Job ID = 1295022 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T02:16:48 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 : 20,518,553 reads read : 20,518,553 reads written : 20,518,553 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: 00:07:32 20518553 reads; of these: 20518553 (100.00%) were unpaired; of these: 1336894 (6.52%) aligned 0 times 14023071 (68.34%) aligned exactly 1 time 5158588 (25.14%) aligned >1 times 93.48% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 1713454 / 19181659 = 0.0893 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 11:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.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 11:41:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:41:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.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 11:41:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:41:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.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 11:41:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:41:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:41:45: 1000000 INFO @ Mon, 03 Jun 2019 11:41:49: 1000000 INFO @ Mon, 03 Jun 2019 11:41:50: 1000000 INFO @ Mon, 03 Jun 2019 11:41:55: 2000000 INFO @ Mon, 03 Jun 2019 11:42:01: 2000000 INFO @ Mon, 03 Jun 2019 11:42:02: 2000000 INFO @ Mon, 03 Jun 2019 11:42:04: 3000000 INFO @ Mon, 03 Jun 2019 11:42:13: 3000000 INFO @ Mon, 03 Jun 2019 11:42:14: 4000000 INFO @ Mon, 03 Jun 2019 11:42:15: 3000000 INFO @ Mon, 03 Jun 2019 11:42:22: 5000000 INFO @ Mon, 03 Jun 2019 11:42:24: 4000000 INFO @ Mon, 03 Jun 2019 11:42:27: 4000000 INFO @ Mon, 03 Jun 2019 11:42:31: 6000000 INFO @ Mon, 03 Jun 2019 11:42:36: 5000000 INFO @ Mon, 03 Jun 2019 11:42:39: 5000000 INFO @ Mon, 03 Jun 2019 11:42:39: 7000000 INFO @ Mon, 03 Jun 2019 11:42:47: 8000000 INFO @ Mon, 03 Jun 2019 11:42:47: 6000000 INFO @ Mon, 03 Jun 2019 11:42:51: 6000000 INFO @ Mon, 03 Jun 2019 11:42:56: 9000000 INFO @ Mon, 03 Jun 2019 11:42:59: 7000000 INFO @ Mon, 03 Jun 2019 11:43:03: 7000000 INFO @ Mon, 03 Jun 2019 11:43:04: 10000000 INFO @ Mon, 03 Jun 2019 11:43:11: 8000000 INFO @ Mon, 03 Jun 2019 11:43:12: 11000000 INFO @ Mon, 03 Jun 2019 11:43:16: 8000000 INFO @ Mon, 03 Jun 2019 11:43:21: 12000000 INFO @ Mon, 03 Jun 2019 11:43:22: 9000000 INFO @ Mon, 03 Jun 2019 11:43:28: 9000000 INFO @ Mon, 03 Jun 2019 11:43:29: 13000000 INFO @ Mon, 03 Jun 2019 11:43:34: 10000000 INFO @ Mon, 03 Jun 2019 11:43:37: 14000000 INFO @ Mon, 03 Jun 2019 11:43:40: 10000000 INFO @ Mon, 03 Jun 2019 11:43:45: 11000000 INFO @ Mon, 03 Jun 2019 11:43:46: 15000000 INFO @ Mon, 03 Jun 2019 11:43:51: 11000000 INFO @ Mon, 03 Jun 2019 11:43:54: 16000000 INFO @ Mon, 03 Jun 2019 11:43:56: 12000000 INFO @ Mon, 03 Jun 2019 11:44:03: 17000000 INFO @ Mon, 03 Jun 2019 11:44:03: 12000000 INFO @ Mon, 03 Jun 2019 11:44:07: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:44:07: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:44:07: #1 total tags in treatment: 17468205 INFO @ Mon, 03 Jun 2019 11:44:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:44:07: #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 11:44:07: #1 tags after filtering in treatment: 17468205 INFO @ Mon, 03 Jun 2019 11:44:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:44:07: #1 finished! INFO @ Mon, 03 Jun 2019 11:44:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:44:08: 13000000 INFO @ Mon, 03 Jun 2019 11:44:09: #2 number of paired peaks: 364 WARNING @ Mon, 03 Jun 2019 11:44:09: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Mon, 03 Jun 2019 11:44:09: start model_add_line... INFO @ Mon, 03 Jun 2019 11:44:09: start X-correlation... INFO @ Mon, 03 Jun 2019 11:44:09: end of X-cor INFO @ Mon, 03 Jun 2019 11:44:09: #2 finished! INFO @ Mon, 03 Jun 2019 11:44:09: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 11:44:09: #2 alternative fragment length(s) may be 4,79 bps INFO @ Mon, 03 Jun 2019 11:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.05_model.r WARNING @ Mon, 03 Jun 2019 11:44:09: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:44:09: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Mon, 03 Jun 2019 11:44:09: #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 