Job ID = 4178484 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:29:45 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 22,790,183 reads read : 22,790,183 reads written : 22,790,183 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:27 22790183 reads; of these: 22790183 (100.00%) were unpaired; of these: 733806 (3.22%) aligned 0 times 13741568 (60.30%) aligned exactly 1 time 8314809 (36.48%) aligned >1 times 96.78% overall alignment rate Time searching: 00:11:28 Overall time: 00:11:28 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] 6077360 / 22056377 = 0.2755 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.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 12:53:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:53:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:53:36: 1000000 INFO @ Thu, 05 Dec 2019 12:53:43: 2000000 INFO @ Thu, 05 Dec 2019 12:53:50: 3000000 INFO @ Thu, 05 Dec 2019 12:53:58: 4000000 INFO @ Thu, 05 Dec 2019 12:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.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 12:53:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:53:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:54:05: 5000000 INFO @ Thu, 05 Dec 2019 12:54:06: 1000000 INFO @ Thu, 05 Dec 2019 12:54:13: 6000000 INFO @ Thu, 05 Dec 2019 12:54:15: 2000000 INFO @ Thu, 05 Dec 2019 12:54:21: 7000000 INFO @ Thu, 05 Dec 2019 12:54:23: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.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 12:54:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:54:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:54:30: 8000000 INFO @ Thu, 05 Dec 2019 12:54:32: 4000000 INFO @ Thu, 05 Dec 2019 12:54:38: 1000000 INFO @ Thu, 05 Dec 2019 12:54:38: 9000000 INFO @ Thu, 05 Dec 2019 12:54:40: 5000000 INFO @ Thu, 05 Dec 2019 12:54:45: 10000000 INFO @ Thu, 05 Dec 2019 12:54:47: 2000000 INFO @ Thu, 05 Dec 2019 12:54:49: 6000000 INFO @ Thu, 05 Dec 2019 12:54:53: 11000000 INFO @ Thu, 05 Dec 2019 12:54:55: 3000000 INFO @ Thu, 05 Dec 2019 12:54:57: 7000000 INFO @ Thu, 05 Dec 2019 12:55:01: 12000000 INFO @ Thu, 05 Dec 2019 12:55:04: 4000000 INFO @ Thu, 05 Dec 2019 12:55:06: 8000000 INFO @ Thu, 05 Dec 2019 12:55:08: 13000000 INFO @ Thu, 05 Dec 2019 12:55:13: 5000000 INFO @ Thu, 05 Dec 2019 12:55:14: 9000000 INFO @ Thu, 05 Dec 2019 12:55:16: 14000000 INFO @ Thu, 05 Dec 2019 12:55:22: 6000000 INFO @ Thu, 05 Dec 2019 12:55:23: 10000000 INFO @ Thu, 05 Dec 2019 12:55:24: 15000000 INFO @ Thu, 05 Dec 2019 12:55:30: 7000000 INFO @ Thu, 05 Dec 2019 12:55:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:55:31: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:55:31: #1 total tags in treatment: 15979017 INFO @ Thu, 05 Dec 2019 12:55:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:55:31: #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 12:55:31: 11000000 INFO @ Thu, 05 Dec 2019 12:55:32: #1 tags after filtering in treatment: 15979017 INFO @ Thu, 05 Dec 2019 12:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:55:32: #1 finished! INFO @ Thu, 05 Dec 2019 12:55:32: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:55:33: #2 number of paired peaks: 129 WARNING @ Thu, 05 Dec 2019 12:55:33: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Thu, 05 Dec 2019 12:55:33: start model_add_line... INFO @ Thu, 05 Dec 2019 12:55:33: start X-correlation... INFO @ Thu, 05 Dec 2019 12:55:33: end of X-cor INFO @ Thu, 05 Dec 2019 12:55:33: #2 finished! INFO @ Thu, 05 Dec 2019 12:55:33: #2 predicted fragment length is 87 bps INFO @ Thu, 05 Dec 2019 12:55:33: #2 alternative fragment length(s) may be 50,55,70,87,112,143,219,285,308,445,543,568,588 bps INFO @ Thu, 05 Dec 2019 12:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.05_model.r WARNING @ Thu, 05 Dec 2019 12:55:33: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:55:33: #2 You may need to consider one of the other alternative d(s): 50,55,70,87,112,143,219,285,308,445,543,568,588 WARNING @ Thu, 05 Dec 2019 12:55:33: #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 12:55:33: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:55:39: 8000000 INFO @ Thu, 05 Dec 2019 12:55:40: 12000000 INFO @ Thu, 05 Dec 2019 12:55:48: 9000000 INFO @ Thu, 05 Dec 2019 12:55:48: 13000000 