Job ID = 2640402 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:07:05 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 : 54,131,290 reads read : 54,131,290 reads written : 54,131,290 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:39:34 54131290 reads; of these: 54131290 (100.00%) were unpaired; of these: 14750409 (27.25%) aligned 0 times 27349784 (50.52%) aligned exactly 1 time 12031097 (22.23%) aligned >1 times 72.75% overall alignment rate Time searching: 00:39:38 Overall time: 00:39:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 22129038 / 39380881 = 0.5619 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:19:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:19:23: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:19:23: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:19:30: 1000000 INFO @ Sat, 24 Aug 2019 17:19:37: 2000000 INFO @ Sat, 24 Aug 2019 17:19:45: 3000000 INFO @ Sat, 24 Aug 2019 17:19:52: 4000000 INFO @ Sat, 24 Aug 2019 17:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:19:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:19:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:19:59: 5000000 INFO @ Sat, 24 Aug 2019 17:20:02: 1000000 INFO @ Sat, 24 Aug 2019 17:20:06: 6000000 INFO @ Sat, 24 Aug 2019 17:20:11: 2000000 INFO @ Sat, 24 Aug 2019 17:20:13: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:20:20: 8000000 INFO @ Sat, 24 Aug 2019 17:20:21: 3000000 INFO @ Sat, 24 Aug 2019 17:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:20:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:20:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:20:28: 9000000 INFO @ Sat, 24 Aug 2019 17:20:30: 4000000 INFO @ Sat, 24 Aug 2019 17:20:31: 1000000 INFO @ Sat, 24 Aug 2019 17:20:35: 10000000 INFO @ Sat, 24 Aug 2019 17:20:39: 5000000 INFO @ Sat, 24 Aug 2019 17:20:40: 2000000 INFO @ Sat, 24 Aug 2019 17:20:42: 11000000 INFO @ Sat, 24 Aug 2019 17:20:48: 3000000 INFO @ Sat, 24 Aug 2019 17:20:49: 6000000 INFO @ Sat, 24 Aug 2019 17:20:49: 12000000 INFO @ Sat, 24 Aug 2019 17:20:56: 13000000 INFO @ Sat, 24 Aug 2019 17:20:57: 4000000 INFO @ Sat, 24 Aug 2019 17:20:58: 7000000 INFO @ Sat, 24 Aug 2019 17:21:03: 14000000 INFO @ Sat, 24 Aug 2019 17:21:05: 5000000 INFO @ Sat, 24 Aug 2019 17:21:08: 8000000 INFO @ Sat, 24 Aug 2019 17:21:10: 15000000 INFO @ Sat, 24 Aug 2019 17:21:14: 6000000 INFO @ Sat, 24 Aug 2019 17:21:17: 16000000 INFO @ Sat, 24 Aug 2019 17:21:18: 9000000 INFO @ Sat, 24 Aug 2019 17:21:22: 7000000 INFO @ Sat, 24 Aug 2019 17:21:25: 17000000 INFO @ Sat, 24 Aug 2019 17:21:26: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:21:26: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:21:26: #1 total tags in treatment: 17251843 INFO @ Sat, 24 Aug 2019 17:21:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:21:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:21:27: #1 tags after filtering in treatment: 17251729 INFO @ Sat, 24 Aug 2019 17:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:21:27: #1 finished! INFO @ Sat, 24 Aug 2019 17:21:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:21:27: 10000000 INFO @ Sat, 24 Aug 2019 17:21:30: #2 number of paired peaks: 13236 INFO @ Sat, 24 Aug 2019 17:21:30: start model_add_line... INFO @ Sat, 24 Aug 2019 17:21:30: start X-correlation... INFO @ Sat, 24 Aug 2019 17:21:30: end of X-cor INFO @ Sat, 24 Aug 2019 17:21:30: #2 finished! INFO @ Sat, 24 Aug 2019 17:21:30: #2 predicted fragment length is 50 bps INFO @ Sat, 24 Aug 2019 17:21:30: #2 alternative fragment length(s) may be 50,229,384,411,500,540 bps INFO @ Sat, 24 Aug 2019 17:21:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.05_model.r WARNING @ Sat, 24 Aug 2019 17:21:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:21:30: #2 You may need to consider one of the other alternative d(s): 50,229,384,411,500,540 WARNING @ Sat, 24 Aug 2019 17:21:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:21:30: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:21:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:21:31: 8000000 INFO @ Sat, 24 Aug 2019 17:21:36: 11000000 INFO @ Sat, 24 Aug 2019 17:21:39: 9000000 INFO @ Sat, 24 Aug 2019 17:21:45: 12000000 INFO @ Sat, 24 Aug 2019 17:21:48: 10000000 INFO @ Sat, 24 Aug 2019 17:21:54: 13000000 INFO @ Sat, 24 Aug 2019 17:21:56: 11000000 INFO @ Sat, 24 Aug 2019 17:22:03: 14000000 INFO @ Sat, 24 Aug 2019 17:22:04: 12000000 INFO @ Sat, 24 Aug 2019 17:22:12: 15000000 INFO @ Sat, 24 Aug 2019 17:22:13: 13000000 INFO @ Sat, 24 Aug 2019 17:22:21: 16000000 INFO @ Sat, 24 Aug 2019 17:22:21: 14000000 INFO @ Sat, 24 Aug 2019 17:22:25: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:22:29: 15000000 INFO @ Sat, 24 Aug 2019 17:22:30: 17000000 INFO @ Sat, 24 Aug 2019 17:22:32: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:22:32: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:22:32: #1 total tags in treatment: 17251843 INFO @ Sat, 24 Aug 2019 17:22:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:22:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:22:33: #1 tags after filtering in treatment: 17251729 INFO @ Sat, 24 Aug 2019 17:22:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:22:33: #1 finished! INFO @ Sat, 24 Aug 2019 17:22:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:22:35: #2 number of paired peaks: 13236 INFO @ Sat, 24 Aug 2019 17:22:35: start model_add_line... INFO @ Sat, 24 Aug 2019 17:22:35: start X-correlation... INFO @ Sat, 24 Aug 2019 17:22:35: end of X-cor INFO @ Sat, 24 Aug 2019 17:22:35: #2 finished! INFO @ Sat, 24 Aug 2019 17:22:35: #2 predicted fragment length is 50 bps INFO @ Sat, 24 Aug 2019 17:22:35: #2 alternative fragment length(s) may be 50,229,384,411,500,540 bps INFO @ Sat, 24 Aug 2019 17:22:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.10_model.r WARNING @ Sat, 24 Aug 2019 17:22:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:22:36: #2 You may need to consider one of the other alternative d(s): 50,229,384,411,500,540 WARNING @ Sat, 24 Aug 2019 17:22:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:22:36: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:22:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:22:37: 16000000 INFO @ Sat, 24 Aug 2019 17:22:45: 17000000 INFO @ Sat, 24 Aug 2019 17:22:47: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:22:47: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:22:47: #1 total tags in treatment: 17251843 INFO @ Sat, 24 Aug 2019 17:22:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:22:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:22:48: #1 tags after filtering in treatment: 17251729 INFO @ Sat, 24 Aug 2019 17:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:22:48: #1 finished! INFO @ Sat, 24 Aug 2019 17:22:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:22:50: #2 number of paired peaks: 13236 INFO @ Sat, 24 Aug 2019 17:22:50: start model_add_line... INFO @ Sat, 24 Aug 2019 17:22:51: start X-correlation... INFO @ Sat, 24 Aug 2019 17:22:51: end of X-cor INFO @ Sat, 24 Aug 2019 17:22:51: #2 finished! INFO @ Sat, 24 Aug 2019 17:22:51: #2 predicted fragment length is 50 bps INFO @ Sat, 24 Aug 2019 17:22:51: #2 alternative fragment length(s) may be 50,229,384,411,500,540 bps INFO @ Sat, 24 Aug 2019 17:22:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.20_model.r WARNING @ Sat, 24 Aug 2019 17:22:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:22:51: #2 You may need to consider one of the other alternative d(s): 50,229,384,411,500,540 WARNING @ Sat, 24 Aug 2019 17:22:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:22:51: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:22:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.05_summits.bed INFO @ Sat, 24 Aug 2019 17:22:53: Done! pass1 - making usageList (68 chroms): 3 millis pass2 - checking and writing primary data (5146 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:23:31: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:23:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.10_summits.bed INFO @ Sat, 24 Aug 2019 17:23:59: Done! pass1 - making usageList (55 chroms): 3 millis pass2 - checking and writing primary data (2589 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:24:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337078/ERX337078.20_summits.bed INFO @ Sat, 24 Aug 2019 17:24:13: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1009 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。