Job ID = 1298865 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:35:38 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' 2019-06-03T08:35:38 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/SRR1164480' 2019-06-03T08:35:47 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1164480' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T08:35:47 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T09:09:33 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 : 40,621,839 reads read : 40,621,839 reads written : 40,621,839 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: 00:22:50 40621839 reads; of these: 40621839 (100.00%) were unpaired; of these: 2403821 (5.92%) aligned 0 times 21964016 (54.07%) aligned exactly 1 time 16254002 (40.01%) aligned >1 times 94.08% overall alignment rate Time searching: 00:22:50 Overall time: 00:22:50 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 16 files... [bam_rmdupse_core] 14263290 / 38218018 = 0.3732 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 18:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.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 18:47:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:47:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.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 18:47:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:47:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.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 18:47:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:47:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:47:12: 1000000 INFO @ Mon, 03 Jun 2019 18:47:13: 1000000 INFO @ Mon, 03 Jun 2019 18:47:13: 1000000 INFO @ Mon, 03 Jun 2019 18:47:19: 2000000 INFO @ Mon, 03 Jun 2019 18:47:21: 2000000 INFO @ Mon, 03 Jun 2019 18:47:21: 2000000 INFO @ Mon, 03 Jun 2019 18:47:26: 3000000 INFO @ Mon, 03 Jun 2019 18:47:28: 3000000 INFO @ Mon, 03 Jun 2019 18:47:28: 3000000 INFO @ Mon, 03 Jun 2019 18:47:33: 4000000 INFO @ Mon, 03 Jun 2019 18:47:36: 4000000 INFO @ Mon, 03 Jun 2019 18:47:36: 4000000 INFO @ Mon, 03 Jun 2019 18:47:39: 5000000 INFO @ Mon, 03 Jun 2019 18:47:44: 5000000 INFO @ Mon, 03 Jun 2019 18:47:44: 5000000 INFO @ Mon, 03 Jun 2019 18:47:46: 6000000 INFO @ Mon, 03 Jun 2019 18:47:51: 6000000 INFO @ Mon, 03 Jun 2019 18:47:51: 6000000 INFO @ Mon, 03 Jun 2019 18:47:53: 7000000 INFO @ Mon, 03 Jun 2019 18:47:59: 7000000 INFO @ Mon, 03 Jun 2019 18:47:59: 7000000 INFO @ Mon, 03 Jun 2019 18:47:59: 8000000 INFO @ Mon, 03 Jun 2019 18:48:06: 8000000 INFO @ Mon, 03 Jun 2019 18:48:06: 9000000 INFO @ Mon, 03 Jun 2019 18:48:06: 8000000 INFO @ Mon, 03 Jun 2019 18:48:13: 10000000 INFO @ Mon, 03 Jun 2019 18:48:14: 9000000 INFO @ Mon, 03 Jun 2019 18:48:14: 9000000 INFO @ Mon, 03 Jun 2019 18:48:20: 11000000 INFO @ Mon, 03 Jun 2019 18:48:21: 10000000 INFO @ Mon, 03 Jun 2019 18:48:21: 10000000 INFO @ Mon, 03 Jun 2019 18:48:26: 12000000 INFO @ Mon, 03 Jun 2019 18:48:28: 11000000 INFO @ Mon, 03 Jun 2019 18:48:29: 11000000 INFO @ Mon, 03 Jun 2019 18:48:33: 13000000 INFO @ Mon, 03 Jun 2019 18:48:36: 12000000 INFO @ Mon, 03 Jun 2019 18:48:36: 12000000 INFO @ Mon, 03 Jun 2019 18:48:40: 14000000 INFO @ Mon, 03 Jun 2019 18:48:43: 13000000 INFO @ Mon, 03 Jun 2019 18:48:44: 13000000 INFO @ Mon, 03 Jun 2019 18:48:46: 15000000 INFO @ Mon, 03 Jun 2019 18:48:51: 14000000 INFO @ Mon, 03 Jun 2019 18:48:51: 14000000 INFO @ Mon, 03 Jun 2019 18:48:53: 16000000 INFO @ Mon, 03 Jun 2019 18:48:58: 15000000 INFO @ Mon, 03 Jun 2019 18:48:59: 15000000 INFO @ Mon, 03 Jun 2019 18:49:00: 17000000 INFO @ Mon, 03 Jun 2019 18:49:06: 16000000 INFO @ Mon, 03 Jun 2019 18:49:06: 16000000 INFO @ Mon, 03 Jun 2019 18:49:06: 18000000 INFO @ Mon, 03 Jun 2019 18:49:13: 19000000 INFO @ Mon, 03 Jun 2019 18:49:13: 17000000 INFO @ Mon, 03 Jun 2019 18:49:13: 17000000 INFO @ Mon, 03 Jun 2019 18:49:20: 20000000 INFO @ Mon, 03 Jun 2019 18:49:21: 18000000 INFO @ Mon, 03 Jun 2019 18:49:21: 18000000 INFO @ Mon, 03 Jun 2019 18:49:26: 21000000 INFO @ Mon, 03 Jun 2019 18:49:28: 19000000 INFO @ Mon, 03 Jun 2019 18:49:28: 19000000 INFO @ Mon, 03 Jun 2019 18:49:33: 22000000 INFO @ Mon, 03 Jun 2019 18:49:35: 20000000 INFO @ Mon, 03 Jun 2019 18:49:36: 20000000 INFO @ Mon, 03 Jun 2019 18:49:40: 23000000 INFO @ Mon, 03 Jun 2019 18:49:43: 21000000 INFO @ Mon, 03 Jun 2019 18:49:44: 21000000 INFO @ Mon, 03 Jun 2019 18:49:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:49:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:49:46: #1 total tags in treatment: 23954728 INFO @ Mon, 03 Jun 2019 18:49:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:49:46: #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 18:49:47: #1 tags after filtering in treatment: 23954728 INFO @ Mon, 03 Jun 2019 18:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:49:47: #1 finished! INFO @ Mon, 03 Jun 2019 18:49:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:49:49: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 18:49:49: Too few paired peaks (39) 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 18:49:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.10_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/SRX467056/SRX467056.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:49:50: 22000000 INFO @ Mon, 03 Jun 2019 18:49:51: 22000000 INFO @ Mon, 03 Jun 2019 18:49:57: 23000000 INFO @ Mon, 03 Jun 2019 18:49:58: 23000000 INFO @ Mon, 03 Jun 2019 18:50:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:50:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:50:04: #1 total tags in treatment: 23954728 INFO @ Mon, 03 Jun 2019 18:50:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:50:04: #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 18:50:04: #1 tags after filtering in treatment: 23954728 INFO @ Mon, 03 Jun 2019 18:50:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:50:04: #1 finished! INFO @ Mon, 03 Jun 2019 18:50:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:50:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:50:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:50:05: #1 total tags in treatment: 23954728 INFO @ Mon, 03 Jun 2019 18:50:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:50:05: #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 18:50:06: #1 tags after filtering in treatment: 23954728 INFO @ Mon, 03 Jun 2019 18:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:50:06: #1 finished! INFO @ Mon, 03 Jun 2019 18:50:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:50:07: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 18:50:07: Too few paired peaks (39) 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 18:50:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.05_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/SRX467056/SRX467056.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:50:08: #2 number of paired peaks: 39 WARNING @ Mon, 03 Jun 2019 18:50:08: Too few paired peaks (39) 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 18:50:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.20_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/SRX467056/SRX467056.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467056/SRX467056.20_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。