Job ID = 1298462 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:21:08 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' 2019-06-03T08:21:08 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/SRR1164459' 2019-06-03T08:21:12 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' 2019-06-03T08:21:12 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/SRR1164459' 2019-06-03T08:21:12 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR1164459', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T08:22:05 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 ) spots read : 17,765,478 reads read : 17,765,478 reads written : 17,765,478 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: 00:05:19 17765478 reads; of these: 17765478 (100.00%) were unpaired; of these: 535897 (3.02%) aligned 0 times 14657731 (82.51%) aligned exactly 1 time 2571850 (14.48%) aligned >1 times 96.98% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 2660215 / 17229581 = 0.1544 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 17:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.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 17:41:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:41:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.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 17:41:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:41:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.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 17:41:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:41:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:41:40: 1000000 INFO @ Mon, 03 Jun 2019 17:41:42: 1000000 INFO @ Mon, 03 Jun 2019 17:41:42: 1000000 INFO @ Mon, 03 Jun 2019 17:41:47: 2000000 INFO @ Mon, 03 Jun 2019 17:41:51: 2000000 INFO @ Mon, 03 Jun 2019 17:41:52: 2000000 INFO @ Mon, 03 Jun 2019 17:41:54: 3000000 INFO @ Mon, 03 Jun 2019 17:42:01: 3000000 INFO @ Mon, 03 Jun 2019 17:42:02: 4000000 INFO @ Mon, 03 Jun 2019 17:42:02: 3000000 INFO @ Mon, 03 Jun 2019 17:42:09: 5000000 INFO @ Mon, 03 Jun 2019 17:42:10: 4000000 INFO @ Mon, 03 Jun 2019 17:42:12: 4000000 INFO @ Mon, 03 Jun 2019 17:42:17: 6000000 INFO @ Mon, 03 Jun 2019 17:42:19: 5000000 INFO @ Mon, 03 Jun 2019 17:42:22: 5000000 INFO @ Mon, 03 Jun 2019 17:42:24: 7000000 INFO @ Mon, 03 Jun 2019 17:42:29: 6000000 INFO @ Mon, 03 Jun 2019 17:42:32: 8000000 INFO @ Mon, 03 Jun 2019 17:42:32: 6000000 INFO @ Mon, 03 Jun 2019 17:42:38: 7000000 INFO @ Mon, 03 Jun 2019 17:42:39: 9000000 INFO @ Mon, 03 Jun 2019 17:42:41: 7000000 INFO @ Mon, 03 Jun 2019 17:42:46: 10000000 INFO @ Mon, 03 Jun 2019 17:42:48: 8000000 INFO @ Mon, 03 Jun 2019 17:42:51: 8000000 INFO @ Mon, 03 Jun 2019 17:42:54: 11000000 INFO @ Mon, 03 Jun 2019 17:42:57: 9000000 INFO @ Mon, 03 Jun 2019 17:43:01: 9000000 INFO @ Mon, 03 Jun 2019 17:43:01: 12000000 INFO @ Mon, 03 Jun 2019 17:43:06: 10000000 INFO @ Mon, 03 Jun 2019 17:43:09: 13000000 INFO @ Mon, 03 Jun 2019 17:43:11: 10000000 INFO @ Mon, 03 Jun 2019 17:43:16: 11000000 INFO @ Mon, 03 Jun 2019 17:43:16: 14000000 INFO @ Mon, 03 Jun 2019 17:43:20: 11000000 INFO @ Mon, 03 Jun 2019 17:43:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:43:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:43:21: #1 total tags in treatment: 14569366 INFO @ Mon, 03 Jun 2019 17:43:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:43:21: #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 17:43:21: #1 tags after filtering in treatment: 14569366 INFO @ Mon, 03 Jun 2019 17:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:43:21: #1 finished! INFO @ Mon, 03 Jun 2019 17:43:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:43:22: #2 number of paired peaks: 33 WARNING @ Mon, 03 Jun 2019 17:43:22: Too few paired peaks (33) 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 17:43:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.05_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/SRX467035/SRX467035.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:43:25: 12000000 INFO @ Mon, 03 Jun 2019 17:43:30: 12000000 INFO @ Mon, 03 Jun 2019 17:43:35: 13000000 INFO @ Mon, 03 Jun 2019 17:43:40: 13000000 INFO @ Mon, 03 Jun 2019 17:43:44: 14000000 INFO @ Mon, 03 Jun 2019 17:43:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:43:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:43:49: #1 total tags in treatment: 14569366 INFO @ Mon, 03 Jun 2019 17:43:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:43:49: #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 17:43:50: #1 tags after filtering in treatment: 14569366 INFO @ Mon, 03 Jun 2019 17:43:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:43:50: #1 finished! INFO @ Mon, 03 Jun 2019 17:43:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:43:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:43:50: 14000000 INFO @ Mon, 03 Jun 2019 17:43:51: #2 number of paired peaks: 33 WARNING @ Mon, 03 Jun 2019 17:43:51: Too few paired peaks (33) 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 17:43:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.10_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/SRX467035/SRX467035.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:43:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:43:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:43:55: #1 total tags in treatment: 14569366 INFO @ Mon, 03 Jun 2019 17:43:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:43:55: #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 17:43:56: #1 tags after filtering in treatment: 14569366 INFO @ Mon, 03 Jun 2019 17:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:43:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:43:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:43:57: #2 number of paired peaks: 33 WARNING @ Mon, 03 Jun 2019 17:43:57: Too few paired peaks (33) 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 17:43:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.20_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/SRX467035/SRX467035.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX467035/SRX467035.20_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。