Job ID = 2590168 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T10:53:27 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 : 24,434,363 reads read : 24,434,363 reads written : 24,434,363 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: 00:05:34 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3205470 (13.12%) aligned 0 times 17392679 (71.18%) aligned exactly 1 time 3836214 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2473095 / 21228893 = 0.1165 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 20:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:16:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:16:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:16:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:16:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:16:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:16:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:16:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:16:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:16:13: 1000000 INFO @ Mon, 12 Aug 2019 20:16:15: 1000000 INFO @ Mon, 12 Aug 2019 20:16:17: 1000000 INFO @ Mon, 12 Aug 2019 20:16:20: 2000000 INFO @ Mon, 12 Aug 2019 20:16:25: 2000000 INFO @ Mon, 12 Aug 2019 20:16:27: 3000000 INFO @ Mon, 12 Aug 2019 20:16:28: 2000000 INFO @ Mon, 12 Aug 2019 20:16:34: 4000000 INFO @ Mon, 12 Aug 2019 20:16:35: 3000000 INFO @ Mon, 12 Aug 2019 20:16:37: 3000000 INFO @ Mon, 12 Aug 2019 20:16:42: 5000000 INFO @ Mon, 12 Aug 2019 20:16:45: 4000000 INFO @ Mon, 12 Aug 2019 20:16:47: 4000000 INFO @ Mon, 12 Aug 2019 20:16:49: 6000000 INFO @ Mon, 12 Aug 2019 20:16:55: 5000000 INFO @ Mon, 12 Aug 2019 20:16:56: 7000000 INFO @ Mon, 12 Aug 2019 20:16:57: 5000000 INFO @ Mon, 12 Aug 2019 20:17:04: 8000000 INFO @ Mon, 12 Aug 2019 20:17:04: 6000000 INFO @ Mon, 12 Aug 2019 20:17:06: 6000000 INFO @ Mon, 12 Aug 2019 20:17:11: 9000000 INFO @ Mon, 12 Aug 2019 20:17:13: 7000000 INFO @ Mon, 12 Aug 2019 20:17:15: 7000000 INFO @ Mon, 12 Aug 2019 20:17:19: 10000000 INFO @ Mon, 12 Aug 2019 20:17:22: 8000000 INFO @ Mon, 12 Aug 2019 20:17:23: 8000000 INFO @ Mon, 12 Aug 2019 20:17:26: 11000000 INFO @ Mon, 12 Aug 2019 20:17:31: 9000000 INFO @ Mon, 12 Aug 2019 20:17:33: 9000000 INFO @ Mon, 12 Aug 2019 20:17:34: 12000000 INFO @ Mon, 12 Aug 2019 20:17:40: 10000000 INFO @ Mon, 12 Aug 2019 20:17:41: 13000000 INFO @ Mon, 12 Aug 2019 20:17:41: 10000000 INFO @ Mon, 12 Aug 2019 20:17:48: 14000000 INFO @ Mon, 12 Aug 2019 20:17:48: 11000000 INFO @ Mon, 12 Aug 2019 20:17:50: 11000000 INFO @ Mon, 12 Aug 2019 20:17:55: 15000000 INFO @ Mon, 12 Aug 2019 20:17:57: 12000000 INFO @ Mon, 12 Aug 2019 20:17:59: 12000000 INFO @ Mon, 12 Aug 2019 20:18:03: 16000000 INFO @ Mon, 12 Aug 2019 20:18:05: 13000000 INFO @ Mon, 12 Aug 2019 20:18:07: 13000000 INFO @ Mon, 12 Aug 2019 20:18:10: 17000000 INFO @ Mon, 12 Aug 2019 20:18:14: 14000000 INFO @ Mon, 12 Aug 2019 20:18:16: 14000000 INFO @ Mon, 12 Aug 2019 20:18:17: 18000000 INFO @ Mon, 12 Aug 2019 20:18:23: 15000000 INFO @ Mon, 12 Aug 2019 20:18:23: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:18:23: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:18:23: #1 total tags in treatment: 18755798 INFO @ Mon, 12 Aug 2019 20:18:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:18:23: #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 20:18:23: #1 tags after filtering in treatment: 18755798 INFO @ Mon, 12 Aug 2019 20:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:18:23: #1 finished! INFO @ Mon, 12 Aug 2019 20:18:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:18:25: 15000000 INFO @ Mon, 12 Aug 2019 20:18:25: #2 number of paired peaks: 246 WARNING @ Mon, 12 Aug 2019 20:18:25: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 12 Aug 2019 20:18:25: start model_add_line... INFO @ Mon, 12 Aug 2019 20:18:25: start X-correlation... INFO @ Mon, 12 Aug 2019 20:18:25: end of X-cor INFO @ Mon, 12 Aug 2019 20:18:25: #2 finished! INFO @ Mon, 12 Aug 2019 20:18:25: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 20:18:25: #2 alternative fragment length(s) may be 2,37,545,577 bps