Job ID = 1294248 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 1900-01-00T00:00:00 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T20:46:34 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T20:49:04 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 : 26,727,264 reads read : 53,454,528 reads written : 26,727,264 reads 0-length : 26,727,264 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: 00:13:42 26727264 reads; of these: 26727264 (100.00%) were unpaired; of these: 924393 (3.46%) aligned 0 times 20874326 (78.10%) aligned exactly 1 time 4928545 (18.44%) aligned >1 times 96.54% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 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 12 files... [bam_rmdupse_core] 7705400 / 25802871 = 0.2986 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 06:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.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 06:18:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:18:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.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 06:18:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:18:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.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 06:18:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:18:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:18:17: 1000000 INFO @ Mon, 03 Jun 2019 06:18:19: 1000000 INFO @ Mon, 03 Jun 2019 06:18:19: 1000000 INFO @ Mon, 03 Jun 2019 06:18:25: 2000000 INFO @ Mon, 03 Jun 2019 06:18:29: 2000000 INFO @ Mon, 03 Jun 2019 06:18:29: 2000000 INFO @ Mon, 03 Jun 2019 06:18:32: 3000000 INFO @ Mon, 03 Jun 2019 06:18:38: 3000000 INFO @ Mon, 03 Jun 2019 06:18:38: 3000000 INFO @ Mon, 03 Jun 2019 06:18:40: 4000000 INFO @ Mon, 03 Jun 2019 06:18:47: 5000000 INFO @ Mon, 03 Jun 2019 06:18:47: 4000000 INFO @ Mon, 03 Jun 2019 06:18:47: 4000000 INFO @ Mon, 03 Jun 2019 06:18:55: 6000000 INFO @ Mon, 03 Jun 2019 06:18:56: 5000000 INFO @ Mon, 03 Jun 2019 06:18:56: 5000000 INFO @ Mon, 03 Jun 2019 06:19:02: 7000000 INFO @ Mon, 03 Jun 2019 06:19:05: 6000000 INFO @ Mon, 03 Jun 2019 06:19:05: 6000000 INFO @ Mon, 03 Jun 2019 06:19:09: 8000000 INFO @ Mon, 03 Jun 2019 06:19:14: 7000000 INFO @ Mon, 03 Jun 2019 06:19:14: 7000000 INFO @ Mon, 03 Jun 2019 06:19:16: 9000000 INFO @ Mon, 03 Jun 2019 06:19:22: 8000000 INFO @ Mon, 03 Jun 2019 06:19:23: 8000000 INFO @ Mon, 03 Jun 2019 06:19:24: 10000000 INFO @ Mon, 03 Jun 2019 06:19:31: 9000000 INFO @ Mon, 03 Jun 2019 06:19:31: 11000000 INFO @ Mon, 03 Jun 2019 06:19:32: 9000000 INFO @ Mon, 03 Jun 2019 06:19:38: 12000000 INFO @ Mon, 03 Jun 2019 06:19:39: 10000000 INFO @ Mon, 03 Jun 2019 06:19:40: 10000000 INFO @ Mon, 03 Jun 2019 06:19:46: 13000000 INFO @ Mon, 03 Jun 2019 06:19:48: 11000000 INFO @ Mon, 03 Jun 2019 06:19:49: 11000000 INFO @ Mon, 03 Jun 2019 06:19:53: 14000000 INFO @ Mon, 03 Jun 2019 06:19:57: 12000000 INFO @ Mon, 03 Jun 2019 06:19:58: 12000000 INFO @ Mon, 03 Jun 2019 06:20:00: 15000000 INFO @ Mon, 03 Jun 2019 06:20:05: 13000000 INFO @ Mon, 03 Jun 2019 06:20:06: 13000000 INFO @ Mon, 03 Jun 2019 06:20:08: 16000000 INFO @ Mon, 03 Jun 2019 06:20:14: 14000000 INFO @ Mon, 03 Jun 2019 06:20:15: 14000000 INFO @ Mon, 03 Jun 2019 06:20:15: 17000000 INFO @ Mon, 03 Jun 2019 06:20:23: 15000000 INFO @ Mon, 03 Jun 2019 06:20:23: 18000000 INFO @ Mon, 03 Jun 2019 06:20:24: 15000000 INFO @ Mon, 03 Jun 2019 06:20:24: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:20:24: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:20:24: #1 total tags in treatment: 18097471 INFO @ Mon, 03 Jun 2019 06:20:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:20:24: #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 06:20:24: #1 tags after filtering in treatment: 18097471 INFO @ Mon, 03 Jun 2019 06:20:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:20:24: #1 finished! INFO @ Mon, 03 Jun 2019 06:20:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:20:26: #2 number of paired peaks: 3441 INFO @ Mon, 03 Jun 2019 06:20:26: start model_add_line... INFO @ Mon, 03 Jun 2019 06:20:26: start X-correlation... INFO @ Mon, 03 Jun 2019 06:20:26: end of X-cor INFO @ Mon, 03 Jun 2019 06:20:26: #2 finished! INFO @ Mon, 03 Jun 2019 06:20:26: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 