Job ID = 1309288 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:28:39 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 ) 2019-06-03T14:28:39 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 : 13,765,503 reads read : 27,531,006 reads written : 13,765,503 reads 0-length : 13,765,503 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: 00:12:50 13765503 reads; of these: 13765503 (100.00%) were unpaired; of these: 773594 (5.62%) aligned 0 times 11136333 (80.90%) aligned exactly 1 time 1855576 (13.48%) aligned >1 times 94.38% overall alignment rate Time searching: 00:12:50 Overall time: 00:12:51 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 12 files... [bam_rmdupse_core] 1955778 / 12991909 = 0.1505 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 23:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.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 23:51:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:51:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.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 23:51:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:51:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.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 23:51:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:51:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:51:35: 1000000 INFO @ Mon, 03 Jun 2019 23:51:37: 1000000 INFO @ Mon, 03 Jun 2019 23:51:38: 1000000 INFO @ Mon, 03 Jun 2019 23:51:45: 2000000 INFO @ Mon, 03 Jun 2019 23:51:48: 2000000 INFO @ Mon, 03 Jun 2019 23:51:51: 2000000 INFO @ Mon, 03 Jun 2019 23:51:54: 3000000 INFO @ Mon, 03 Jun 2019 23:51:59: 3000000 INFO @ Mon, 03 Jun 2019 23:52:03: 3000000 INFO @ Mon, 03 Jun 2019 23:52:04: 4000000 INFO @ Mon, 03 Jun 2019 23:52:09: 4000000 INFO @ Mon, 03 Jun 2019 23:52:14: 5000000 INFO @ Mon, 03 Jun 2019 23:52:15: 4000000 INFO @ Mon, 03 Jun 2019 23:52:20: 5000000 INFO @ Mon, 03 Jun 2019 23:52:24: 6000000 INFO @ Mon, 03 Jun 2019 23:52:26: 5000000 INFO @ Mon, 03 Jun 2019 23:52:31: 6000000 INFO @ Mon, 03 Jun 2019 23:52:33: 7000000 INFO @ Mon, 03 Jun 2019 23:52:37: 6000000 INFO @ Mon, 03 Jun 2019 23:52:42: 7000000 INFO @ Mon, 03 Jun 2019 23:52:43: 8000000 INFO @ Mon, 03 Jun 2019 23:52:48: 7000000 INFO @ Mon, 03 Jun 2019 23:52:53: 9000000 INFO @ Mon, 03 Jun 2019 23:52:53: 8000000 INFO @ Mon, 03 Jun 2019 23:52:59: 8000000 INFO @ Mon, 03 Jun 2019 23:53:03: 10000000 INFO @ Mon, 03 Jun 2019 23:53:04: 9000000 INFO @ Mon, 03 Jun 2019 23:53:10: 9000000 INFO @ Mon, 03 Jun 2019 23:53:12: 11000000 INFO @ Mon, 03 Jun 2019 23:53:13: #1 tag size is determined as 146 bps INFO @ Mon, 03 Jun 2019 23:53:13: #1 tag size = 146 INFO @ Mon, 03 Jun 2019 23:53:13: #1 total tags in treatment: 11036131 INFO @ Mon, 03 Jun 2019 23:53:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:53:13: #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 23:53:13: #1 tags after filtering in treatment: 11036131 INFO @ Mon, 03 Jun 2019 23:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:53:13: #1 finished! INFO @ Mon, 03 Jun 2019 23:53:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:53:14: #2 number of paired peaks: 2460 INFO @ Mon, 03 Jun 2019 23:53:14: start model_add_line... INFO @ Mon, 03 Jun 2019 23:53:14: start X-correlation... INFO @ Mon, 03 Jun 2019 23:53:14: end of X-cor INFO @ Mon, 03 Jun 2019 23:53:14: #2 finished! INFO @ Mon, 03 Jun 2019 23:53:14: #2 predicted fragment length is 176 bps INFO @ Mon, 03 Jun 2019 23:53:14: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 03 Jun 2019 23:53:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.05_model.r WARNING @ Mon, 03 Jun 2019 23:53:14: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:53:14: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Mon, 03 Jun 2019 23:53:14: #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 23:53:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:53:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:53:15: 10000000 INFO @ Mon, 03 Jun 2019 23:53:21: 10000000 INFO @ Mon, 03 Jun 2019 23:53:26: 11000000 INFO @ Mon, 03 Jun 2019 23:53:26: #1 tag size is determined as 146 bps INFO @ Mon, 03 Jun 2019 23:53:26: #1 tag size = 146 INFO @ Mon, 03 Jun 2019 23:53:26: #1 total tags in treatment: 11036131 INFO @ Mon, 03 Jun 2019 23:53:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:53:26: #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 23:53:27: #1 tags after filtering in treatment: 11036131 INFO @ Mon, 03 Jun 2019 23:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:53:27: #1 finished! INFO @ Mon, 03 Jun 2019 23:53:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:53:28: #2 number of paired peaks: 2460 INFO @ Mon, 03 Jun 2019 23:53:28: start model_add_line... INFO @ Mon, 03 Jun 2019 23:53:28: start X-correlation... INFO @ Mon, 03 Jun 2019 23:53:28: end of X-cor INFO @ Mon, 03 Jun 2019 23:53:28: #2 finished! INFO @ Mon, 03 Jun 2019 23:53:28: #2 predicted fragment length is 176 bps INFO @ Mon, 03 Jun 2019 23:53:28: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 03 Jun 2019 23:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.10_model.r WARNING @ Mon, 03 Jun 2019 23:53:28: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:53:28: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Mon, 03 Jun 2019 23:53:28: #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 23:53:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:53:31: 11000000 INFO @ Mon, 03 Jun 2019 23:53:32: #1 tag size is determined as 146 bps INFO @ Mon, 03 Jun 2019 23:53:32: #1 tag size = 146 INFO @ Mon, 03 Jun 2019 23:53:32: #1 total tags in treatment: 11036131 INFO @ Mon, 03 Jun 2019 23:53:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:53:32: #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 23:53:32: #1 tags after filtering in treatment: 11036131 INFO @ Mon, 03 Jun 2019 23:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:53:32: #1 finished! INFO @ Mon, 03 Jun 2019 23:53:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:53:33: #2 number of paired peaks: 2460 INFO @ Mon, 03 Jun 2019 23:53:33: start model_add_line... INFO @ Mon, 03 Jun 2019 23:53:33: start X-correlation... INFO @ Mon, 03 Jun 2019 23:53:33: end of X-cor INFO @ Mon, 03 Jun 2019 23:53:33: #2 finished! INFO @ Mon, 03 Jun 2019 23:53:33: #2 predicted fragment length is 176 bps INFO @ Mon, 03 Jun 2019 23:53:33: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 03 Jun 2019 23:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.20_model.r WARNING @ Mon, 03 Jun 2019 23:53:33: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:53:33: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Mon, 03 Jun 2019 23:53:33: #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 23:53:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:53:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:54:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.05_summits.bed INFO @ Mon, 03 Jun 2019 23:54:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (11162 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:54:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:54:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:54:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:54:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.10_summits.bed INFO @ Mon, 03 Jun 2019 23:54:20: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (7673 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:54:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:54:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:54:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864531/SRX864531.20_summits.bed INFO @ Mon, 03 Jun 2019 23:54:25: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4340 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。