Job ID = 1300032 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:44:49 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 : 19,478,435 reads read : 19,478,435 reads written : 19,478,435 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:09 19478435 reads; of these: 19478435 (100.00%) were unpaired; of these: 698637 (3.59%) aligned 0 times 12844225 (65.94%) aligned exactly 1 time 5935573 (30.47%) aligned >1 times 96.41% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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 8 files... [bam_rmdupse_core] 2218870 / 18779798 = 0.1182 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 19:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.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 19:11:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:11:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.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 19:11:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:11:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.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 19:11:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:11:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:11:37: 1000000 INFO @ Mon, 03 Jun 2019 19:11:38: 1000000 INFO @ Mon, 03 Jun 2019 19:11:38: 1000000 INFO @ Mon, 03 Jun 2019 19:11:44: 2000000 INFO @ Mon, 03 Jun 2019 19:11:47: 2000000 INFO @ Mon, 03 Jun 2019 19:11:47: 2000000 INFO @ Mon, 03 Jun 2019 19:11:52: 3000000 INFO @ Mon, 03 Jun 2019 19:11:55: 3000000 INFO @ Mon, 03 Jun 2019 19:11:55: 3000000 INFO @ Mon, 03 Jun 2019 19:11:59: 4000000 INFO @ Mon, 03 Jun 2019 19:12:04: 4000000 INFO @ Mon, 03 Jun 2019 19:12:04: 4000000 INFO @ Mon, 03 Jun 2019 19:12:06: 5000000 INFO @ Mon, 03 Jun 2019 19:12:13: 5000000 INFO @ Mon, 03 Jun 2019 19:12:13: 5000000 INFO @ Mon, 03 Jun 2019 19:12:14: 6000000 INFO @ Mon, 03 Jun 2019 19:12:21: 7000000 INFO @ Mon, 03 Jun 2019 19:12:21: 6000000 INFO @ Mon, 03 Jun 2019 19:12:21: 6000000 INFO @ Mon, 03 Jun 2019 19:12:28: 8000000 INFO @ Mon, 03 Jun 2019 19:12:30: 7000000 INFO @ Mon, 03 Jun 2019 19:12:30: 7000000 INFO @ Mon, 03 Jun 2019 19:12:36: 9000000 INFO @ Mon, 03 Jun 2019 19:12:38: 8000000 INFO @ Mon, 03 Jun 2019 19:12:39: 8000000 INFO @ Mon, 03 Jun 2019 19:12:43: 10000000 INFO @ Mon, 03 Jun 2019 19:12:47: 9000000 INFO @ Mon, 03 Jun 2019 19:12:47: 9000000 INFO @ Mon, 03 Jun 2019 19:12:50: 11000000 INFO @ Mon, 03 Jun 2019 19:12:55: 10000000 INFO @ Mon, 03 Jun 2019 19:12:56: 10000000 INFO @ Mon, 03 Jun 2019 19:12:58: 12000000 INFO @ Mon, 03 Jun 2019 19:13:03: 11000000 INFO @ Mon, 03 Jun 2019 19:13:04: 11000000 INFO @ Mon, 03 Jun 2019 19:13:05: 13000000 INFO @ Mon, 03 Jun 2019 19:13:12: 12000000 INFO @ Mon, 03 Jun 2019 19:13:12: 14000000 INFO @ Mon, 03 Jun 2019 19:13:12: 12000000 INFO @ Mon, 03 Jun 2019 19:13:20: 15000000 INFO @ Mon, 03 Jun 2019 19:13:20: 13000000 INFO @ Mon, 03 Jun 2019 19:13:21: 13000000 INFO @ Mon, 03 Jun 2019 19:13:27: 16000000 INFO @ Mon, 03 Jun 2019 19:13:29: 14000000 INFO @ Mon, 03 Jun 2019 19:13:29: 14000000 INFO @ Mon, 03 Jun 2019 19:13:31: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:13:31: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:13:31: #1 total tags in treatment: 16560928 INFO @ Mon, 03 Jun 2019 19:13:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:13:31: #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 19:13:31: #1 tags after filtering in treatment: 16560928 INFO @ Mon, 03 Jun 2019 19:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:13:31: #1 finished! INFO @ Mon, 03 Jun 2019 19:13:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:13:33: #2 number of paired peaks: 819 WARNING @ Mon, 03 Jun 2019 19:13:33: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Mon, 03 Jun 2019 19:13:33: start model_add_line... INFO @ Mon, 03 Jun 2019 19:13:33: start X-correlation... INFO @ Mon, 03 Jun 2019 19:13:33: end of X-cor INFO @ Mon, 03 Jun 2019 19:13:33: #2 finished! INFO @ Mon, 03 Jun 2019 19:13:33: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 19:13:33: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 19:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.20_model.r WARNING @ Mon, 03 Jun 2019 