Job ID = 2590611 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T13:44:19 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 : 38,112,094 reads read : 76,224,188 reads written : 38,112,094 reads 0-length : 38,112,094 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: 00:26:29 38112094 reads; of these: 38112094 (100.00%) were unpaired; of these: 701708 (1.84%) aligned 0 times 8460827 (22.20%) aligned exactly 1 time 28949559 (75.96%) aligned >1 times 98.16% overall alignment rate Time searching: 00:26:29 Overall time: 00:26:29 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] 16420284 / 37410386 = 0.4389 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, 12 Aug 2019 23:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.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, 12 Aug 2019 23:21:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:21:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:21:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.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, 12 Aug 2019 23:21:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:21:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.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, 12 Aug 2019 23:21:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:21:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:21:41: 1000000 INFO @ Mon, 12 Aug 2019 23:21:42: 1000000 INFO @ Mon, 12 Aug 2019 23:21:45: 1000000 INFO @ Mon, 12 Aug 2019 23:21:48: 2000000 INFO @ Mon, 12 Aug 2019 23:21:50: 2000000 INFO @ Mon, 12 Aug 2019 23:21:54: 2000000 INFO @ Mon, 12 Aug 2019 23:21:56: 3000000 INFO @ Mon, 12 Aug 2019 23:21:57: 3000000 INFO @ Mon, 12 Aug 2019 23:22:03: 3000000 INFO @ Mon, 12 Aug 2019 23:22:04: 4000000 INFO @ Mon, 12 Aug 2019 23:22:05: 4000000 INFO @ Mon, 12 Aug 2019 23:22:12: 4000000 INFO @ Mon, 12 Aug 2019 23:22:12: 5000000 INFO @ Mon, 12 Aug 2019 23:22:13: 5000000 INFO @ Mon, 12 Aug 2019 23:22:20: 6000000 INFO @ Mon, 12 Aug 2019 23:22:21: 6000000 INFO @ Mon, 12 Aug 2019 23:22:21: 5000000 INFO @ Mon, 12 Aug 2019 23:22:28: 7000000 INFO @ Mon, 12 Aug 2019 23:22:29: 7000000 INFO @ Mon, 12 Aug 2019 23:22:30: 6000000 INFO @ Mon, 12 Aug 2019 23:22:36: 8000000 INFO @ Mon, 12 Aug 2019 23:22:37: 8000000 INFO @ Mon, 12 Aug 2019 23:22:40: 7000000 INFO @ Mon, 12 Aug 2019 23:22:44: 9000000 INFO @ Mon, 12 Aug 2019 23:22:45: 9000000 INFO @ Mon, 12 Aug 2019 23:22:50: 8000000 INFO @ Mon, 12 Aug 2019 23:22:52: 10000000 INFO @ Mon, 12 Aug 2019 23:22:53: 10000000 INFO @ Mon, 12 Aug 2019 23:22:59: 9000000 INFO @ Mon, 12 Aug 2019 23:23:00: 11000000 INFO @ Mon, 12 Aug 2019 23:23:00: 11000000 INFO @ Mon, 12 Aug 2019 23:23:07: 12000000 INFO @ Mon, 12 Aug 2019 23:23:08: 12000000 INFO @ Mon, 12 Aug 2019 23:23:09: 10000000 INFO @ Mon, 12 Aug 2019 23:23:15: 13000000 INFO @ Mon, 12 Aug 2019 23:23:16: 13000000 INFO @ Mon, 12 Aug 2019 23:23:18: 11000000 INFO @ Mon, 12 Aug 2019 23:23:23: 14000000 INFO @ Mon, 12 Aug 2019 23:23:23: 14000000 INFO @ Mon, 12 Aug 2019 23:23:27: 12000000 INFO @ Mon, 12 Aug 2019 23:23:30: 15000000 INFO @ Mon, 12 Aug 2019 23:23:31: 15000000 INFO @ Mon, 12 Aug 2019 23:23:36: 13000000 INFO @ Mon, 12 Aug 2019 23:23:38: 16000000 INFO @ Mon, 12 Aug 2019 23:23:38: 16000000 INFO @ Mon, 12 Aug 2019 23:23:45: 14000000 INFO @ Mon, 12 Aug 2019 23:23:45: 17000000 INFO @ Mon, 12 Aug 2019 23:23:46: 17000000 INFO @ Mon, 12 Aug 2019 23:23:53: 18000000 INFO @ Mon, 12 Aug 2019 23:23:53: 18000000 INFO @ Mon, 12 Aug 2019 23:23:54: 15000000 INFO @ Mon, 12 Aug 2019 23:24:00: 19000000 INFO @ Mon, 12 Aug 2019 23:24:01: 19000000 INFO @ Mon, 12 Aug 2019 23:24:03: 16000000 INFO @ Mon, 12 Aug 2019 23:24:07: 20000000 INFO @ Mon, 12 Aug 2019 23:24:08: 20000000 INFO @ Mon, 12 Aug 2019 23:24:11: 17000000 INFO @ Mon, 12 Aug 2019 23:24:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:24:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:24:15: #1 total tags in treatment: 20990102 INFO @ Mon, 12 Aug 2019 23:24:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:24:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:24:15: #1 tags after filtering in treatment: 20990102 INFO @ Mon, 12 Aug 2019 23:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:24:15: #1 finished! INFO @ Mon, 12 Aug 2019 