11:44:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:44:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:44:15: 13000000 INFO @ Mon, 03 Jun 2019 11:44:19: 14000000 INFO @ Mon, 03 Jun 2019 11:44:27: 14000000 INFO @ Mon, 03 Jun 2019 11:44:31: 15000000 INFO @ Mon, 03 Jun 2019 11:44:39: 15000000 INFO @ Mon, 03 Jun 2019 11:44:42: 16000000 INFO @ Mon, 03 Jun 2019 11:44:51: 16000000 INFO @ Mon, 03 Jun 2019 11:44:54: 17000000 INFO @ Mon, 03 Jun 2019 11:44:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:44:59: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:44:59: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:44:59: #1 total tags in treatment: 17468205 INFO @ Mon, 03 Jun 2019 11:44:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:44:59: #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 11:44:59: #1 tags after filtering in treatment: 17468205 INFO @ Mon, 03 Jun 2019 11:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:44:59: #1 finished! INFO @ Mon, 03 Jun 2019 11:44:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:45:01: #2 number of paired peaks: 364 WARNING @ Mon, 03 Jun 2019 11:45:01: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Mon, 03 Jun 2019 11:45:01: start model_add_line... INFO @ Mon, 03 Jun 2019 11:45:01: start X-correlation... INFO @ Mon, 03 Jun 2019 11:45:01: end of X-cor INFO @ Mon, 03 Jun 2019 11:45:01: #2 finished! INFO @ Mon, 03 Jun 2019 11:45:01: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 11:45:01: #2 alternative fragment length(s) may be 4,79 bps INFO @ Mon, 03 Jun 2019 11:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.10_model.r WARNING @ Mon, 03 Jun 2019 11:45:01: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:45:01: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Mon, 03 Jun 2019 11:45:01: #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 11:45:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:45:02: 17000000 INFO @ Mon, 03 Jun 2019 11:45:08: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:45:08: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:45:08: #1 total tags in treatment: 17468205 INFO @ Mon, 03 Jun 2019 11:45:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:45:08: #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 11:45:08: #1 tags after filtering in treatment: 17468205 INFO @ Mon, 03 Jun 2019 11:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:45:08: #1 finished! INFO @ Mon, 03 Jun 2019 11:45:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:45:10: #2 number of paired peaks: 364 WARNING @ Mon, 03 Jun 2019 11:45:10: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Mon, 03 Jun 2019 11:45:10: start model_add_line... INFO @ Mon, 03 Jun 2019 11:45:10: start X-correlation... INFO @ Mon, 03 Jun 2019 11:45:10: end of X-cor INFO @ Mon, 03 Jun 2019 11:45:10: #2 finished! INFO @ Mon, 03 Jun 2019 11:45:10: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 11:45:10: #2 alternative fragment length(s) may be 4,79 bps INFO @ Mon, 03 Jun 2019 11:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.20_model.r WARNING @ Mon, 03 Jun 2019 11:45:10: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:45:10: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Mon, 03 Jun 2019 11:45:10: #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 11:45:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:45:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:45:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:45:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.05_summits.bed INFO @ Mon, 03 Jun 2019 11:45:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4060 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:45:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:45:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:46:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:46:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:46:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.10_summits.bed INFO @ Mon, 03 Jun 2019 11:46:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2529 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306193/SRX306193.20_summits.bed INFO @ Mon, 03 Jun 2019 11:46:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1284 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。