19:13:33: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:13:33: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 19:13:33: #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 19:13:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:13:37: 15000000 INFO @ Mon, 03 Jun 2019 19:13:38: 15000000 INFO @ Mon, 03 Jun 2019 19:13:45: 16000000 INFO @ Mon, 03 Jun 2019 19:13:46: 16000000 INFO @ Mon, 03 Jun 2019 19:13:49: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:13:49: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:13:49: #1 total tags in treatment: 16560928 INFO @ Mon, 03 Jun 2019 19:13:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:13:49: #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 19:13:50: #1 tags after filtering in treatment: 16560928 INFO @ Mon, 03 Jun 2019 19:13:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:13:50: #1 finished! INFO @ Mon, 03 Jun 2019 19:13:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:13:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:13:50: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:13:50: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:13:50: #1 total tags in treatment: 16560928 INFO @ Mon, 03 Jun 2019 19:13:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:13:50: #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 19:13:51: #1 tags after filtering in treatment: 16560928 INFO @ Mon, 03 Jun 2019 19:13:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:13:51: #1 finished! INFO @ Mon, 03 Jun 2019 19:13:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:13:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:13:51: #2 number of paired peaks: 819 WARNING @ Mon, 03 Jun 2019 19:13:51: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Mon, 03 Jun 2019 19:13:51: start model_add_line... INFO @ Mon, 03 Jun 2019 19:13:51: start X-correlation... INFO @ Mon, 03 Jun 2019 19:13:51: end of X-cor INFO @ Mon, 03 Jun 2019 19:13:51: #2 finished! INFO @ Mon, 03 Jun 2019 19:13:51: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 19:13:51: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 19:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.10_model.r WARNING @ Mon, 03 Jun 2019 19:13:51: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:13:51: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 19:13:51: #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 19:13:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:13:52: #2 number of paired peaks: 819 WARNING @ Mon, 03 Jun 2019 19:13:52: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Mon, 03 Jun 2019 19:13:52: start model_add_line... INFO @ Mon, 03 Jun 2019 19:13:52: start X-correlation... INFO @ Mon, 03 Jun 2019 19:13:52: end of X-cor INFO @ Mon, 03 Jun 2019 19:13:52: #2 finished! INFO @ Mon, 03 Jun 2019 19:13:52: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 19:13:52: #2 alternative fragment length(s) may be 3,66 bps INFO @ Mon, 03 Jun 2019 19:13:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.05_model.r WARNING @ Mon, 03 Jun 2019 19:13:52: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:13:52: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Mon, 03 Jun 2019 19:13:52: #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 19:13:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:13:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:14:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:14:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:14:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:14:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.20_summits.bed INFO @ Mon, 03 Jun 2019 19:14:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1004 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.10_summits.bed INFO @ Mon, 03 Jun 2019 19:14:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2181 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:15:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:15:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:15:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801803/SRX4801803.05_summits.bed INFO @ Mon, 03 Jun 2019 19:15:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3768 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。