Job ID = 4178555 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T04:03:55 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 : 30,297,835 reads read : 60,595,670 reads written : 30,297,835 reads 0-length : 30,297,835 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: 00:09:00 30297835 reads; of these: 30297835 (100.00%) were unpaired; of these: 9727484 (32.11%) aligned 0 times 15995310 (52.79%) aligned exactly 1 time 4575041 (15.10%) aligned >1 times 67.89% overall alignment rate Time searching: 00:09:00 Overall time: 00:09:00 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] 10822532 / 20570351 = 0.5261 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.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 13:27:56: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:27:56: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:28:03: 1000000 INFO @ Thu, 05 Dec 2019 13:28:11: 2000000 INFO @ Thu, 05 Dec 2019 13:28:17: 3000000 INFO @ Thu, 05 Dec 2019 13:28:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.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 13:28:24: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:28:24: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:28:24: 4000000 INFO @ Thu, 05 Dec 2019 13:28:29: 1000000 INFO @ Thu, 05 Dec 2019 13:28:31: 5000000 INFO @ Thu, 05 Dec 2019 13:28:34: 2000000 INFO @ Thu, 05 Dec 2019 13:28:38: 6000000 INFO @ Thu, 05 Dec 2019 13:28:40: 3000000 INFO @ Thu, 05 Dec 2019 13:28:45: 7000000 INFO @ Thu, 05 Dec 2019 13:28:45: 4000000 INFO @ Thu, 05 Dec 2019 13:28:50: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:28:51: 8000000 INFO @ Thu, 05 Dec 2019 13:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.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 13:28:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:28:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:28:57: 6000000 INFO @ Thu, 05 Dec 2019 13:28:58: 9000000 INFO @ Thu, 05 Dec 2019 13:29:00: 1000000 INFO @ Thu, 05 Dec 2019 13:29:03: 7000000 INFO @ Thu, 05 Dec 2019 13:29:03: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:29:03: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:29:03: #1 total tags in treatment: 9747819 INFO @ Thu, 05 Dec 2019 13:29:03: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:29:03: #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 13:29:04: #1 tags after filtering in treatment: 9747819 INFO @ Thu, 05 Dec 2019 13:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:29:04: #1 finished! INFO @ Thu, 05 Dec 2019 13:29:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:29:04: #2 number of paired peaks: 339 WARNING @ Thu, 05 Dec 2019 13:29:04: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Thu, 05 Dec 2019 13:29:04: start model_add_line... INFO @ Thu, 05 Dec 2019 13:29:04: start X-correlation... INFO @ Thu, 05 Dec 2019 13:29:05: end of X-cor INFO @ Thu, 05 Dec 2019 13:29:05: #2 finished! INFO @ Thu, 05 Dec 2019 13:29:05: #2 predicted fragment length is 58 bps INFO @ Thu, 05 Dec 2019 13:29:05: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 05 Dec 2019 13:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.05_model.r WARNING @ Thu, 05 Dec 2019 13:29:05: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:29:05: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 05 Dec 2019 13:29:05: #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 13:29:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:29:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:29:06: 2000000 INFO @ Thu, 05 Dec 2019 13:29:09: 8000000 INFO @ Thu, 05 Dec 2019 13:29:12: 3000000 INFO @ Thu, 05 Dec 2019 13:29:14: 9000000 INFO @ Thu, 05 Dec 2019 13:29:17: 4000000 INFO @ Thu, 05 Dec 2019 13:29:18: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:29:18: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:29:18: #1 total tags in treatment: 9747819 INFO @ Thu, 05 Dec 2019 13:29:18: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:29:18: #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 13:29:18: #1 tags after filtering in treatment: 9747819 INFO @ Thu, 05 Dec 2019 13:29:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:29:18: #1 finished! INFO @ Thu, 05 Dec 2019 13:29:18: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:29:19: #2 number of paired peaks: 339 WARNING @ Thu, 05 Dec 2019 13:29:19: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Thu, 05 Dec 2019 13:29:19: start model_add_line... INFO @ Thu, 05 Dec 2019 13:29:19: start X-correlation... INFO @ Thu, 05 Dec 2019 13:29:19: end of X-cor INFO @ Thu, 05 Dec 2019 13:29:19: #2 finished! INFO @ Thu, 05 Dec 2019 13:29:19: #2 predicted fragment length is 58 bps INFO @ Thu, 05 Dec 2019 13:29:19: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 05 Dec 2019 13:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.10_model.r WARNING @ Thu, 05 Dec 2019 13:29:19: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:29:19: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 05 Dec 2019 13:29:19: #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 13:29:19: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:29:22: 5000000 INFO @ Thu, 05 Dec 2019 13:29:23: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:29:29: 6000000 INFO @ Thu, 05 Dec 2019 13:29:34: 7000000 INFO @ Thu, 05 Dec 2019 13:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.05_summits.bed INFO @ Thu, 05 Dec 2019 13:29:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1924 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:29:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:29:41: 8000000 INFO @ Thu, 05 Dec 2019 13:29:46: 9000000 INFO @ Thu, 05 Dec 2019 13:29:49: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:29:49: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:29:49: #1 total tags in treatment: 9747819 INFO @ Thu, 05 Dec 2019 13:29:49: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:29:49: #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 13:29:49: #1 tags after filtering in treatment: 9747819 INFO @ Thu, 05 Dec 2019 13:29:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:29:49: #1 finished! INFO @ Thu, 05 Dec 2019 13:29:49: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.10_summits.bed INFO @ Thu, 05 Dec 2019 13:29:50: Done! INFO @ Thu, 05 Dec 2019 13:29:50: #2 number of paired peaks: 339 WARNING @ Thu, 05 Dec 2019 13:29:50: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Thu, 05 Dec 2019 13:29:50: start model_add_line... INFO @ Thu, 05 Dec 2019 13:29:50: start X-correlation... pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1211 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:29:50: end of X-cor INFO @ Thu, 05 Dec 2019 13:29:50: #2 finished! INFO @ Thu, 05 Dec 2019 13:29:50: #2 predicted fragment length is 58 bps INFO @ Thu, 05 Dec 2019 13:29:50: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 05 Dec 2019 13:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.20_model.r WARNING @ Thu, 05 Dec 2019 13:29:50: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:29:50: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 05 Dec 2019 13:29:50: #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 13:29:50: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:30:08: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:30:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:30:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:30:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827827/SRX5827827.20_summits.bed INFO @ Thu, 05 Dec 2019 13:30:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (749 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。