Job ID = 2011863 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:54:16 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 ) 2019-07-05T17:57:46 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 ) 2019-07-05T17:57:46 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 ) 2019-07-05T17:57:46 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 ) 2019-07-05T18:06:10 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 : 32,986,316 reads read : 65,972,632 reads written : 65,972,632 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: 00:26:10 32986316 reads; of these: 32986316 (100.00%) were paired; of these: 2687361 (8.15%) aligned concordantly 0 times 26104816 (79.14%) aligned concordantly exactly 1 time 4194139 (12.71%) aligned concordantly >1 times ---- 2687361 pairs aligned concordantly 0 times; of these: 189315 (7.04%) aligned discordantly 1 time ---- 2498046 pairs aligned 0 times concordantly or discordantly; of these: 4996092 mates make up the pairs; of these: 4011255 (80.29%) aligned 0 times 775737 (15.53%) aligned exactly 1 time 209100 (4.19%) aligned >1 times 93.92% overall alignment rate Time searching: 00:26:10 Overall time: 00:26:10 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 28 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] 3931745 / 30349389 = 0.1295 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 03:56:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.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 03:56:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:56:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.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 03:56:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:56:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.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 03:56:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:56:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:57:01: 1000000 INFO @ Sat, 06 Jul 2019 03:57:02: 1000000 INFO @ Sat, 06 Jul 2019 03:57:05: 1000000 INFO @ Sat, 06 Jul 2019 03:57:07: 2000000 INFO @ Sat, 06 Jul 2019 03:57:10: 2000000 INFO @ Sat, 06 Jul 2019 03:57:13: 3000000 INFO @ Sat, 06 Jul 2019 03:57:14: 2000000 INFO @ Sat, 06 Jul 2019 03:57:17: 3000000 INFO @ Sat, 06 Jul 2019 03:57:20: 4000000 INFO @ Sat, 06 Jul 2019 03:57:23: 3000000 INFO @ Sat, 06 Jul 2019 03:57:24: 4000000 INFO @ Sat, 06 Jul 2019 03:57:26: 5000000 INFO @ Sat, 06 Jul 2019 03:57:31: 5000000 INFO @ Sat, 06 Jul 2019 03:57:32: 4000000 INFO @ Sat, 06 Jul 2019 03:57:33: 6000000 INFO @ Sat, 06 Jul 2019 03:57:39: 6000000 INFO @ Sat, 06 Jul 2019 03:57:39: 7000000 INFO @ Sat, 06 Jul 2019 03:57:40: 5000000 INFO @ Sat, 06 Jul 2019 03:57:45: 8000000 INFO @ Sat, 06 Jul 2019 03:57:46: 7000000 INFO @ Sat, 06 Jul 2019 03:57:49: 6000000 INFO @ Sat, 06 Jul 2019 03:57:52: 9000000 INFO @ Sat, 06 Jul 2019 03:57:53: 8000000 INFO @ Sat, 06 Jul 2019 03:57:58: 7000000 INFO @ Sat, 06 Jul 2019 03:57:58: 10000000 INFO @ Sat, 06 Jul 2019 03:58:00: 9000000 INFO @ Sat, 06 Jul 2019 03:58:05: 11000000 INFO @ Sat, 06 Jul 2019 03:58:06: 8000000 INFO @ Sat, 06 Jul 2019 03:58:08: 10000000 INFO @ Sat, 06 Jul 2019 03:58:11: 12000000 INFO @ Sat, 06 Jul 2019 03:58:15: 11000000 INFO @ Sat, 06 Jul 2019 03:58:15: 9000000 INFO @ Sat, 06 Jul 2019 03:58:18: 13000000 INFO @ Sat, 06 Jul 2019 03:58:22: 12000000 INFO @ Sat, 06 Jul 2019 03:58:24: 14000000 INFO @ Sat, 06 Jul 2019 03:58:24: 10000000 INFO @ Sat, 06 Jul 2019 03:58:29: 13000000 INFO @ Sat, 06 Jul 2019 03:58:30: 15000000 INFO @ Sat, 06 Jul 2019 03:58:33: 11000000 INFO @ Sat, 06 Jul 2019 03:58:36: 14000000 INFO @ Sat, 06 Jul 2019 03:58:37: 16000000 INFO @ Sat, 06 Jul 2019 03:58:42: 12000000 INFO @ Sat, 06 Jul 2019 03:58:43: 17000000 INFO @ Sat, 06 Jul 2019 03:58:43: 15000000 INFO @ Sat, 06 Jul 2019 03:58:49: 18000000 INFO @ Sat, 06 Jul 2019 03:58:50: 13000000 INFO @ Sat, 06 Jul 2019 