Job ID = 1293732 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:58:43 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 ) 2019-06-02T16:58:44 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 : 23,604,057 reads read : 23,604,057 reads written : 23,604,057 2019-06-02T17:06:55 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 ) 2019-06-02T17:07:33 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T17:07:33 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 17,978,113 reads read : 17,978,113 reads written : 17,978,113 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: 00:15:15 41582170 reads; of these: 41582170 (100.00%) were unpaired; of these: 2668993 (6.42%) aligned 0 times 26883229 (64.65%) aligned exactly 1 time 12029948 (28.93%) aligned >1 times 93.58% overall alignment rate Time searching: 00:15:15 Overall time: 00:15:15 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 12 files... [bam_rmdupse_core] 13363993 / 38913177 = 0.3434 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 02:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.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 02:38:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:38:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.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 02:38:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:38:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.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 02:38:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:38:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:38:26: 1000000 INFO @ Mon, 03 Jun 2019 02:38:26: 1000000 INFO @ Mon, 03 Jun 2019 02:38:27: 1000000 INFO @ Mon, 03 Jun 2019 02:38:35: 2000000 INFO @ Mon, 03 Jun 2019 02:38:35: 2000000 INFO @ Mon, 03 Jun 2019 02:38:37: 2000000 INFO @ Mon, 03 Jun 2019 02:38:45: 3000000 INFO @ Mon, 03 Jun 2019 02:38:45: 3000000 INFO @ Mon, 03 Jun 2019 02:38:47: 3000000 INFO @ Mon, 03 Jun 2019 02:38:54: 4000000 INFO @ Mon, 03 Jun 2019 02:38:54: 4000000 INFO @ Mon, 03 Jun 2019 02:38:57: 4000000 INFO @ Mon, 03 Jun 2019 02:39:02: 5000000 INFO @ Mon, 03 Jun 2019 02:39:02: 5000000 INFO @ Mon, 03 Jun 2019 02:39:07: 5000000 INFO @ Mon, 03 Jun 2019 02:39:11: 6000000 INFO @ Mon, 03 Jun 2019 02:39:11: 6000000 INFO @ Mon, 03 Jun 2019 02:39:16: 6000000 INFO @ Mon, 03 Jun 2019 02:39:20: 7000000 INFO @ Mon, 03 Jun 2019 02:39:20: 7000000 INFO @ Mon, 03 Jun 2019 02:39:26: 7000000 INFO @ Mon, 03 Jun 2019 02:39:29: 8000000 INFO @ Mon, 03 Jun 2019 02:39:29: 8000000 INFO @ Mon, 03 Jun 2019 02:39:36: 8000000 INFO @ Mon, 03 Jun 2019 02:39:38: 9000000 INFO @ Mon, 03 Jun 2019 02:39:38: 9000000 INFO @ Mon, 03 Jun 2019 02:39:46: 9000000 INFO @ Mon, 03 Jun 2019 02:39:47: 10000000 INFO @ Mon, 03 Jun 2019 02:39:47: 10000000 INFO @ Mon, 03 Jun 2019 02:39:56: 11000000 INFO @ Mon, 03 Jun 2019 02:39:56: 11000000 INFO @ Mon, 03 Jun 2019 02:39:56: 10000000 INFO @ Mon, 03 Jun 2019 02:40:03: 12000000 INFO @ Mon, 03 Jun 2019 02:40:03: 12000000 INFO @ Mon, 03 Jun 2019 02:40:05: 11000000 INFO @ Mon, 03 Jun 2019 02:40:11: 13000000 INFO @ Mon, 03 Jun 2019 02:40:11: 13000000 INFO @ Mon, 03 Jun 2019 02:40:15: 12000000 INFO @ Mon, 03 Jun 2019 02:40:18: 14000000 INFO @ Mon, 03 Jun 2019 02:40:18: 14000000 INFO @ Mon, 03 Jun 2019 02:40:25: 13000000 INFO @ Mon, 03 Jun 2019 02:40:26: 15000000 INFO @ Mon, 03 Jun 2019 02:40:26: 15000000 INFO @ Mon, 03 Jun 2019 02:40:33: 16000000 INFO @ Mon, 03 Jun 2019 02:40:34: 16000000 INFO @ Mon, 03 Jun 2019 02:40:34: 14000000 INFO @ Mon, 03 Jun 2019 02:40:41: 17000000 INFO @ Mon, 03 Jun 2019 02:40:42: 17000000 INFO @ Mon, 03 Jun 2019 02:40:44: 15000000 INFO @ Mon, 03 Jun 2019 02:40:49: 18000000 INFO @ Mon, 03 Jun 2019 