Job ID = 1308702 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:06:25 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 : 35,833,079 reads read : 71,666,158 reads written : 35,833,079 reads 0-length : 35,833,079 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: 00:13:40 35833079 reads; of these: 35833079 (100.00%) were unpaired; of these: 5378689 (15.01%) aligned 0 times 24813931 (69.25%) aligned exactly 1 time 5640459 (15.74%) aligned >1 times 84.99% overall alignment rate Time searching: 00:13:40 Overall time: 00:13:40 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 16 files... [bam_rmdupse_core] 16152040 / 30454390 = 0.5304 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 23:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.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 23:29:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.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 23:29:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.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 23:29:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:29:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:30:07: 1000000 INFO @ Mon, 03 Jun 2019 23:30:07: 1000000 INFO @ Mon, 03 Jun 2019 23:30:07: 1000000 INFO @ Mon, 03 Jun 2019 23:30:16: 2000000 INFO @ Mon, 03 Jun 2019 23:30:17: 2000000 INFO @ Mon, 03 Jun 2019 23:30:17: 2000000 INFO @ Mon, 03 Jun 2019 23:30:26: 3000000 INFO @ Mon, 03 Jun 2019 23:30:27: 3000000 INFO @ Mon, 03 Jun 2019 23:30:27: 3000000 INFO @ Mon, 03 Jun 2019 23:30:35: 4000000 INFO @ Mon, 03 Jun 2019 23:30:36: 4000000 INFO @ Mon, 03 Jun 2019 23:30:36: 4000000 INFO @ Mon, 03 Jun 2019 23:30:44: 5000000 INFO @ Mon, 03 Jun 2019 23:30:46: 5000000 INFO @ Mon, 03 Jun 2019 23:30:47: 5000000 INFO @ Mon, 03 Jun 2019 23:30:53: 6000000 INFO @ Mon, 03 Jun 2019 23:30:55: 6000000 INFO @ Mon, 03 Jun 2019 23:30:56: 6000000 INFO @ Mon, 03 Jun 2019 23:31:01: 7000000 INFO @ Mon, 03 Jun 2019 23:31:04: 7000000 INFO @ Mon, 03 Jun 2019 23:31:05: 7000000 INFO @ Mon, 03 Jun 2019 23:31:10: 8000000 INFO @ Mon, 03 Jun 2019 23:31:13: 8000000 INFO @ Mon, 03 Jun 2019 23:31:15: 8000000 INFO @ Mon, 03 Jun 2019 23:31:19: 9000000 INFO @ Mon, 03 Jun 2019 23:31:22: 9000000 INFO @ Mon, 03 Jun 2019 23:31:24: 9000000 INFO @ Mon, 03 Jun 2019 23:31:28: 10000000 INFO @ Mon, 03 Jun 2019 23:31:31: 10000000 INFO @ Mon, 03 Jun 2019 23:31:34: 10000000 INFO @ Mon, 03 Jun 2019 23:31:37: 11000000 INFO @ Mon, 03 Jun 2019 23:31:40: 11000000 INFO @ Mon, 03 Jun 2019 23:31:43: 11000000 INFO @ Mon, 03 Jun 2019 23:31:46: 12000000 INFO @ Mon, 03 Jun 2019 23:31:50: 12000000 INFO @ Mon, 03 Jun 2019 23:31:53: 12000000 INFO @ Mon, 03 Jun 2019 23:31:55: 13000000 INFO @ Mon, 03 Jun 2019 23:32:00: 13000000 INFO @ Mon, 03 Jun 2019 23:32:03: 13000000 INFO @ Mon, 03 Jun 2019 23:32:04: 14000000 INFO @ Mon, 03 Jun 2019 23:32:07: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:32:07: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:32:07: #1 total tags in treatment: 14302350 INFO @ Mon, 03 Jun 2019 23:32:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:32:07: #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 23:32:07: #1 tags after filtering in treatment: 14302350 INFO @ Mon, 03 Jun 2019 23:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:32:07: #1 finished! INFO @ Mon, 03 Jun 2019 23:32:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:32:09: 14000000 INFO @ Mon, 03 Jun 2019 23:32:09: #2 number of paired peaks: 1465 INFO @ Mon, 03 Jun 2019 23:32:09: start model_add_line... INFO @ Mon, 03 Jun 2019 23:32:09: start X-correlation... INFO @ Mon, 03 Jun 2019 23:32:09: end of X-cor INFO @ Mon, 03 Jun 2019 23:32:09: #2 finished! INFO @ Mon, 03 Jun 2019 23:32:09: #2 predicted fragment length is 89 bps INFO @ Mon, 03 Jun 2019 23:32:09: #2 alternative fragment length(s) may be 4,89,579 bps INFO @ Mon, 03 Jun 2019 23:32:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.10_model.r WARNING @ Mon, 03 Jun 2019 23:32:09: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:32:09: #2 You may need to consider one of the other alternative d(s): 4,89,579 WARNING @ Mon, 03 Jun 2019 23:32:09: #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 23:32:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:32:12: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:32:12: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:32:12: #1 total tags in treatment: 14302350 INFO @ Mon, 03 Jun 2019 23:32:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:32:12: #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 23:32:12: #1 tags after filtering in treatment: 14302350 INFO @ Mon, 03 Jun 2019 23:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:32:12: #1 finished! INFO @ Mon, 03 Jun 2019 23:32:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:32:12: 14000000 INFO @ Mon, 03 Jun 2019 23:32:13: #2 number of paired peaks: 1465 INFO @ Mon, 03 Jun 2019 23:32:13: start model_add_line... INFO @ Mon, 03 Jun 2019 23:32:14: start X-correlation... INFO @ Mon, 03 Jun 2019 23:32:14: end of X-cor INFO @ Mon, 03 Jun 2019 23:32:14: #2 finished! INFO @ Mon, 03 Jun 2019 23:32:14: #2 predicted fragment length is 89 bps INFO @ Mon, 03 Jun 2019 23:32:14: #2 alternative fragment length(s) may be 4,89,579 bps INFO @ Mon, 03 Jun 2019 23:32:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.20_model.r WARNING @ Mon, 03 Jun 2019 23:32:14: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:32:14: #2 You may need to consider one of the other alternative d(s): 4,89,579 WARNING @ Mon, 03 Jun 2019 23:32:14: #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 23:32:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:32:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:32:15: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:32:15: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:32:15: #1 total tags in treatment: 14302350 INFO @ Mon, 03 Jun 2019 23:32:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:32:15: #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 23:32:16: #1 tags after filtering in treatment: 14302350 INFO @ Mon, 03 Jun 2019 23:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:32:16: #1 finished! INFO @ Mon, 03 Jun 2019 23:32:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:32:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:32:17: #2 number of paired peaks: 1465 INFO @ Mon, 03 Jun 2019 23:32:17: start model_add_line... INFO @ Mon, 03 Jun 2019 23:32:17: start X-correlation... INFO @ Mon, 03 Jun 2019 23:32:17: end of X-cor INFO @ Mon, 03 Jun 2019 23:32:17: #2 finished! INFO @ Mon, 03 Jun 2019 23:32:17: #2 predicted fragment length is 89 bps INFO @ Mon, 03 Jun 2019 23:32:17: #2 alternative fragment length(s) may be 4,89,579 bps INFO @ Mon, 03 Jun 2019 23:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.05_model.r WARNING @ Mon, 03 Jun 2019 23:32:17: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:32:17: #2 You may need to consider one of the other alternative d(s): 4,89,579 WARNING @ Mon, 03 Jun 2019 23:32:17: #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 23:32:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:32:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:32:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:32:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.10_summits.bed INFO @ Mon, 03 Jun 2019 23:33:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3491 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.20_summits.bed INFO @ Mon, 03 Jun 2019 23:33:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1125 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343159/SRX5343159.05_summits.bed INFO @ Mon, 03 Jun 2019 23:33:18: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8134 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。