03:58:50: 16000000 INFO @ Sat, 06 Jul 2019 03:58:56: 19000000 INFO @ Sat, 06 Jul 2019 03:58:57: 17000000 INFO @ Sat, 06 Jul 2019 03:58:59: 14000000 INFO @ Sat, 06 Jul 2019 03:59:02: 20000000 INFO @ Sat, 06 Jul 2019 03:59:05: 18000000 INFO @ Sat, 06 Jul 2019 03:59:07: 15000000 INFO @ Sat, 06 Jul 2019 03:59:08: 21000000 INFO @ Sat, 06 Jul 2019 03:59:12: 19000000 INFO @ Sat, 06 Jul 2019 03:59:15: 22000000 INFO @ Sat, 06 Jul 2019 03:59:16: 16000000 INFO @ Sat, 06 Jul 2019 03:59:19: 20000000 INFO @ Sat, 06 Jul 2019 03:59:21: 23000000 INFO @ Sat, 06 Jul 2019 03:59:24: 17000000 INFO @ Sat, 06 Jul 2019 03:59:26: 21000000 INFO @ Sat, 06 Jul 2019 03:59:28: 24000000 INFO @ Sat, 06 Jul 2019 03:59:32: 18000000 INFO @ Sat, 06 Jul 2019 03:59:33: 22000000 INFO @ Sat, 06 Jul 2019 03:59:34: 25000000 INFO @ Sat, 06 Jul 2019 03:59:40: 26000000 INFO @ Sat, 06 Jul 2019 03:59:41: 23000000 INFO @ Sat, 06 Jul 2019 03:59:41: 19000000 INFO @ Sat, 06 Jul 2019 03:59:47: 27000000 INFO @ Sat, 06 Jul 2019 03:59:48: 24000000 INFO @ Sat, 06 Jul 2019 03:59:50: 20000000 INFO @ Sat, 06 Jul 2019 03:59:53: 28000000 INFO @ Sat, 06 Jul 2019 03:59:55: 25000000 INFO @ Sat, 06 Jul 2019 03:59:59: 21000000 INFO @ Sat, 06 Jul 2019 03:59:59: 29000000 INFO @ Sat, 06 Jul 2019 04:00:02: 26000000 INFO @ Sat, 06 Jul 2019 04:00:06: 30000000 INFO @ Sat, 06 Jul 2019 04:00:07: 22000000 INFO @ Sat, 06 Jul 2019 04:00:09: 27000000 INFO @ Sat, 06 Jul 2019 04:00:12: 31000000 INFO @ Sat, 06 Jul 2019 04:00:16: 23000000 INFO @ Sat, 06 Jul 2019 04:00:16: 28000000 INFO @ Sat, 06 Jul 2019 04:00:19: 32000000 INFO @ Sat, 06 Jul 2019 04:00:24: 29000000 INFO @ Sat, 06 Jul 2019 04:00:25: 24000000 INFO @ Sat, 06 Jul 2019 04:00:25: 33000000 INFO @ Sat, 06 Jul 2019 04:00:31: 30000000 INFO @ Sat, 06 Jul 2019 04:00:31: 34000000 INFO @ Sat, 06 Jul 2019 04:00:33: 25000000 INFO @ Sat, 06 Jul 2019 04:00:38: 35000000 INFO @ Sat, 06 Jul 2019 04:00:38: 31000000 INFO @ Sat, 06 Jul 2019 04:00:42: 26000000 INFO @ Sat, 06 Jul 2019 04:00:44: 36000000 INFO @ Sat, 06 Jul 2019 04:00:45: 32000000 INFO @ Sat, 06 Jul 2019 04:00:50: 37000000 INFO @ Sat, 06 Jul 2019 04:00:51: 27000000 INFO @ Sat, 06 Jul 2019 04:00:52: 33000000 INFO @ Sat, 06 Jul 2019 04:00:56: 38000000 INFO @ Sat, 06 Jul 2019 04:00:59: 34000000 INFO @ Sat, 06 Jul 2019 04:01:00: 28000000 INFO @ Sat, 06 Jul 2019 04:01:03: 39000000 INFO @ Sat, 06 Jul 2019 04:01:06: 35000000 INFO @ Sat, 06 Jul 2019 04:01:08: 29000000 INFO @ Sat, 06 Jul 2019 04:01:09: 40000000 INFO @ Sat, 06 Jul 2019 04:01:13: 36000000 INFO @ Sat, 06 Jul 2019 04:01:15: 41000000 INFO @ Sat, 06 Jul 2019 04:01:17: 30000000 INFO @ Sat, 06 Jul 2019 04:01:20: 37000000 INFO @ Sat, 06 Jul 2019 04:01:21: 42000000 INFO @ Sat, 06 Jul 2019 04:01:26: 31000000 INFO @ Sat, 06 Jul 2019 04:01:27: 38000000 INFO @ Sat, 06 Jul 2019 04:01:27: 43000000 INFO @ Sat, 06 Jul 2019 04:01:34: 39000000 INFO @ Sat, 06 Jul 2019 04:01:34: 44000000 INFO @ Sat, 06 Jul 2019 04:01:35: 32000000 INFO @ Sat, 06 Jul 2019 04:01:40: 45000000 INFO @ Sat, 06 Jul 2019 04:01:40: 40000000 INFO @ Sat, 06 Jul 2019 04:01:44: 33000000 INFO @ Sat, 06 Jul 2019 04:01:46: 46000000 INFO @ Sat, 06 Jul 2019 04:01:47: 41000000 INFO @ Sat, 06 Jul 2019 04:01:52: 34000000 INFO @ Sat, 06 Jul 2019 04:01:52: 47000000 INFO @ Sat, 06 Jul 2019 04:01:54: 42000000 INFO @ Sat, 06 Jul 2019 04:01:58: 48000000 INFO @ Sat, 06 Jul 2019 04:02:00: 35000000 INFO @ Sat, 06 Jul 2019 04:02:01: 43000000 INFO @ Sat, 06 Jul 2019 04:02:05: 49000000 INFO @ Sat, 06 Jul 2019 04:02:08: 44000000 INFO @ Sat, 06 Jul 2019 04:02:08: 36000000 INFO @ Sat, 06 Jul 2019 04:02:11: 50000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 04:02:15: 45000000 INFO @ Sat, 06 Jul 2019 04:02:17: 37000000 INFO @ Sat, 06 Jul 2019 04:02:17: 51000000 INFO @ Sat, 06 Jul 2019 04:02:22: 46000000 INFO @ Sat, 06 Jul 2019 04:02:23: 52000000 INFO @ Sat, 06 Jul 2019 04:02:25: 38000000 INFO @ Sat, 06 Jul 2019 