Job ID = 1294727 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:50:20 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 ) 2019-06-03T00:50:21 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 ) 2019-06-03T00:50:21 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 ) 2019-06-03T00:50:21 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 ) 2019-06-03T00:50:21 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 ) 2019-06-03T00:51:02 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 ) 2019-06-03T00:53:22 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 ) 2019-06-03T00:53:22 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 : 13,389,851 reads read : 13,389,851 reads written : 13,389,851 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: 00:07:43 13389851 reads; of these: 13389851 (100.00%) were unpaired; of these: 780807 (5.83%) aligned 0 times 8324651 (62.17%) aligned exactly 1 time 4284393 (32.00%) aligned >1 times 94.17% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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] 1578280 / 12609044 = 0.1252 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 10:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.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 10:06:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:06:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.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 10:06:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:06:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.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 10:06:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:06:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:06:37: 1000000 INFO @ Mon, 03 Jun 2019 10:06:38: 1000000 INFO @ Mon, 03 Jun 2019 10:06:38: 1000000 INFO @ Mon, 03 Jun 2019 10:06:46: 2000000 INFO @ Mon, 03 Jun 2019 10:06:47: 2000000 INFO @ Mon, 03 Jun 2019 10:06:48: 2000000 INFO @ Mon, 03 Jun 2019 10:06:55: 3000000 INFO @ Mon, 03 Jun 2019 10:06:58: 3000000 INFO @ Mon, 03 Jun 2019 10:06:58: 3000000 INFO @ Mon, 03 Jun 2019 10:07:04: 4000000 INFO @ Mon, 03 Jun 2019 10:07:07: 4000000 INFO @ Mon, 03 Jun 2019 10:07:08: 4000000 INFO @ Mon, 03 Jun 2019 10:07:12: 5000000 INFO @ Mon, 03 Jun 2019 10:07:17: 5000000 INFO @ Mon, 03 Jun 2019 10:07:19: 5000000 INFO @ Mon, 03 Jun 2019 10:07:22: 6000000 INFO @ Mon, 03 Jun 2019 10:07:27: 6000000 INFO @ Mon, 03 Jun 2019 10:07:29: 6000000 INFO @ Mon, 03 Jun 2019 10:07:31: 7000000 INFO @ Mon, 03 Jun 2019 10:07:37: 7000000 INFO @ Mon, 03 Jun 2019 10:07:39: 7000000 INFO @ Mon, 03 Jun 2019 10:07:40: 8000000 INFO @ Mon, 03 Jun 2019 10:07:47: 8000000 INFO @ Mon, 03 Jun 2019 10:07:48: 9000000 INFO @ Mon, 03 Jun 2019 10:07:49: 8000000 INFO @ Mon, 03 Jun 2019 10:07:56: 9000000 INFO @ Mon, 03 Jun 2019 10:07:57: 10000000 INFO @ Mon, 03 Jun 2019 10:07:59: 9000000 INFO @ Mon, 03 Jun 2019 10:08:05: 11000000 INFO @ Mon, 03 Jun 2019 10:08:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:08:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:08:06: #1 total tags in treatment: 11030764 INFO @ Mon, 03 Jun 2019 10:08:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:08:06: #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 10:08:06: #1 tags after filtering in treatment: 11030764 INFO @ Mon, 03 Jun 2019 10:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:08:06: #1 finished! INFO @ Mon, 03 Jun 2019 10:08:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:08:06: 10000000 INFO @ Mon, 03 Jun 2019 10:08:07: #2 number of paired peaks: 476 WARNING @ Mon, 03 Jun 2019 10:08:07: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 03 Jun 2019 10:08:07: start model_add_line... INFO @ Mon, 03 Jun 2019 10:08:07: start X-correlation... INFO @ Mon, 03 Jun 2019 10:08:07: end of X-cor INFO @ Mon, 03 Jun 2019 10:08:07: #2 finished! INFO @ Mon, 03 Jun 2019 10:08:07: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 10:08:07: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 10:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.20_model.r WARNING @ Mon, 03 Jun 2019 10:08:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:08:08: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 10:08:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:08:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:08:09: 10000000 INFO @ Mon, 03 Jun 2019 10:08:16: 11000000 INFO @ Mon, 03 Jun 2019 10:08:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:08:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:08:16: #1 total tags in treatment: 11030764 INFO @ Mon, 03 Jun 2019 10:08:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:08:16: #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 10:08:16: #1 tags after filtering in treatment: 11030764 INFO @ Mon, 03 Jun 2019 10:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:08:16: #1 finished! INFO @ Mon, 03 Jun 2019 10:08:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:08:18: #2 number of paired peaks: 476 WARNING @ Mon, 03 Jun 2019 10:08:18: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 03 Jun 2019 10:08:18: start model_add_line... INFO @ Mon, 03 Jun 2019 10:08:18: start X-correlation... INFO @ Mon, 03 Jun 2019 10:08:18: end of X-cor INFO @ Mon, 03 Jun 2019 10:08:18: #2 finished! INFO @ Mon, 03 Jun 2019 10:08:18: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 10:08:18: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 10:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.10_model.r WARNING @ Mon, 03 Jun 2019 10:08:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:08:18: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 10:08:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:08:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:08:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:08:19: 11000000 INFO @ Mon, 03 Jun 2019 10:08:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:08:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:08:19: #1 total tags in treatment: 11030764 INFO @ Mon, 03 Jun 2019 10:08:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:08:19: #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 10:08:19: #1 tags after filtering in treatment: 11030764 INFO @ Mon, 03 Jun 2019 10:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:08:19: #1 finished! INFO @ Mon, 03 Jun 2019 10:08:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:08:20: #2 number of paired peaks: 476 WARNING @ Mon, 03 Jun 2019 10:08:20: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 03 Jun 2019 10:08:20: start model_add_line... INFO @ Mon, 03 Jun 2019 10:08:21: start X-correlation... INFO @ Mon, 03 Jun 2019 10:08:21: end of X-cor INFO @ Mon, 03 Jun 2019 10:08:21: #2 finished! INFO @ Mon, 03 Jun 2019 10:08:21: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 10:08:21: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 10:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.05_model.r WARNING @ Mon, 03 Jun 2019 10:08:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:08:21: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 10:08:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:08:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:08:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:08:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:08:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.20_summits.bed INFO @ Mon, 03 Jun 2019 10:08:59: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1345 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.10_summits.bed INFO @ Mon, 03 Jun 2019 10:09:08: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1780 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287842/SRX287842.05_summits.bed INFO @ Mon, 03 Jun 2019 10:09:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2053 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。