INFO @ Mon, 12 Aug 2019 20:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.10_model.r WARNING @ Mon, 12 Aug 2019 20:18:25: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:18:25: #2 You may need to consider one of the other alternative d(s): 2,37,545,577 WARNING @ Mon, 12 Aug 2019 20:18:25: #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 20:18:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:18:31: 16000000 INFO @ Mon, 12 Aug 2019 20:18:33: 16000000 INFO @ Mon, 12 Aug 2019 20:18:40: 17000000 INFO @ Mon, 12 Aug 2019 20:18:42: 17000000 INFO @ Mon, 12 Aug 2019 20:18:49: 18000000 INFO @ Mon, 12 Aug 2019 20:18:50: 18000000 INFO @ Mon, 12 Aug 2019 20:18:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:18:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:18:55: #1 total tags in treatment: 18755798 INFO @ Mon, 12 Aug 2019 20:18:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:18:55: #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 20:18:56: #1 tags after filtering in treatment: 18755798 INFO @ Mon, 12 Aug 2019 20:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:18:56: #1 finished! INFO @ Mon, 12 Aug 2019 20:18:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:18:57: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:18:57: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:18:57: #1 total tags in treatment: 18755798 INFO @ Mon, 12 Aug 2019 20:18:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:18:57: #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 20:18:57: #2 number of paired peaks: 246 WARNING @ Mon, 12 Aug 2019 20:18:57: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 12 Aug 2019 20:18:57: start model_add_line... INFO @ Mon, 12 Aug 2019 20:18:57: #1 tags after filtering in treatment: 18755798 INFO @ Mon, 12 Aug 2019 20:18:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:18:57: #1 finished! INFO @ Mon, 12 Aug 2019 20:18:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:18:58: start X-correlation... INFO @ Mon, 12 Aug 2019 20:18:58: end of X-cor INFO @ Mon, 12 Aug 2019 20:18:58: #2 finished! INFO @ Mon, 12 Aug 2019 20:18:58: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 20:18:58: #2 alternative fragment length(s) may be 2,37,545,577 bps INFO @ Mon, 12 Aug 2019 20:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.05_model.r WARNING @ Mon, 12 Aug 2019 20:18:58: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:18:58: #2 You may need to consider one of the other alternative d(s): 2,37,545,577 WARNING @ Mon, 12 Aug 2019 20:18:58: #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 20:18:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:18:59: #2 number of paired peaks: 246 WARNING @ Mon, 12 Aug 2019 20:18:59: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 12 Aug 2019 20:18:59: start model_add_line... INFO @ Mon, 12 Aug 2019 20:18:59: start X-correlation... INFO @ Mon, 12 Aug 2019 20:18:59: end of X-cor INFO @ Mon, 12 Aug 2019 20:18:59: #2 finished! INFO @ Mon, 12 Aug 2019 20:18:59: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 20:18:59: #2 alternative fragment length(s) may be 2,37,545,577 bps INFO @ Mon, 12 Aug 2019 20:18:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.20_model.r WARNING @ Mon, 12 Aug 2019 20:18:59: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:18:59: #2 You may need to consider one of the other alternative d(s): 2,37,545,577 WARNING @ Mon, 12 Aug 2019 20:18:59: #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 20:18:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:19:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.10_summits.bed INFO @ Mon, 12 Aug 2019 20:19:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:19:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:19:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.05_summits.bed INFO @ Mon, 12 Aug 2019 20:20:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (799 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495042/SRX495042.20_summits.bed INFO @ Mon, 12 Aug 2019 20:20:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。