, 05 Jul 2019 23:27:43: 30000000 INFO @ Fri, 05 Jul 2019 23:27:44: 37000000 INFO @ Fri, 05 Jul 2019 23:27:45: 30000000 INFO @ Fri, 05 Jul 2019 23:27:50: 31000000 INFO @ Fri, 05 Jul 2019 23:27:51: 38000000 INFO @ Fri, 05 Jul 2019 23:27:52: 31000000 INFO @ Fri, 05 Jul 2019 23:27:57: 39000000 INFO @ Fri, 05 Jul 2019 23:27:58: 32000000 INFO @ Fri, 05 Jul 2019 23:27:59: 32000000 INFO @ Fri, 05 Jul 2019 23:28:04: 40000000 INFO @ Fri, 05 Jul 2019 23:28:05: 33000000 INFO @ Fri, 05 Jul 2019 23:28:07: 33000000 INFO @ Fri, 05 Jul 2019 23:28:10: 41000000 INFO @ Fri, 05 Jul 2019 23:28:12: 34000000 INFO @ Fri, 05 Jul 2019 23:28:14: 34000000 INFO @ Fri, 05 Jul 2019 23:28:16: 42000000 INFO @ Fri, 05 Jul 2019 23:28:19: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:28:21: 35000000 INFO @ Fri, 05 Jul 2019 23:28:23: 43000000 INFO @ Fri, 05 Jul 2019 23:28:27: 36000000 INFO @ Fri, 05 Jul 2019 23:28:28: 36000000 INFO @ Fri, 05 Jul 2019 23:28:29: 44000000 INFO @ Fri, 05 Jul 2019 23:28:34: 37000000 INFO @ Fri, 05 Jul 2019 23:28:36: 37000000 INFO @ Fri, 05 Jul 2019 23:28:36: 45000000 INFO @ Fri, 05 Jul 2019 23:28:41: 38000000 INFO @ Fri, 05 Jul 2019 23:28:42: 46000000 INFO @ Fri, 05 Jul 2019 23:28:43: 38000000 INFO @ Fri, 05 Jul 2019 23:28:48: 39000000 INFO @ Fri, 05 Jul 2019 23:28:49: 47000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:28:50: 39000000 INFO @ Fri, 05 Jul 2019 23:28:55: 48000000 INFO @ Fri, 05 Jul 2019 23:28:56: 40000000 INFO @ Fri, 05 Jul 2019 23:28:58: 40000000 INFO @ Fri, 05 Jul 2019 23:29:02: 49000000 INFO @ Fri, 05 Jul 2019 23:29:03: 41000000 INFO @ Fri, 05 Jul 2019 23:29:05: 41000000 INFO @ Fri, 05 Jul 2019 23:29:08: 50000000 INFO @ Fri, 05 Jul 2019 23:29:10: 42000000 INFO @ Fri, 05 Jul 2019 23:29:12: 42000000 INFO @ Fri, 05 Jul 2019 23:29:14: 51000000 INFO @ Fri, 05 Jul 2019 23:29:18: 43000000 INFO @ Fri, 05 Jul 2019 23:29:19: 43000000 INFO @ Fri, 05 Jul 2019 23:29:21: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 23:29:21: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 23:29:21: #1 total tags in treatment: 25463681 INFO @ Fri, 05 Jul 2019 23:29:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:21: #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 23:29:22: #1 tags after filtering in treatment: 13812182 INFO @ Fri, 05 Jul 2019 23:29:22: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 23:29:22: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:23: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:29:23: 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 23:29:23: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:29:25: 44000000 INFO @ Fri, 05 Jul 2019 23:29:27: 44000000 INFO @ Fri, 05 Jul 2019 23:29:32: 45000000 INFO @ Fri, 05 Jul 2019 23:29:34: 45000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.10_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/SRX363272/SRX363272.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:29:39: 46000000 INFO @ Fri, 05 Jul 2019 23:29:41: 46000000 INFO @ Fri, 05 Jul 2019 23:29:47: 47000000 INFO @ Fri, 05 Jul 2019 23:29:48: 47000000 INFO @ Fri, 05 Jul 2019 23:29:54: 48000000 INFO @ Fri, 05 Jul 2019 23:29:56: 48000000 INFO @ Fri, 05 Jul 2019 23:30:01: 49000000 INFO @ Fri, 05 Jul 2019 23:30:03: 49000000 INFO @ Fri, 05 Jul 2019 23:30:08: 50000000 INFO @ Fri, 05 Jul 2019 23:30:10: 50000000 INFO @ Fri, 05 Jul 2019 23:30:15: 51000000 INFO @ Fri, 05 Jul 2019 23:30:17: 51000000 INFO @ Fri, 05 Jul 2019 23:30:23: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 23:30:23: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 23:30:23: #1 total tags in treatment: 25463681 INFO @ Fri, 05 Jul 2019 23:30:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:30:23: #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 23:30:23: #1 tags after filtering in treatment: 13812182 INFO @ Fri, 05 Jul 2019 23:30:23: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 23:30:23: #1 finished! INFO @ Fri, 05 Jul 2019 23:30:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:30:24: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 23:30:24: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 23:30:24: #1 total tags in treatment: 25463681 INFO @ Fri, 05 Jul 2019 23:30:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:30:24: #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 23:30:24: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:30:24: 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 23:30:24: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:30:25: #1 tags after filtering in treatment: 13812182 INFO @ Fri, 05 Jul 2019 23:30:25: #1 Redundant rate of treatment: 0.46 INFO @ Fri, 05 Jul 2019 23:30:25: #1 finished! INFO @ Fri, 05 Jul 2019 23:30:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:30:26: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:30:26: 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 @ Fri, 05 Jul 2019 23:30:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.20_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/SRX363272/SRX363272.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX363272/SRX363272.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling