Job ID = 4178485 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:31:08 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 : 23,764,924 reads read : 23,764,924 reads written : 23,764,924 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:44 23764924 reads; of these: 23764924 (100.00%) were unpaired; of these: 559661 (2.35%) aligned 0 times 19247992 (80.99%) aligned exactly 1 time 3957271 (16.65%) aligned >1 times 97.65% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 7720647 / 23205263 = 0.3327 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.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 @ Thu, 05 Dec 2019 12:45:11: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:45:11: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:45:17: 1000000 INFO @ Thu, 05 Dec 2019 12:45:23: 2000000 INFO @ Thu, 05 Dec 2019 12:45:28: 3000000 INFO @ Thu, 05 Dec 2019 12:45:34: 4000000 INFO @ Thu, 05 Dec 2019 12:45:39: 5000000 INFO @ Thu, 05 Dec 2019 12:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.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 @ Thu, 05 Dec 2019 12:45:40: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:45:40: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:45:45: 6000000 INFO @ Thu, 05 Dec 2019 12:45:46: 1000000 INFO @ Thu, 05 Dec 2019 12:45:50: 7000000 INFO @ Thu, 05 Dec 2019 12:45:51: 2000000 INFO @ Thu, 05 Dec 2019 12:45:56: 8000000 INFO @ Thu, 05 Dec 2019 12:45:57: 3000000 INFO @ Thu, 05 Dec 2019 12:46:01: 9000000 INFO @ Thu, 05 Dec 2019 12:46:03: 4000000 INFO @ Thu, 05 Dec 2019 12:46:06: 10000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:46:09: 5000000 INFO @ Thu, 05 Dec 2019 12:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.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 @ Thu, 05 Dec 2019 12:46:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:46:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:46:11: 11000000 INFO @ Thu, 05 Dec 2019 12:46:15: 6000000 INFO @ Thu, 05 Dec 2019 12:46:16: 1000000 INFO @ Thu, 05 Dec 2019 12:46:17: 12000000 INFO @ Thu, 05 Dec 2019 12:46:21: 7000000 INFO @ Thu, 05 Dec 2019 12:46:22: 13000000 INFO @ Thu, 05 Dec 2019 12:46:23: 2000000 INFO @ Thu, 05 Dec 2019 12:46:27: 8000000 INFO @ Thu, 05 Dec 2019 12:46:28: 14000000 INFO @ Thu, 05 Dec 2019 12:46:29: 3000000 INFO @ Thu, 05 Dec 2019 12:46:33: 15000000 INFO @ Thu, 05 Dec 2019 12:46:34: 9000000 INFO @ Thu, 05 Dec 2019 12:46:35: 4000000 INFO @ Thu, 05 Dec 2019 12:46:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:46:36: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:46:36: #1 total tags in treatment: 15484616 INFO @ Thu, 05 Dec 2019 12:46:36: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:46:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:46:36: #1 tags after filtering in treatment: 15484616 INFO @ Thu, 05 Dec 2019 12:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:46:36: #1 finished! INFO @ Thu, 05 Dec 2019 12:46:36: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:46:37: #2 number of paired peaks: 160 WARNING @ Thu, 05 Dec 2019 12:46:37: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Thu, 05 Dec 2019 12:46:37: start model_add_line... INFO @ Thu, 05 Dec 2019 12:46:37: start X-correlation... INFO @ Thu, 05 Dec 2019 12:46:37: end of X-cor INFO @ Thu, 05 Dec 2019 12:46:37: #2 finished! INFO @ Thu, 05 Dec 2019 12:46:37: #2 predicted fragment length is 72 bps INFO @ Thu, 05 Dec 2019 12:46:37: #2 alternative fragment length(s) may be 50,54,72,131,133,140,165,190,237,264,313,340,387,421,467,497,513,562,594 bps INFO @ Thu, 05 Dec 2019 12:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.05_model.r WARNING @ Thu, 05 Dec 2019 12:46:37: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:46:37: #2 You may need to consider one of the other alternative d(s): 50,54,72,131,133,140,165,190,237,264,313,340,387,421,467,497,513,562,594 WARNING @ Thu, 05 Dec 2019 12:46:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:46:37: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:46:40: 10000000 INFO @ Thu, 05 Dec 2019 12:46:41: 5000000 INFO @ Thu, 05 Dec 2019 12:46:46: 11000000 INFO @ Thu, 05 Dec 2019 12:46:47: 6000000 INFO @ Thu, 05 Dec 2019 12:46:52: 12000000 INFO @ Thu, 05 Dec 2019 12:46:53: 7000000 INFO @ Thu, 05 Dec 2019 12:46:58: 13000000 INFO @ Thu, 05 Dec 2019 12:47:00: 8000000 INFO @ Thu, 05 Dec 2019 12:47:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:47:04: 14000000 INFO @ Thu, 05 Dec 2019 12:47:05: 9000000 INFO @ Thu, 05 Dec 2019 12:47:10: 15000000 INFO @ Thu, 05 Dec 2019 12:47:11: 10000000 INFO @ Thu, 05 Dec 2019 12:47:13: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:47:13: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:47:13: #1 total tags in treatment: 15484616 INFO @ Thu, 05 Dec 2019 12:47:13: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:47:13: #1 tags after filtering in treatment: 15484616 INFO @ Thu, 05 Dec 2019 12:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:47:13: #1 finished! INFO @ Thu, 05 Dec 2019 12:47:13: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:47:14: #2 number of paired peaks: 160 WARNING @ Thu, 05 Dec 2019 12:47:14: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Thu, 05 Dec 2019 12:47:14: start model_add_line... INFO @ Thu, 05 Dec 2019 12:47:14: start X-correlation... INFO @ Thu, 05 Dec 2019 12:47:14: end of X-cor INFO @ Thu, 05 Dec 2019 12:47:14: #2 finished! INFO @ Thu, 05 Dec 2019 12:47:14: #2 predicted fragment length is 72 bps INFO @ Thu, 05 Dec 2019 12:47:14: #2 alternative fragment length(s) may be 50,54,72,131,133,140,165,190,237,264,313,340,387,421,467,497,513,562,594 bps INFO @ Thu, 05 Dec 2019 12:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.10_model.r WARNING @ Thu, 05 Dec 2019 12:47:14: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:47:14: #2 You may need to consider one of the other alternative d(s): 50,54,72,131,133,140,165,190,237,264,313,340,387,421,467,497,513,562,594 WARNING @ Thu, 05 Dec 2019 12:47:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:47:14: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:47:17: 11000000 INFO @ Thu, 05 Dec 2019 12:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.05_summits.bed INFO @ Thu, 05 Dec 2019 12:47:18: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (1718 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:47:23: 12000000 INFO @ Thu, 05 Dec 2019 12:47:28: 13000000 INFO @ Thu, 05 Dec 2019 12:47:34: 14000000 INFO @ Thu, 05 Dec 2019 12:47:39: 15000000 INFO @ Thu, 05 Dec 2019 12:47:42: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:47:42: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:47:42: #1 total tags in treatment: 15484616 INFO @ Thu, 05 Dec 2019 12:47:42: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:47:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:47:42: #1 tags after filtering in treatment: 15484616 INFO @ Thu, 05 Dec 2019 12:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:47:42: #1 finished! INFO @ Thu, 05 Dec 2019 12:47:42: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:47:42: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:47:43: #2 number of paired peaks: 160 WARNING @ Thu, 05 Dec 2019 12:47:43: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Thu, 05 Dec 2019 12:47:43: start model_add_line... INFO @ Thu, 05 Dec 2019 12:47:43: start X-correlation... INFO @ Thu, 05 Dec 2019 12:47:43: end of X-cor INFO @ Thu, 05 Dec 2019 12:47:43: #2 finished! INFO @ Thu, 05 Dec 2019 12:47:43: #2 predicted fragment length is 72 bps INFO @ Thu, 05 Dec 2019 12:47:43: #2 alternative fragment length(s) may be 50,54,72,131,133,140,165,190,237,264,313,340,387,421,467,497,513,562,594 bps INFO @ Thu, 05 Dec 2019 12:47:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.20_model.r WARNING @ Thu, 05 Dec 2019 12:47:43: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:47:43: #2 You may need to consider one of the other alternative d(s): 50,54,72,131,133,140,165,190,237,264,313,340,387,421,467,497,513,562,594 WARNING @ Thu, 05 Dec 2019 12:47:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:47:43: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.10_summits.bed INFO @ Thu, 05 Dec 2019 12:47:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (794 records, 4 fields): 487 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:48:10: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535386/SRX5535386.20_summits.bed INFO @ Thu, 05 Dec 2019 12:48:26: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (131 records, 4 fields): 459 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。