Job ID = 1294416 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:37:16 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 : 21,149,406 reads read : 21,149,406 reads written : 21,149,406 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: 00:09:35 21149406 reads; of these: 21149406 (100.00%) were unpaired; of these: 1292870 (6.11%) aligned 0 times 13945510 (65.94%) aligned exactly 1 time 5911026 (27.95%) aligned >1 times 93.89% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 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] 4303106 / 19856536 = 0.2167 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 07:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.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 07:54:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:54:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.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 07:54:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:54:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.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 07:54:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:54:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:54:18: 1000000 INFO @ Mon, 03 Jun 2019 07:54:18: 1000000 INFO @ Mon, 03 Jun 2019 07:54:19: 1000000 INFO @ Mon, 03 Jun 2019 07:54:26: 2000000 INFO @ Mon, 03 Jun 2019 07:54:26: 2000000 INFO @ Mon, 03 Jun 2019 07:54:27: 2000000 INFO @ Mon, 03 Jun 2019 07:54:34: 3000000 INFO @ Mon, 03 Jun 2019 07:54:34: 3000000 INFO @ Mon, 03 Jun 2019 07:54:36: 3000000 INFO @ Mon, 03 Jun 2019 07:54:42: 4000000 INFO @ Mon, 03 Jun 2019 07:54:42: 4000000 INFO @ Mon, 03 Jun 2019 07:54:44: 4000000 INFO @ Mon, 03 Jun 2019 07:54:49: 5000000 INFO @ Mon, 03 Jun 2019 07:54:49: 5000000 INFO @ Mon, 03 Jun 2019 07:54:52: 5000000 INFO @ Mon, 03 Jun 2019 07:54:57: 6000000 INFO @ Mon, 03 Jun 2019 07:54:57: 6000000 INFO @ Mon, 03 Jun 2019 07:55:00: 6000000 INFO @ Mon, 03 Jun 2019 07:55:05: 7000000 INFO @ Mon, 03 Jun 2019 07:55:05: 7000000 INFO @ Mon, 03 Jun 2019 07:55:08: 7000000 INFO @ Mon, 03 Jun 2019 07:55:13: 8000000 INFO @ Mon, 03 Jun 2019 07:55:13: 8000000 INFO @ Mon, 03 Jun 2019 07:55:17: 8000000 INFO @ Mon, 03 Jun 2019 07:55:21: 9000000 INFO @ Mon, 03 Jun 2019 07:55:21: 9000000 INFO @ Mon, 03 Jun 2019 07:55:25: 9000000 INFO @ Mon, 03 Jun 2019 07:55:29: 10000000 INFO @ Mon, 03 Jun 2019 07:55:29: 10000000 INFO @ Mon, 03 Jun 2019 07:55:33: 10000000 INFO @ Mon, 03 Jun 2019 07:55:36: 11000000 INFO @ Mon, 03 Jun 2019 07:55:36: 11000000 INFO @ Mon, 03 Jun 2019 07:55:41: 11000000 INFO @ Mon, 03 Jun 2019 07:55:44: 12000000 INFO @ Mon, 03 Jun 2019 07:55:44: 12000000 INFO @ Mon, 03 Jun 2019 07:55:49: 12000000 INFO @ Mon, 03 Jun 2019 07:55:52: 13000000 INFO @ Mon, 03 Jun 2019 07:55:52: 13000000 INFO @ Mon, 03 Jun 2019 07:55:58: 13000000 INFO @ Mon, 03 Jun 2019 07:56:00: 14000000 INFO @ Mon, 03 Jun 2019 07:56:00: 14000000 INFO @ Mon, 03 Jun 2019 07:56:06: 14000000 INFO @ Mon, 03 Jun 2019 07:56:08: 15000000 INFO @ Mon, 03 Jun 2019 07:56:08: 15000000 INFO @ Mon, 03 Jun 2019 07:56:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:56:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:56:12: #1 total tags in treatment: 15553430 INFO @ Mon, 03 Jun 2019 07:56:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:56:12: #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 07:56:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:56:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:56:13: #1 total tags in treatment: 15553430 INFO @ Mon, 03 Jun 2019 07:56:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:56:13: #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 07:56:13: #1 tags after filtering in treatment: 15553430 INFO @ Mon, 03 Jun 2019 07:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:56:13: #1 finished! INFO @ Mon, 03 Jun 2019 07:56:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:56:13: #1 tags after filtering in treatment: 15553430 INFO @ Mon, 03 Jun 2019 07:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:56:13: #1 finished! INFO @ Mon, 03 Jun 2019 07:56:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:56:14: 