02:40:49: 18000000 INFO @ Mon, 03 Jun 2019 02:40:53: 16000000 INFO @ Mon, 03 Jun 2019 02:40:56: 19000000 INFO @ Mon, 03 Jun 2019 02:40:57: 19000000 INFO @ Mon, 03 Jun 2019 02:41:03: 17000000 INFO @ Mon, 03 Jun 2019 02:41:04: 20000000 INFO @ Mon, 03 Jun 2019 02:41:04: 20000000 INFO @ Mon, 03 Jun 2019 02:41:12: 21000000 INFO @ Mon, 03 Jun 2019 02:41:12: 21000000 INFO @ Mon, 03 Jun 2019 02:41:13: 18000000 INFO @ Mon, 03 Jun 2019 02:41:19: 22000000 INFO @ Mon, 03 Jun 2019 02:41:20: 22000000 INFO @ Mon, 03 Jun 2019 02:41:23: 19000000 INFO @ Mon, 03 Jun 2019 02:41:27: 23000000 INFO @ Mon, 03 Jun 2019 02:41:27: 23000000 INFO @ Mon, 03 Jun 2019 02:41:33: 20000000 INFO @ Mon, 03 Jun 2019 02:41:34: 24000000 INFO @ Mon, 03 Jun 2019 02:41:35: 24000000 INFO @ Mon, 03 Jun 2019 02:41:42: 25000000 INFO @ Mon, 03 Jun 2019 02:41:43: 21000000 INFO @ Mon, 03 Jun 2019 02:41:43: 25000000 INFO @ Mon, 03 Jun 2019 02:41:46: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:41:46: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:41:46: #1 total tags in treatment: 25549184 INFO @ Mon, 03 Jun 2019 02:41:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:46: #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 02:41:46: #1 tags after filtering in treatment: 25549184 INFO @ Mon, 03 Jun 2019 02:41:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:46: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:47: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:41:47: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:41:47: #1 total tags in treatment: 25549184 INFO @ Mon, 03 Jun 2019 02:41:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:47: #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 02:41:47: #1 tags after filtering in treatment: 25549184 INFO @ Mon, 03 Jun 2019 02:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:47: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:48: #2 number of paired peaks: 5 WARNING @ Mon, 03 Jun 2019 02:41:48: Too few paired peaks (5) 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 02:41:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.05_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/SRX111814/SRX111814.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:41:50: #2 number of paired peaks: 5 WARNING @ Mon, 03 Jun 2019 02:41:50: Too few paired peaks (5) 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 02:41:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.20_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/SRX111814/SRX111814.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:41:52: 22000000 INFO @ Mon, 03 Jun 2019 02:42:01: 23000000 INFO @ Mon, 03 Jun 2019 02:42:11: 24000000 INFO @ Mon, 03 Jun 2019 02:42:20: 25000000 INFO @ Mon, 03 Jun 2019 02:42:24: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:42:24: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:42:24: #1 total tags in treatment: 25549184 INFO @ Mon, 03 Jun 2019 02:42:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:42:24: #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 02:42:25: #1 tags after filtering in treatment: 25549184 INFO @ Mon, 03 Jun 2019 02:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:42:25: #1 finished! INFO @ Mon, 03 Jun 2019 02:42:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:42:27: #2 number of paired peaks: 5 WARNING @ Mon, 03 Jun 2019 02:42:27: Too few paired peaks (5) 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 02:42:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.10_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/SRX111814/SRX111814.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX111814/SRX111814.10_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。