04:02:28: 47000000 INFO @ Sat, 06 Jul 2019 04:02:29: 53000000 INFO @ Sat, 06 Jul 2019 04:02:33: 39000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 04:02:35: 48000000 INFO @ Sat, 06 Jul 2019 04:02:37: 54000000 INFO @ Sat, 06 Jul 2019 04:02:38: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 04:02:38: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 04:02:38: #1 total tags in treatment: 26370371 INFO @ Sat, 06 Jul 2019 04:02:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:02:38: #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 04:02:38: #1 tags after filtering in treatment: 12284310 INFO @ Sat, 06 Jul 2019 04:02:38: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 06 Jul 2019 04:02:38: #1 finished! INFO @ Sat, 06 Jul 2019 04:02:38: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:02:39: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:02:39: 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 04:02:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.05_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/SRX5170660/SRX5170660.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:02:42: 40000000 INFO @ Sat, 06 Jul 2019 04:02:42: 49000000 INFO @ Sat, 06 Jul 2019 04:02:49: 50000000 INFO @ Sat, 06 Jul 2019 04:02:50: 41000000 INFO @ Sat, 06 Jul 2019 04:02:56: 51000000 INFO @ Sat, 06 Jul 2019 04:02:58: 42000000 INFO @ Sat, 06 Jul 2019 04:03:02: 52000000 INFO @ Sat, 06 Jul 2019 04:03:06: 43000000 INFO @ Sat, 06 Jul 2019 04:03:09: 53000000 INFO @ Sat, 06 Jul 2019 04:03:14: 44000000 INFO @ Sat, 06 Jul 2019 04:03:16: 54000000 INFO @ Sat, 06 Jul 2019 04:03:17: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 04:03:17: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 04:03:17: #1 total tags in treatment: 26370371 INFO @ Sat, 06 Jul 2019 04:03:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:03:17: #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 04:03:18: #1 tags after filtering in treatment: 12284310 INFO @ Sat, 06 Jul 2019 04:03:18: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 06 Jul 2019 04:03:18: #1 finished! INFO @ Sat, 06 Jul 2019 04:03:18: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:03:19: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:03:19: 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 04:03:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.10_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/SRX5170660/SRX5170660.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:03:22: 45000000 INFO @ Sat, 06 Jul 2019 04:03:30: 46000000 INFO @ Sat, 06 Jul 2019 04:03:38: 47000000 INFO @ Sat, 06 Jul 2019 04:03:46: 48000000 INFO @ Sat, 06 Jul 2019 04:03:54: 49000000 INFO @ Sat, 06 Jul 2019 04:04:02: 50000000 INFO @ Sat, 06 Jul 2019 04:04:11: 51000000 INFO @ Sat, 06 Jul 2019 04:04:19: 52000000 INFO @ Sat, 06 Jul 2019 04:04:27: 53000000 INFO @ Sat, 06 Jul 2019 04:04:35: 54000000 INFO @ Sat, 06 Jul 2019 04:04:36: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 04:04:36: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 04:04:36: #1 total tags in treatment: 26370371 INFO @ Sat, 06 Jul 2019 04:04:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:04:36: #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 04:04:36: #1 tags after filtering in treatment: 12284310 INFO @ Sat, 06 Jul 2019 04:04:36: #1 Redundant rate of treatment: 0.53 INFO @ Sat, 06 Jul 2019 04:04:36: #1 finished! INFO @ Sat, 06 Jul 2019 04:04:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:04:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:04:37: 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 04:04:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.20_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/SRX5170660/SRX5170660.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5170660/SRX5170660.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling