Job ID = 1301043 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:37:41 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 ) 2019-06-03T10:37:41 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 : 73,535,040 reads read : 147,070,080 reads written : 73,535,040 reads 0-length : 73,535,040 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:24:13 73535040 reads; of these: 73535040 (100.00%) were unpaired; of these: 3456606 (4.70%) aligned 0 times 56202852 (76.43%) aligned exactly 1 time 13875582 (18.87%) aligned >1 times 95.30% overall alignment rate Time searching: 00:24:13 Overall time: 00:24:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 32 files... [bam_rmdupse_core] 17252592 / 70078434 = 0.2462 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 @ Mon, 03 Jun 2019 20:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:32:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:32:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:32:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:32:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:32:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:32:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:32:44: 1000000 INFO @ Mon, 03 Jun 2019 20:32:44: 1000000 INFO @ Mon, 03 Jun 2019 20:32:45: 1000000 INFO @ Mon, 03 Jun 2019 20:32:52: 2000000 INFO @ Mon, 03 Jun 2019 20:32:52: 2000000 INFO @ Mon, 03 Jun 2019 20:32:53: 2000000 INFO @ Mon, 03 Jun 2019 20:33:01: 3000000 INFO @ Mon, 03 Jun 2019 20:33:01: 3000000 INFO @ Mon, 03 Jun 2019 20:33:02: 3000000 INFO @ Mon, 03 Jun 2019 20:33:09: 4000000 INFO @ Mon, 03 Jun 2019 20:33:09: 4000000 INFO @ Mon, 03 Jun 2019 20:33:10: 4000000 INFO @ Mon, 03 Jun 2019 20:33:17: 5000000 INFO @ Mon, 03 Jun 2019 20:33:17: 5000000 INFO @ Mon, 03 Jun 2019 20:33:19: 5000000 INFO @ Mon, 03 Jun 2019 20:33:25: 6000000 INFO @ Mon, 03 Jun 2019 20:33:25: 6000000 INFO @ Mon, 03 Jun 2019 20:33:28: 6000000 INFO @ Mon, 03 Jun 2019 20:33:34: 7000000 INFO @ Mon, 03 Jun 2019 20:33:34: 7000000 INFO @ Mon, 03 Jun 2019 20:33:36: 7000000 INFO @ Mon, 03 Jun 2019 20:33:42: 8000000 INFO @ Mon, 03 Jun 2019 20:33:42: 8000000 INFO @ Mon, 03 Jun 2019 20:33:45: 8000000 INFO @ Mon, 03 Jun 2019 20:33:50: 9000000 INFO @ Mon, 03 Jun 2019 20:33:50: 9000000 INFO @ Mon, 03 Jun 2019 20:33:53: 9000000 INFO @ Mon, 03 Jun 2019 20:33:58: 10000000 INFO @ Mon, 03 Jun 2019 20:33:58: 10000000 INFO @ Mon, 03 Jun 2019 20:34:02: 10000000 INFO @ Mon, 03 Jun 2019 20:34:06: 11000000 INFO @ Mon, 03 Jun 2019 20:34:06: 11000000 INFO @ Mon, 03 Jun 2019 20:34:10: 11000000 INFO @ Mon, 03 Jun 2019 20:34:13: 12000000 INFO @ Mon, 03 Jun 2019 20:34:13: 12000000 INFO @ Mon, 03 Jun 2019 20:34:19: 12000000 INFO @ Mon, 03 Jun 2019 20:34:20: 13000000 INFO @ Mon, 03 Jun 2019 20:34:20: 13000000 INFO @ Mon, 03 Jun 2019 20:34:27: 13000000 INFO @ Mon, 03 Jun 2019 20:34:27: 14000000 INFO @ Mon, 03 Jun 2019 20:34:28: 14000000 INFO @ Mon, 03 Jun 2019 20:34:35: 15000000 INFO @ Mon, 03 Jun 2019 20:34:35: 15000000 INFO @ Mon, 03 Jun 2019 20:34:35: 14000000 INFO @ Mon, 03 Jun 2019 20:34:42: 16000000 INFO @ Mon, 03 Jun 2019 20:34:42: 16000000 INFO @ Mon, 03 Jun 2019 20:34:44: 15000000 INFO @ Mon, 03 Jun 2019 20:34:49: 17000000 INFO @ Mon, 03 Jun 2019 20:34:50: 17000000 INFO @ Mon, 03 Jun 2019 20:34:52: 16000000 INFO @ Mon, 03 Jun 2019 20:34:56: 18000000 INFO @ Mon, 03 Jun 2019 20:34:57: 18000000 INFO @ Mon, 03 Jun 2019 20:35:01: 17000000 INFO @ Mon, 03 Jun 2019 20:35:04: 19000000 INFO @ Mon, 03 Jun 2019 20:35:04: 19000000 INFO @ Mon, 03 Jun 2019 20:35:09: 18000000 INFO @ Mon, 