INFO @ Thu, 05 Dec 2019 12:55:57: 10000000 INFO @ Thu, 05 Dec 2019 12:55:58: 14000000 INFO @ Thu, 05 Dec 2019 12:56:06: 11000000 INFO @ Thu, 05 Dec 2019 12:56:07: 15000000 INFO @ Thu, 05 Dec 2019 12:56:15: 12000000 INFO @ Thu, 05 Dec 2019 12:56:16: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:56:16: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:56:16: #1 total tags in treatment: 15979017 INFO @ Thu, 05 Dec 2019 12:56:16: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:56:16: #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 12:56:16: #1 tags after filtering in treatment: 15979017 INFO @ Thu, 05 Dec 2019 12:56:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:56:16: #1 finished! INFO @ Thu, 05 Dec 2019 12:56:16: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:56:18: #2 number of paired peaks: 129 WARNING @ Thu, 05 Dec 2019 12:56:18: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Thu, 05 Dec 2019 12:56:18: start model_add_line... INFO @ Thu, 05 Dec 2019 12:56:18: start X-correlation... INFO @ Thu, 05 Dec 2019 12:56:18: end of X-cor INFO @ Thu, 05 Dec 2019 12:56:18: #2 finished! INFO @ Thu, 05 Dec 2019 12:56:18: #2 predicted fragment length is 87 bps INFO @ Thu, 05 Dec 2019 12:56:18: #2 alternative fragment length(s) may be 50,55,70,87,112,143,219,285,308,445,543,568,588 bps INFO @ Thu, 05 Dec 2019 12:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.10_model.r WARNING @ Thu, 05 Dec 2019 12:56:18: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:56:18: #2 You may need to consider one of the other alternative d(s): 50,55,70,87,112,143,219,285,308,445,543,568,588 WARNING @ Thu, 05 Dec 2019 12:56:18: #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 12:56:18: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:56:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:56:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:56:23: 13000000 INFO @ Thu, 05 Dec 2019 12:56:32: 14000000 INFO @ Thu, 05 Dec 2019 12:56:40: 15000000 INFO @ Thu, 05 Dec 2019 12:56:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:56:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:56:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.05_summits.bed INFO @ Thu, 05 Dec 2019 12:56:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2078 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:56:49: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:56:49: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:56:49: #1 total tags in treatment: 15979017 INFO @ Thu, 05 Dec 2019 12:56:49: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:56:49: #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 12:56:49: #1 tags after filtering in treatment: 15979017 INFO @ Thu, 05 Dec 2019 12:56:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:56:49: #1 finished! INFO @ Thu, 05 Dec 2019 12:56:49: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:56:51: #2 number of paired peaks: 129 WARNING @ Thu, 05 Dec 2019 12:56:51: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Thu, 05 Dec 2019 12:56:51: start model_add_line... INFO @ Thu, 05 Dec 2019 12:56:51: start X-correlation... INFO @ Thu, 05 Dec 2019 12:56:51: end of X-cor INFO @ Thu, 05 Dec 2019 12:56:51: #2 finished! INFO @ Thu, 05 Dec 2019 12:56:51: #2 predicted fragment length is 87 bps INFO @ Thu, 05 Dec 2019 12:56:51: #2 alternative fragment length(s) may be 50,55,70,87,112,143,219,285,308,445,543,568,588 bps INFO @ Thu, 05 Dec 2019 12:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.20_model.r WARNING @ Thu, 05 Dec 2019 12:56:51: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:56:51: #2 You may need to consider one of the other alternative d(s): 50,55,70,87,112,143,219,285,308,445,543,568,588 WARNING @ Thu, 05 Dec 2019 12:56:51: #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 12:56:51: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:57:05: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.10_summits.bed INFO @ Thu, 05 Dec 2019 12:57:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1112 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:57:38: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535385/SRX5535385.20_summits.bed INFO @ Thu, 05 Dec 2019 12:58:02: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。