Job ID = 3785857 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:35:38 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 ) 2019-11-01T05:35:38 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( UNKNOWN ERROR CODE (004NET - Reading information from the socket failed ) 2019-11-01T05:35:38 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( UNKNOWN ERROR CODE (004NET - Reading information from the socket failed ) 2019-11-01T05:35:38 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 ) 2019-11-01T05:35:39 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 ) 2019-11-01T05:35:39 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 ) 2019-11-01T05:38:04 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 ) 2019-11-01T05:39:29 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 ) 2019-11-01T05:41:13 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 ) 2019-11-01T05:41:13 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 ) 2019-11-01T05:41:13 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 ) 2019-11-01T05:41:13 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 ) 2019-11-01T05:42:44 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 ) 2019-11-01T05:44:05 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 ) 2019-11-01T05:44:05 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 ) 2019-11-01T05:44:54 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 ) 2019-11-01T05:46:16 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 ) spots read : 12,776,510 reads read : 12,776,510 reads written : 12,776,510 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: 00:03:36 12776510 reads; of these: 12776510 (100.00%) were unpaired; of these: 1020355 (7.99%) aligned 0 times 10008003 (78.33%) aligned exactly 1 time 1748152 (13.68%) aligned >1 times 92.01% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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 8 files... [bam_rmdupse_core] 982094 / 11756155 = 0.0835 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.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 @ Fri, 01 Nov 2019 14:56:20: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:56:20: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:56:30: 1000000 INFO @ Fri, 01 Nov 2019 14:56:39: 2000000 INFO @ Fri, 01 Nov 2019 14:56:47: 3000000 INFO @ Fri, 01 Nov 2019 14:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.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 @ Fri, 01 Nov 2019 14:56:49: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:56:49: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:56:56: 4000000 INFO @ Fri, 01 Nov 2019 14:56:59: 1000000 INFO @ Fri, 01 Nov 2019 14:57:05: 5000000 INFO @ Fri, 01 Nov 2019 14:57:09: 2000000 INFO @ Fri, 01 Nov 2019 14:57:14: 6000000 BedGraph に変換中... INFO @ Fri, 01 Nov 2019 14:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.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 @ Fri, 01 Nov 2019 14:57:19: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:57:19: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:57:19: 3000000 INFO @ Fri, 01 Nov 2019 14:57:23: 7000000 INFO @ Fri, 01 Nov 2019 14:57:29: 1000000 INFO @ Fri, 01 Nov 2019 14:57:30: 4000000 INFO @ Fri, 01 Nov 2019 14:57:32: 8000000 INFO @ Fri, 01 Nov 2019 14:57:37: 2000000 INFO @ Fri, 01 Nov 2019 14:57:40: 5000000 INFO @ Fri, 01 Nov 2019 14:57:41: 9000000 INFO @ Fri, 01 Nov 2019 14:57:45: 3000000 INFO @ Fri, 01 Nov 2019 14:57:50: 10000000 INFO @ Fri, 01 Nov 2019 14:57:50: 6000000 INFO @ Fri, 01 Nov 2019 14:57:52: 4000000 INFO @ Fri, 01 Nov 2019 14:57:56: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:57:56: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:57:56: #1 total tags in treatment: 10774061 INFO @ Fri, 01 Nov 2019 14:57:56: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:57:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:57:57: #1 tags after filtering in treatment: 10774061 INFO @ Fri, 01 Nov 2019 14:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:57:57: #1 finished! INFO @ Fri, 01 Nov 2019 14:57:57: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:57:58: #2 number of paired peaks: 81 WARNING @ Fri, 01 Nov 2019 14:57:58: Too few paired peaks (81) 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, 01 Nov 2019 14:57:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.05_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/SRX5247952/SRX5247952.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:58:00: 5000000 INFO @ Fri, 01 Nov 2019 14:58:01: 7000000 INFO @ Fri, 01 Nov 2019 14:58:08: 6000000 INFO @ Fri, 01 Nov 2019 14:58:11: 8000000 INFO @ Fri, 01 Nov 2019 14:58:16: 7000000 INFO @ Fri, 01 Nov 2019 14:58:21: 9000000 INFO @ Fri, 01 Nov 2019 14:58:23: 8000000 INFO @ Fri, 01 Nov 2019 14:58:31: 9000000 INFO @ Fri, 01 Nov 2019 14:58:31: 10000000 INFO @ Fri, 01 Nov 2019 14:58:39: 10000000 INFO @ Fri, 01 Nov 2019 14:58:39: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:58:39: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:58:39: #1 total tags in treatment: 10774061 INFO @ Fri, 01 Nov 2019 14:58:39: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:58:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:58:39: #1 tags after filtering in treatment: 10774061 INFO @ Fri, 01 Nov 2019 14:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:58:39: #1 finished! INFO @ Fri, 01 Nov 2019 14:58:39: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:58:40: #2 number of paired peaks: 81 WARNING @ Fri, 01 Nov 2019 14:58:40: Too few paired peaks (81) 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, 01 Nov 2019 14:58:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.10_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/SRX5247952/SRX5247952.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:58:45: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:58:45: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:58:45: #1 total tags in treatment: 10774061 INFO @ Fri, 01 Nov 2019 14:58:45: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:58:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:58:45: #1 tags after filtering in treatment: 10774061 INFO @ Fri, 01 Nov 2019 14:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:58:45: #1 finished! INFO @ Fri, 01 Nov 2019 14:58:45: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:58:46: #2 number of paired peaks: 81 WARNING @ Fri, 01 Nov 2019 14:58:46: Too few paired peaks (81) 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, 01 Nov 2019 14:58:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.20_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/dm3/SRX5247952/SRX5247952.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX5247952/SRX5247952.20_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。