Job ID = 2640602 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:01:53 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 ) 2019-08-24T09:01:53 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 : 18,466,938 reads read : 36,933,876 reads written : 18,466,938 reads 0-length : 18,466,938 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:20 18466938 reads; of these: 18466938 (100.00%) were unpaired; of these: 452654 (2.45%) aligned 0 times 13063955 (70.74%) aligned exactly 1 time 4950329 (26.81%) aligned >1 times 97.55% overall alignment rate Time searching: 00:15:23 Overall time: 00:15:23 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 8 files... [bam_rmdupse_core] 7695660 / 18014284 = 0.4272 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.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 18:25:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:25:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:25:25: 1000000 INFO @ Sat, 24 Aug 2019 18:25:33: 2000000 INFO @ Sat, 24 Aug 2019 18:25:42: 3000000 INFO @ Sat, 24 Aug 2019 18:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.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 18:25:47: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:25:47: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:25:49: 4000000 INFO @ Sat, 24 Aug 2019 18:25:56: 1000000 INFO @ Sat, 24 Aug 2019 18:25:57: 5000000 INFO @ Sat, 24 Aug 2019 18:26:04: 6000000 INFO @ Sat, 24 Aug 2019 18:26:05: 2000000 INFO @ Sat, 24 Aug 2019 18:26:11: 7000000 INFO @ Sat, 24 Aug 2019 18:26:14: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.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 18:26:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:26:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:26:19: 8000000 INFO @ Sat, 24 Aug 2019 18:26:23: 4000000 INFO @ Sat, 24 Aug 2019 18:26:28: 1000000 INFO @ Sat, 24 Aug 2019 18:26:28: 9000000 INFO @ Sat, 24 Aug 2019 18:26:31: 5000000 INFO @ Sat, 24 Aug 2019 18:26:36: 10000000 INFO @ Sat, 24 Aug 2019 18:26:37: 2000000 INFO @ Sat, 24 Aug 2019 18:26:38: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:26:38: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:26:38: #1 total tags in treatment: 10318624 INFO @ Sat, 24 Aug 2019 18:26:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:26:38: #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 18:26:39: #1 tags after filtering in treatment: 10318440 INFO @ Sat, 24 Aug 2019 18:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:26:39: #1 finished! INFO @ Sat, 24 Aug 2019 18:26:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:26:40: 6000000 INFO @ Sat, 24 Aug 2019 18:26:41: #2 number of paired peaks: 11599 INFO @ Sat, 24 Aug 2019 18:26:41: start model_add_line... INFO @ Sat, 24 Aug 2019 18:26:41: start X-correlation... INFO @ Sat, 24 Aug 2019 18:26:41: end of X-cor INFO @ Sat, 24 Aug 2019 18:26:41: #2 finished! INFO @ Sat, 24 Aug 2019 18:26:41: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:26:41: #2 alternative fragment length(s) may be 52,106 bps INFO @ Sat, 24 Aug 2019 18:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.05_model.r WARNING @ Sat, 24 Aug 2019 18:26:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:26:41: #2 You may need to consider one of the other alternative d(s): 52,106 WARNING @ Sat, 24 Aug 2019 18:26:41: #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 18:26:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:26:46: 3000000 INFO @ Sat, 24 Aug 2019 18:26:48: 7000000 INFO @ Sat, 24 Aug 2019 18:26:56: 4000000 INFO @ Sat, 24 Aug 2019 18:26:57: 8000000 INFO @ Sat, 24 Aug 2019 18:27:05: 9000000 INFO @ Sat, 24 Aug 2019 18:27:05: 5000000 INFO @ Sat, 24 Aug 2019 18:27:13: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:27:14: 10000000 INFO @ Sat, 24 Aug 2019 18:27:15: 6000000 INFO @ Sat, 24 Aug 2019 18:27:16: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:27:16: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:27:16: #1 total tags in treatment: 10318624 INFO @ Sat, 24 Aug 2019 18:27:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:27:16: #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 18:27:17: #1 tags after filtering in treatment: 10318440 INFO @ Sat, 24 Aug 2019 18:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:27:17: #1 finished! INFO @ Sat, 24 Aug 2019 18:27:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:27:18: #2 number of paired peaks: 11599 INFO @ Sat, 24 Aug 2019 18:27:18: start model_add_line... INFO @ Sat, 24 Aug 2019 18:27:19: start X-correlation... INFO @ Sat, 24 Aug 2019 18:27:19: end of X-cor INFO @ Sat, 24 Aug 2019 18:27:19: #2 finished! INFO @ Sat, 24 Aug 2019 18:27:19: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:27:19: #2 alternative fragment length(s) may be 52,106 bps INFO @ Sat, 24 Aug 2019 18:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.10_model.r WARNING @ Sat, 24 Aug 2019 18:27:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:27:19: #2 You may need to consider one of the other alternative d(s): 52,106 WARNING @ Sat, 24 Aug 2019 18:27:19: #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 18:27:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:27:24: 7000000 INFO @ Sat, 24 Aug 2019 18:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.05_summits.bed INFO @ Sat, 24 Aug 2019 18:27:30: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (1022 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:27:33: 8000000 INFO @ Sat, 24 Aug 2019 18:27:42: 9000000 INFO @ Sat, 24 Aug 2019 18:27:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:27:52: 10000000 INFO @ Sat, 24 Aug 2019 18:27:55: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:27:55: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:27:55: #1 total tags in treatment: 10318624 INFO @ Sat, 24 Aug 2019 18:27:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:27:55: #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 18:27:55: #1 tags after filtering in treatment: 10318440 INFO @ Sat, 24 Aug 2019 18:27:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:27:55: #1 finished! INFO @ Sat, 24 Aug 2019 18:27:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:27:57: #2 number of paired peaks: 11599 INFO @ Sat, 24 Aug 2019 18:27:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:27:57: start X-correlation... INFO @ Sat, 24 Aug 2019 18:27:57: end of X-cor INFO @ Sat, 24 Aug 2019 18:27:57: #2 finished! INFO @ Sat, 24 Aug 2019 18:27:57: #2 predicted fragment length is 52 bps INFO @ Sat, 24 Aug 2019 18:27:57: #2 alternative fragment length(s) may be 52,106 bps INFO @ Sat, 24 Aug 2019 18:27:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.20_model.r WARNING @ Sat, 24 Aug 2019 18:27:57: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:27:57: #2 You may need to consider one of the other alternative d(s): 52,106 WARNING @ Sat, 24 Aug 2019 18:27:57: #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 18:27:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:27:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.10_summits.bed INFO @ Sat, 24 Aug 2019 18:28:08: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (579 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:28:29: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:28:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:28:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:28:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375032/SRX5375032.20_summits.bed INFO @ Sat, 24 Aug 2019 18:28:46: Done! pass1 - making usageList (23 chroms): 2 millis pass2 - checking and writing primary data (264 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。