06:20:26: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 06:20:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.10_model.r WARNING @ Mon, 03 Jun 2019 06:20:26: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:20:26: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 06:20:26: #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 06:20:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:20:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:20:31: 16000000 INFO @ Mon, 03 Jun 2019 06:20:32: 16000000 INFO @ Mon, 03 Jun 2019 06:20:39: 17000000 INFO @ Mon, 03 Jun 2019 06:20:40: 17000000 INFO @ Mon, 03 Jun 2019 06:20:48: 18000000 INFO @ Mon, 03 Jun 2019 06:20:49: 18000000 INFO @ Mon, 03 Jun 2019 06:20:49: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:20:49: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:20:49: #1 total tags in treatment: 18097471 INFO @ Mon, 03 Jun 2019 06:20:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:20:49: #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 06:20:49: #1 tags after filtering in treatment: 18097471 INFO @ Mon, 03 Jun 2019 06:20:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:20:49: #1 finished! INFO @ Mon, 03 Jun 2019 06:20:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:20:50: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 06:20:50: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 06:20:50: #1 total tags in treatment: 18097471 INFO @ Mon, 03 Jun 2019 06:20:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:20:50: #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 06:20:50: #1 tags after filtering in treatment: 18097471 INFO @ Mon, 03 Jun 2019 06:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:20:50: #1 finished! INFO @ Mon, 03 Jun 2019 06:20:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:20:51: #2 number of paired peaks: 3441 INFO @ Mon, 03 Jun 2019 06:20:51: start model_add_line... INFO @ Mon, 03 Jun 2019 06:20:51: start X-correlation... INFO @ Mon, 03 Jun 2019 06:20:52: end of X-cor INFO @ Mon, 03 Jun 2019 06:20:52: #2 finished! INFO @ Mon, 03 Jun 2019 06:20:52: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 06:20:52: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 06:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.05_model.r WARNING @ Mon, 03 Jun 2019 06:20:52: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:20:52: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 06:20:52: #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 06:20:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:20:52: #2 number of paired peaks: 3441 INFO @ Mon, 03 Jun 2019 06:20:52: start model_add_line... INFO @ Mon, 03 Jun 2019 06:20:52: start X-correlation... INFO @ Mon, 03 Jun 2019 06:20:52: end of X-cor INFO @ Mon, 03 Jun 2019 06:20:52: #2 finished! INFO @ Mon, 03 Jun 2019 06:20:52: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 06:20:52: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 06:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.20_model.r WARNING @ Mon, 03 Jun 2019 06:20:52: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:20:52: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 06:20:52: #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 06:20:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:21:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.10_summits.bed INFO @ Mon, 03 Jun 2019 06:21:44: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11747 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:21:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:21:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:22:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:22:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:22:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.05_summits.bed INFO @ Mon, 03 Jun 2019 06:22:09: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (15098 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:22:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:22:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:22:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035279/SRX2035279.20_summits.bed INFO @ Mon, 03 Jun 2019 06:22:10: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (8359 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。