Job ID = 1298438 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:20:43 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' 2019-06-03T08:20:43 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/sra36/SRR/001137/SRR1164457' 2019-06-03T08:20:43 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' 2019-06-03T08:20:43 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/sra36/SRR/001137/SRR1164457' 2019-06-03T08:20:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1164457' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T08:20:52 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T08:20:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1164457' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T08:20:52 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T08:29:54 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 ) 2019-06-03T08:38:31 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 : 16,584,363 reads read : 16,584,363 reads written : 16,584,363 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: 00:03:24 16584363 reads; of these: 16584363 (100.00%) were unpaired; of these: 6341730 (38.24%) aligned 0 times 9024662 (54.42%) aligned exactly 1 time 1217971 (7.34%) aligned >1 times 61.76% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 1235425 / 10242633 = 0.1206 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 17:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.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 17:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.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 17:47:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:47:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:47:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:47:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.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 17:47:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:47:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:47:48: 1000000 INFO @ Mon, 03 Jun 2019 17:47:49: 1000000 INFO @ Mon, 03 Jun 2019 17:47:49: 1000000 INFO @ Mon, 03 Jun 2019 17:47:55: 2000000 INFO @ Mon, 03 Jun 2019 17:47:58: 2000000 INFO @ Mon, 03 Jun 2019 17:47:58: 2000000 INFO @ Mon, 03 Jun 2019 17:48:02: 3000000 INFO @ Mon, 03 Jun 2019 17:48:06: 3000000 INFO @ Mon, 03 Jun 2019 17:48:06: 3000000 INFO @ Mon, 03 Jun 2019 17:48:09: 4000000 INFO @ Mon, 03 Jun 2019 17:48:15: 4000000 INFO @ Mon, 03 Jun 2019 17:48:15: 4000000 INFO @ Mon, 03 Jun 2019 17:48:16: 5000000 INFO @ Mon, 03 Jun 2019 17:48:23: 5000000 INFO @ Mon, 03 Jun 2019 17:48:23: 5000000 INFO @ Mon, 03 Jun 2019 17:48:23: 6000000 INFO @ Mon, 03 Jun 2019 17:48:30: 7000000 INFO @ Mon, 03 Jun 2019 17:48:31: 6000000 INFO @ Mon, 03 Jun 2019 17:48:31: 6000000 INFO @ Mon, 03 Jun 2019 17:48:37: 8000000 INFO @ Mon, 03 Jun 2019 17:48:39: 7000000 INFO @ Mon, 03 Jun 2019 17:48:39: 7000000 INFO @ Mon, 03 Jun 2019 17:48:44: 9000000 INFO @ Mon, 03 Jun 2019 17:48:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:48:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:48:45: #1 total tags in treatment: 9007208 INFO @ Mon, 03 Jun 2019 17:48:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:48:45: #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 17:48:45: #1 tags after filtering in treatment: 9007208 INFO @ Mon, 03 Jun 2019 17:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:48:45: #1 finished! INFO @ Mon, 03 Jun 2019 17:48:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:48:46: #2 number of paired peaks: 30 WARNING @ Mon, 03 Jun 2019 17:48:46: Too few paired peaks (30) 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 17:48:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.10_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/SRX467033/SRX467033.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:48:47: 8000000 INFO @ Mon, 03 Jun 2019 17:48:47: 8000000 INFO @ Mon, 03 Jun 2019 17:48:56: 9000000 INFO @ Mon, 03 Jun 2019 17:48:56: 9000000 INFO @ Mon, 03 Jun 2019 17:48:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:48:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:48:56: #1 total tags in treatment: 9007208 INFO @ Mon, 03 Jun 2019 17:48:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:48:56: #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 17:48:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:48:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:48:56: #1 total tags in treatment: 9007208 INFO @ Mon, 03 Jun 2019 17:48:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:48:56: #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 17:48:56: #1 tags after filtering in treatment: 9007208 INFO @ Mon, 03 Jun 2019 17:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:48:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:48:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:48:56: #1 tags after filtering in treatment: 9007208 INFO @ Mon, 03 Jun 2019 17:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:48:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:48:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:48:57: #2 number of paired peaks: 30 WARNING @ Mon, 03 Jun 2019 17:48:57: Too few paired peaks (30) 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 17:48:57: Process for pairing-model is terminated! INFO @ Mon, 03 Jun 2019 17:48:57: #2 number of paired peaks: 30 WARNING @ Mon, 03 Jun 2019 17:48:57: Too few paired peaks (30) 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 17:48:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.20_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/SRX467033/SRX467033.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.05_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/SRX467033/SRX467033.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467033/SRX467033.05_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。