15000000 INFO @ Mon, 03 Jun 2019 07:56:14: #2 number of paired peaks: 208 WARNING @ Mon, 03 Jun 2019 07:56:14: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 03 Jun 2019 07:56:14: start model_add_line... INFO @ Mon, 03 Jun 2019 07:56:14: #2 number of paired peaks: 208 WARNING @ Mon, 03 Jun 2019 07:56:14: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 03 Jun 2019 07:56:14: start model_add_line... INFO @ Mon, 03 Jun 2019 07:56:14: start X-correlation... INFO @ Mon, 03 Jun 2019 07:56:14: end of X-cor INFO @ Mon, 03 Jun 2019 07:56:14: #2 finished! INFO @ Mon, 03 Jun 2019 07:56:14: #2 predicted fragment length is 97 bps INFO @ Mon, 03 Jun 2019 07:56:14: #2 alternative fragment length(s) may be 97 bps INFO @ Mon, 03 Jun 2019 07:56:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.10_model.r WARNING @ Mon, 03 Jun 2019 07:56:14: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:56:14: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Mon, 03 Jun 2019 07:56:14: #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 07:56:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:56:14: start X-correlation... INFO @ Mon, 03 Jun 2019 07:56:14: end of X-cor INFO @ Mon, 03 Jun 2019 07:56:14: #2 finished! INFO @ Mon, 03 Jun 2019 07:56:14: #2 predicted fragment length is 97 bps INFO @ Mon, 03 Jun 2019 07:56:14: #2 alternative fragment length(s) may be 97 bps INFO @ Mon, 03 Jun 2019 07:56:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.05_model.r WARNING @ Mon, 03 Jun 2019 07:56:14: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:56:14: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Mon, 03 Jun 2019 07:56:14: #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 07:56:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:56:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:56:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:56:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:56:18: #1 total tags in treatment: 15553430 INFO @ Mon, 03 Jun 2019 07:56:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:56:18: #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 07:56:19: #1 tags after filtering in treatment: 15553430 INFO @ Mon, 03 Jun 2019 07:56:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:56:19: #1 finished! INFO @ Mon, 03 Jun 2019 07:56:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:56:20: #2 number of paired peaks: 208 WARNING @ Mon, 03 Jun 2019 07:56:20: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Mon, 03 Jun 2019 07:56:20: start model_add_line... INFO @ Mon, 03 Jun 2019 07:56:20: start X-correlation... INFO @ Mon, 03 Jun 2019 07:56:20: end of X-cor INFO @ Mon, 03 Jun 2019 07:56:20: #2 finished! INFO @ Mon, 03 Jun 2019 07:56:20: #2 predicted fragment length is 97 bps INFO @ Mon, 03 Jun 2019 07:56:20: #2 alternative fragment length(s) may be 97 bps INFO @ Mon, 03 Jun 2019 07:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.20_model.r WARNING @ Mon, 03 Jun 2019 07:56:20: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:56:20: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Mon, 03 Jun 2019 07:56:20: #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 07:56:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:56:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:56:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:57:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:57:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:57:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.05_summits.bed INFO @ Mon, 03 Jun 2019 07:57:16: Done! INFO @ Mon, 03 Jun 2019 07:57:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:57:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.10_summits.bed INFO @ Mon, 03 Jun 2019 07:57:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3954 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2524 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287588/SRX287588.20_summits.bed INFO @ Mon, 03 Jun 2019 07:57:21: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1436 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。