Job ID = 1300103 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:59:10 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 ) 2019-06-03T09:59:10 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 ) 2019-06-03T09:59:10 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 : 12,595,880 reads read : 12,595,880 reads written : 12,595,880 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:37 12595880 reads; of these: 12595880 (100.00%) were unpaired; of these: 292992 (2.33%) aligned 0 times 7612483 (60.44%) aligned exactly 1 time 4690405 (37.24%) aligned >1 times 97.67% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 1234341 / 12302888 = 0.1003 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 19:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.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 19:11:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:11:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.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 19:11:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:11:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.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 19:11:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:11:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:12:00: 1000000 INFO @ Mon, 03 Jun 2019 19:12:01: 1000000 INFO @ Mon, 03 Jun 2019 19:12:02: 1000000 INFO @ Mon, 03 Jun 2019 19:12:07: 2000000 INFO @ Mon, 03 Jun 2019 19:12:08: 2000000 INFO @ Mon, 03 Jun 2019 19:12:11: 2000000 INFO @ Mon, 03 Jun 2019 19:12:14: 3000000 INFO @ Mon, 03 Jun 2019 19:12:16: 3000000 INFO @ Mon, 03 Jun 2019 19:12:20: 3000000 INFO @ Mon, 03 Jun 2019 19:12:21: 4000000 INFO @ Mon, 03 Jun 2019 19:12:24: 4000000 INFO @ Mon, 03 Jun 2019 19:12:28: 5000000 INFO @ Mon, 03 Jun 2019 19:12:30: 4000000 INFO @ Mon, 03 Jun 2019 19:12:32: 5000000 INFO @ Mon, 03 Jun 2019 19:12:35: 6000000 INFO @ Mon, 03 Jun 2019 19:12:39: 5000000 INFO @ Mon, 03 Jun 2019 19:12:40: 6000000 INFO @ Mon, 03 Jun 2019 19:12:42: 7000000 INFO @ Mon, 03 Jun 2019 19:12:47: 7000000 INFO @ Mon, 03 Jun 2019 19:12:48: 6000000 INFO @ Mon, 03 Jun 2019 19:12:50: 8000000 INFO @ Mon, 03 Jun 2019 19:12:55: 8000000 INFO @ Mon, 03 Jun 2019 19:12:57: 9000000 INFO @ Mon, 03 Jun 2019 19:12:57: 7000000 INFO @ Mon, 03 Jun 2019 19:13:03: 9000000 INFO @ Mon, 03 Jun 2019 19:13:04: 10000000 INFO @ Mon, 03 Jun 2019 19:13:06: 8000000 INFO @ Mon, 03 Jun 2019 19:13:11: 10000000 INFO @ Mon, 03 Jun 2019 19:13:11: 11000000 INFO @ Mon, 03 Jun 2019 19:13:11: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:13:11: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:13:11: #1 total tags in treatment: 11068547 INFO @ Mon, 03 Jun 2019 19:13:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:13:11: #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 19:13:12: #1 tags after filtering in treatment: 11068547 INFO @ Mon, 03 Jun 2019 19:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:13:12: #1 finished! INFO @ Mon, 03 Jun 2019 19:13:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:13:13: #2 number of paired peaks: 1288 INFO @ Mon, 03 Jun 2019 19:13:13: start model_add_line... INFO @ Mon, 03 Jun 2019 19:13:13: start X-correlation... INFO @ Mon, 03 Jun 2019 19:13:13: end of X-cor INFO @ Mon, 03 Jun 2019 19:13:13: #2 finished! INFO @ Mon, 03 Jun 2019 19:13:13: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 19:13:13: #2 alternative fragment length(s) may be 4,79 bps INFO @ Mon, 03 Jun 2019 19:13:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.10_model.r WARNING @ Mon, 03 Jun 2019 19:13:13: #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 19:13:13: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Mon, 03 Jun 2019 19:13:13: #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 19:13:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:13:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:13:15: 9000000 INFO @ Mon, 03 Jun 2019 19:13:18: 11000000 INFO @ Mon, 03 Jun 2019 19:13:19: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:13:19: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:13:19: #1 total tags in treatment: 11068547 INFO @ Mon, 03 Jun 2019 19:13:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:13:19: #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 19:13:19: #1 tags after filtering in treatment: 11068547 INFO @ Mon, 03 Jun 2019 19:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:13:19: #1 finished! INFO @ Mon, 03 Jun 2019 19:13:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:13:20: #2 number of paired peaks: 1288 INFO @ Mon, 03 Jun 2019 19:13:20: start model_add_line... INFO @ Mon, 03 Jun 2019 19:13:21: start X-correlation... INFO @ Mon, 03 Jun 2019 19:13:21: end of X-cor INFO @ Mon, 03 Jun 2019 19:13:21: #2 finished! INFO @ Mon, 03 Jun 2019 19:13:21: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 19:13:21: #2 alternative fragment length(s) may be 4,79 bps INFO @ Mon, 03 Jun 2019 19:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.20_model.r WARNING @ Mon, 03 Jun 2019 19:13:21: #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 19:13:21: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Mon, 03 Jun 2019 19:13:21: #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 19:13:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:13:24: 10000000 INFO @ Mon, 03 Jun 2019 19:13:33: 11000000 INFO @ Mon, 03 Jun 2019 19:13:34: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:13:34: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:13:34: #1 total tags in treatment: 11068547 INFO @ Mon, 03 Jun 2019 19:13:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:13:34: #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 19:13:34: #1 tags after filtering in treatment: 11068547 INFO @ Mon, 03 Jun 2019 19:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:13:34: #1 finished! INFO @ Mon, 03 Jun 2019 19:13:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:13:35: #2 number of paired peaks: 1288 INFO @ Mon, 03 Jun 2019 19:13:35: start model_add_line... INFO @ Mon, 03 Jun 2019 19:13:35: start X-correlation... INFO @ Mon, 03 Jun 2019 19:13:35: end of X-cor INFO @ Mon, 03 Jun 2019 19:13:35: #2 finished! INFO @ Mon, 03 Jun 2019 19:13:35: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 19:13:35: #2 alternative fragment length(s) may be 4,79 bps INFO @ Mon, 03 Jun 2019 19:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.05_model.r WARNING @ Mon, 03 Jun 2019 19:13:35: #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 19:13:35: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Mon, 03 Jun 2019 19:13:35: #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 19:13:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:13:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:13:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:13:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.10_summits.bed INFO @ Mon, 03 Jun 2019 19:14:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2173 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:14:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.20_summits.bed INFO @ Mon, 03 Jun 2019 19:14:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1227 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:14:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:14:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:14:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801808/SRX4801808.05_summits.bed INFO @ Mon, 03 Jun 2019 19:14:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3808 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。