23:24:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:24:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:24:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:24:16: #1 total tags in treatment: 20990102 INFO @ Mon, 12 Aug 2019 23:24:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:24:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:24:16: #1 tags after filtering in treatment: 20990102 INFO @ Mon, 12 Aug 2019 23:24:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:24:16: #1 finished! INFO @ Mon, 12 Aug 2019 23:24:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:24:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:24:18: #2 number of paired peaks: 4176 INFO @ Mon, 12 Aug 2019 23:24:18: start model_add_line... INFO @ Mon, 12 Aug 2019 23:24:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:24:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:24:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:24:18: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 23:24:18: #2 alternative fragment length(s) may be 3,40 bps INFO @ Mon, 12 Aug 2019 23:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.05_model.r WARNING @ Mon, 12 Aug 2019 23:24:18: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:24:18: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Mon, 12 Aug 2019 23:24:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:24:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:24:19: #2 number of paired peaks: 4176 INFO @ Mon, 12 Aug 2019 23:24:19: start model_add_line... INFO @ Mon, 12 Aug 2019 23:24:19: start X-correlation... INFO @ Mon, 12 Aug 2019 23:24:19: end of X-cor INFO @ Mon, 12 Aug 2019 23:24:19: #2 finished! INFO @ Mon, 12 Aug 2019 23:24:19: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 23:24:19: #2 alternative fragment length(s) may be 3,40 bps INFO @ Mon, 12 Aug 2019 23:24:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.10_model.r WARNING @ Mon, 12 Aug 2019 23:24:19: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:24:19: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Mon, 12 Aug 2019 23:24:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:24:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:24:20: 18000000 INFO @ Mon, 12 Aug 2019 23:24:28: 19000000 INFO @ Mon, 12 Aug 2019 23:24:37: 20000000 INFO @ Mon, 12 Aug 2019 23:24:45: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:24:45: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:24:45: #1 total tags in treatment: 20990102 INFO @ Mon, 12 Aug 2019 23:24:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:24:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:24:46: #1 tags after filtering in treatment: 20990102 INFO @ Mon, 12 Aug 2019 23:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:24:46: #1 finished! INFO @ Mon, 12 Aug 2019 23:24:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:24:48: #2 number of paired peaks: 4176 INFO @ Mon, 12 Aug 2019 23:24:48: start model_add_line... INFO @ Mon, 12 Aug 2019 23:24:49: start X-correlation... INFO @ Mon, 12 Aug 2019 23:24:49: end of X-cor INFO @ Mon, 12 Aug 2019 23:24:49: #2 finished! INFO @ Mon, 12 Aug 2019 23:24:49: #2 predicted fragment length is 40 bps INFO @ Mon, 12 Aug 2019 23:24:49: #2 alternative fragment length(s) may be 3,40 bps INFO @ Mon, 12 Aug 2019 23:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.20_model.r WARNING @ Mon, 12 Aug 2019 23:24:49: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:24:49: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Mon, 12 Aug 2019 23:24:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:24:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:25:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:25:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.05_summits.bed INFO @ Mon, 12 Aug 2019 23:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.10_summits.bed INFO @ Mon, 12 Aug 2019 23:25:31: Done! INFO @ Mon, 12 Aug 2019 23:25:31: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9656 records, 4 fields): 16 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (20843 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:25:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923195/SRX4923195.20_summits.bed INFO @ Mon, 12 Aug 2019 23:26:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1743 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。