Job ID = 1294550 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:45:29 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T23:45:29 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra12/SRR/000849/SRR869925' 2019-06-02T23:45:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869925' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:47:23 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 ) 2019-06-02T23:47:37 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 ) 2019-06-02T23:47:37 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 ) 2019-06-02T23:49:13 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 ) 2019-06-02T23:49:36 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 ) 2019-06-02T23:49:36 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 ) 2019-06-02T23:50:44 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 : 17,631,207 reads read : 17,631,207 reads written : 17,631,207 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: 00:04:37 17631207 reads; of these: 17631207 (100.00%) were unpaired; of these: 968746 (5.49%) aligned 0 times 14880083 (84.40%) aligned exactly 1 time 1782378 (10.11%) aligned >1 times 94.51% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 1470496 / 16662461 = 0.0883 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 09:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.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 09:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.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 09:06:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:06:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:06:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:06:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.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 09:06:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:06:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:06:44: 1000000 INFO @ Mon, 03 Jun 2019 09:06:44: 1000000 INFO @ Mon, 03 Jun 2019 09:06:46: 1000000 INFO @ Mon, 03 Jun 2019 09:06:51: 2000000 INFO @ Mon, 03 Jun 2019 09:06:51: 2000000 INFO @ Mon, 03 Jun 2019 09:06:56: 2000000 INFO @ Mon, 03 Jun 2019 09:06:58: 3000000 INFO @ Mon, 03 Jun 2019 09:06:58: 3000000 INFO @ Mon, 03 Jun 2019 09:07:06: 4000000 INFO @ Mon, 03 Jun 2019 09:07:06: 3000000 INFO @ Mon, 03 Jun 2019 09:07:06: 4000000 INFO @ Mon, 03 Jun 2019 09:07:13: 5000000 INFO @ Mon, 03 Jun 2019 09:07:13: 5000000 INFO @ Mon, 03 Jun 2019 09:07:15: 4000000 INFO @ Mon, 03 Jun 2019 09:07:20: 6000000 INFO @ Mon, 03 Jun 2019 09:07:21: 6000000 INFO @ Mon, 03 Jun 2019 09:07:25: 5000000 INFO @ Mon, 03 Jun 2019 09:07:28: 7000000 INFO @ Mon, 03 Jun 2019 09:07:28: 7000000 INFO @ Mon, 03 Jun 2019 09:07:35: 6000000 INFO @ Mon, 03 Jun 2019 09:07:36: 8000000 INFO @ Mon, 03 Jun 2019 09:07:36: 8000000 INFO @ Mon, 03 Jun 2019 09:07:45: 9000000 INFO @ Mon, 03 Jun 2019 09:07:45: 9000000 INFO @ Mon, 03 Jun 2019 09:07:45: 7000000 INFO @ Mon, 03 Jun 2019 09:07:53: 10000000 INFO @ Mon, 03 Jun 2019 09:07:53: 10000000 INFO @ Mon, 03 Jun 2019 09:07:56: 8000000 INFO @ Mon, 03 Jun 2019 09:08:01: 11000000 INFO @ Mon, 03 Jun 2019 09:08:02: 11000000 INFO @ Mon, 03 Jun 2019 09:08:07: 9000000 INFO @ Mon, 03 Jun 2019 09:08:09: 12000000 INFO @ Mon, 03 Jun 2019 09:08:10: 12000000 INFO @ Mon, 03 Jun 2019 09:08:17: 13000000 INFO @ Mon, 03 Jun 2019 09:08:18: 10000000 INFO @ Mon, 03 Jun 2019 09:08:18: 13000000 INFO @ Mon, 03 Jun 2019 09:08:25: 14000000 INFO @ Mon, 03 Jun 2019 09:08:26: 14000000 INFO @ Mon, 03 Jun 2019 09:08:28: 11000000 INFO @ Mon, 03 Jun 2019 09:08:33: 15000000 INFO @ Mon, 03 Jun 2019 09:08:33: 15000000 INFO @ Mon, 03 Jun 2019 09:08:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:08:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:08:34: #1 total tags in treatment: 15191965 INFO @ Mon, 03 Jun 2019 09:08:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:08:34: #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 09:08:34: #1 tags after filtering in treatment: 15191965 INFO @ Mon, 03 Jun 2019 09:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:08:34: #1 finished! INFO @ Mon, 03 Jun 2019 09:08:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:08:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:08:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:08:35: #1 total tags in treatment: 15191965 INFO @ Mon, 03 Jun 2019 09:08:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:08:35: #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 09:08:35: #1 tags after filtering in treatment: 15191965 INFO @ Mon, 03 Jun 2019 09:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:08:35: #1 finished! INFO @ Mon, 03 Jun 2019 09:08:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:08:36: #2 number of paired peaks: 1 WARNING @ Mon, 03 Jun 2019 09:08:36: Too few paired peaks (1) 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 09:08:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.05_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/SRX287736/SRX287736.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:08:37: #2 number of paired peaks: 1 WARNING @ Mon, 03 Jun 2019 09:08:37: Too few paired peaks (1) 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 09:08:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.10_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/dm3/SRX287736/SRX287736.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:08:38: 12000000 INFO @ Mon, 03 Jun 2019 09:08:48: 13000000 INFO @ Mon, 03 Jun 2019 09:08:57: 14000000 INFO @ Mon, 03 Jun 2019 09:09:07: 15000000 INFO @ Mon, 03 Jun 2019 09:09:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:09:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:09:09: #1 total tags in treatment: 15191965 INFO @ Mon, 03 Jun 2019 09:09:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:09:09: #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 09:09:09: #1 tags after filtering in treatment: 15191965 INFO @ Mon, 03 Jun 2019 09:09:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:09:09: #1 finished! INFO @ Mon, 03 Jun 2019 09:09:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:09:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:09:10: #2 number of paired peaks: 1 WARNING @ Mon, 03 Jun 2019 09:09:10: Too few paired peaks (1) 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 09:09:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.20_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/SRX287736/SRX287736.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX287736/SRX287736.20_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。