03 Jun 2019 20:35:11: 20000000 INFO @ Mon, 03 Jun 2019 20:35:11: 20000000 INFO @ Mon, 03 Jun 2019 20:35:18: 19000000 INFO @ Mon, 03 Jun 2019 20:35:18: 21000000 INFO @ Mon, 03 Jun 2019 20:35:18: 21000000 INFO @ Mon, 03 Jun 2019 20:35:25: 22000000 INFO @ Mon, 03 Jun 2019 20:35:26: 22000000 INFO @ Mon, 03 Jun 2019 20:35:26: 20000000 INFO @ Mon, 03 Jun 2019 20:35:33: 23000000 INFO @ Mon, 03 Jun 2019 20:35:33: 23000000 INFO @ Mon, 03 Jun 2019 20:35:34: 21000000 INFO @ Mon, 03 Jun 2019 20:35:40: 24000000 INFO @ Mon, 03 Jun 2019 20:35:40: 24000000 INFO @ Mon, 03 Jun 2019 20:35:43: 22000000 INFO @ Mon, 03 Jun 2019 20:35:47: 25000000 INFO @ Mon, 03 Jun 2019 20:35:47: 25000000 INFO @ Mon, 03 Jun 2019 20:35:51: 23000000 INFO @ Mon, 03 Jun 2019 20:35:54: 26000000 INFO @ Mon, 03 Jun 2019 20:35:55: 26000000 INFO @ Mon, 03 Jun 2019 20:36:00: 24000000 INFO @ Mon, 03 Jun 2019 20:36:01: 27000000 INFO @ Mon, 03 Jun 2019 20:36:02: 27000000 INFO @ Mon, 03 Jun 2019 20:36:08: 25000000 INFO @ Mon, 03 Jun 2019 20:36:09: 28000000 INFO @ Mon, 03 Jun 2019 20:36:09: 28000000 INFO @ Mon, 03 Jun 2019 20:36:16: 29000000 INFO @ Mon, 03 Jun 2019 20:36:16: 29000000 INFO @ Mon, 03 Jun 2019 20:36:16: 26000000 INFO @ Mon, 03 Jun 2019 20:36:23: 30000000 INFO @ Mon, 03 Jun 2019 20:36:23: 30000000 INFO @ Mon, 03 Jun 2019 20:36:25: 27000000 INFO @ Mon, 03 Jun 2019 20:36:30: 31000000 INFO @ Mon, 03 Jun 2019 20:36:30: 31000000 INFO @ Mon, 03 Jun 2019 20:36:33: 28000000 INFO @ Mon, 03 Jun 2019 20:36:37: 32000000 INFO @ Mon, 03 Jun 2019 20:36:38: 32000000 INFO @ Mon, 03 Jun 2019 20:36:42: 29000000 INFO @ Mon, 03 Jun 2019 20:36:44: 33000000 INFO @ Mon, 03 Jun 2019 20:36:45: 33000000 INFO @ Mon, 03 Jun 2019 20:36:50: 30000000 INFO @ Mon, 03 Jun 2019 20:36:52: 34000000 INFO @ Mon, 03 Jun 2019 20:36:52: 34000000 INFO @ Mon, 03 Jun 2019 20:36:58: 31000000 INFO @ Mon, 03 Jun 2019 20:36:59: 35000000 INFO @ Mon, 03 Jun 2019 20:36:59: 35000000 INFO @ Mon, 03 Jun 2019 20:37:06: 36000000 INFO @ Mon, 03 Jun 2019 20:37:06: 36000000 INFO @ Mon, 03 Jun 2019 20:37:07: 32000000 INFO @ Mon, 03 Jun 2019 20:37:13: 37000000 INFO @ Mon, 03 Jun 2019 20:37:13: 37000000 INFO @ Mon, 03 Jun 2019 20:37:15: 33000000 INFO @ Mon, 03 Jun 2019 20:37:20: 38000000 INFO @ Mon, 03 Jun 2019 20:37:21: 38000000 INFO @ Mon, 03 Jun 2019 20:37:23: 34000000 INFO @ Mon, 03 Jun 2019 20:37:27: 39000000 INFO @ Mon, 03 Jun 2019 20:37:28: 39000000 INFO @ Mon, 03 Jun 2019 20:37:32: 35000000 INFO @ Mon, 03 Jun 2019 20:37:35: 40000000 INFO @ Mon, 03 Jun 2019 20:37:35: 40000000 INFO @ Mon, 03 Jun 2019 20:37:40: 36000000 INFO @ Mon, 03 Jun 2019 20:37:42: 41000000 INFO @ Mon, 03 Jun 2019 20:37:42: 41000000 INFO @ Mon, 03 Jun 2019 20:37:48: 37000000 INFO @ Mon, 03 Jun 2019 20:37:49: 42000000 INFO @ Mon, 03 Jun 2019 20:37:49: 42000000 INFO @ Mon, 03 Jun 2019 20:37:56: 43000000 INFO @ Mon, 03 Jun 2019 20:37:57: 38000000 INFO @ Mon, 03 Jun 2019 20:37:57: 43000000 INFO @ Mon, 03 Jun 2019 20:38:04: 44000000 INFO @ Mon, 03 Jun 2019 20:38:04: 44000000 INFO @ Mon, 03 Jun 2019 20:38:05: 39000000 INFO @ Mon, 03 Jun 2019 20:38:11: 45000000 INFO @ Mon, 03 Jun 2019 20:38:11: 45000000 INFO @ Mon, 03 Jun 2019 20:38:14: 40000000 INFO @ Mon, 03 Jun 2019 20:38:18: 46000000 INFO @ Mon, 03 Jun 2019 20:38:18: 46000000 INFO @ Mon, 03 Jun 2019 20:38:22: 41000000 INFO @ Mon, 03 Jun 2019 20:38:25: 47000000 INFO @ Mon, 03 Jun 2019 20:38:26: 47000000 INFO @ Mon, 03 Jun 2019 20:38:31: 42000000 INFO @ Mon, 03 Jun 2019 20:38:33: 48000000 INFO @ Mon, 03 Jun 2019 20:38:34: 48000000 INFO @ Mon, 03 Jun 2019 20:38:40: 43000000 INFO @ Mon, 03 Jun 2019 20:38:42: 49000000 INFO @ Mon, 03 Jun 2019 20:38:42: 49000000 INFO @ Mon, 03 Jun 2019 20:38:48: 44000000 INFO @ Mon, 03 Jun 2019 20:38:50: 50000000 INFO @ Mon, 03 Jun 2019 20:38:50: 50000000 INFO @ Mon, 03 Jun 2019 20:38:57: 45000000 INFO @ Mon, 03 Jun 2019 20:38:57: 51000000 INFO @ Mon, 03 Jun 2019 20:38:58: 51000000 INFO @ Mon, 03 Jun 2019 20:39:05: 52000000 INFO @ Mon, 03 Jun 2019 20:39:05: 52000000 INFO @ Mon, 03 Jun 2019 20:39:05: 46000000 INFO @ Mon, 03 Jun 2019 20:39:11: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 20:39:11: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 20:39:11: #1 total tags in treatment: 52825842 INFO @ Mon, 03 Jun 2019 20:39:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:39:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:39:12: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 20:39:12: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 20:39:12: #1 total tags in treatment: 52825842 INFO @ Mon, 03 Jun 2019 20:39:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:39:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:39:12: #1 tags after filtering in treatment: 52825842 INFO @ Mon, 03 Jun 2019 20:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:39:12: #1 finished! INFO @ Mon, 03 Jun 2019 20:39:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:39:13: #1 tags after filtering in treatment: 52825842 INFO @ Mon, 03 Jun 2019 20:39:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:39:13: #1 finished! INFO @ Mon, 03 Jun 2019 20:39:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:39:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:39:13: 47000000 INFO @ Mon, 03 Jun 2019 20:39:16: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 20:39:16: 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 @ Mon, 03 Jun 2019 20:39:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.05_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/dm3/SRX4828018/SRX4828018.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:39:17: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 20:39:17: 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 @ Mon, 03 Jun 2019 20:39:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.10_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/dm3/SRX4828018/SRX4828018.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:39:22: 48000000 INFO @ Mon, 03 Jun 2019 20:39:30: 49000000 INFO @ Mon, 03 Jun 2019 20:39:38: 50000000 INFO @ Mon, 03 Jun 2019 20:39:46: 51000000 INFO @ Mon, 03 Jun 2019 20:39:54: 52000000 INFO @ Mon, 03 Jun 2019 20:40:02: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 20:40:02: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 20:40:02: #1 total tags in treatment: 52825842 INFO @ Mon, 03 Jun 2019 20:40:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:40:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:40:03: #1 tags after filtering in treatment: 52825842 INFO @ Mon, 03 Jun 2019 20:40:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:40:03: #1 finished! INFO @ Mon, 03 Jun 2019 20:40:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:40:07: #2 number of paired peaks: 0 WARNING @ Mon, 03 Jun 2019 20:40:07: 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 @ Mon, 03 Jun 2019 20:40:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.20_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/dm3/SRX4828018/SRX4828018.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX4828018/SRX4828018.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。