Job ID = 1291873 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:58:58 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 ) 2019-06-02T07:58:58 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 : 28,372,619 reads read : 28,372,619 reads written : 28,372,619 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: 00:06:38 28372619 reads; of these: 28372619 (100.00%) were unpaired; of these: 78398 (0.28%) aligned 0 times 23642218 (83.33%) aligned exactly 1 time 4652003 (16.40%) aligned >1 times 99.72% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4182915 / 28294221 = 0.1478 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 @ Sun, 02 Jun 2019 17:16:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.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 @ Sun, 02 Jun 2019 17:16:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.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 @ Sun, 02 Jun 2019 17:16:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.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 @ Sun, 02 Jun 2019 17:16:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:40: 1000000 INFO @ Sun, 02 Jun 2019 17:16:42: 1000000 INFO @ Sun, 02 Jun 2019 17:16:42: 1000000 INFO @ Sun, 02 Jun 2019 17:16:47: 2000000 INFO @ Sun, 02 Jun 2019 17:16:52: 2000000 INFO @ Sun, 02 Jun 2019 17:16:52: 2000000 INFO @ Sun, 02 Jun 2019 17:16:54: 3000000 INFO @ Sun, 02 Jun 2019 17:17:01: 3000000 INFO @ Sun, 02 Jun 2019 17:17:01: 3000000 INFO @ Sun, 02 Jun 2019 17:17:02: 4000000 INFO @ Sun, 02 Jun 2019 17:17:09: 5000000 INFO @ Sun, 02 Jun 2019 17:17:10: 4000000 INFO @ Sun, 02 Jun 2019 17:17:10: 4000000 INFO @ Sun, 02 Jun 2019 17:17:16: 6000000 INFO @ Sun, 02 Jun 2019 17:17:20: 5000000 INFO @ Sun, 02 Jun 2019 17:17:20: 5000000 INFO @ Sun, 02 Jun 2019 17:17:23: 7000000 INFO @ Sun, 02 Jun 2019 17:17:30: 6000000 INFO @ Sun, 02 Jun 2019 17:17:30: 6000000 INFO @ Sun, 02 Jun 2019 17:17:30: 8000000 INFO @ Sun, 02 Jun 2019 17:17:37: 9000000 INFO @ Sun, 02 Jun 2019 17:17:39: 7000000 INFO @ Sun, 02 Jun 2019 17:17:40: 7000000 INFO @ Sun, 02 Jun 2019 17:17:44: 10000000 INFO @ Sun, 02 Jun 2019 17:17:49: 8000000 INFO @ Sun, 02 Jun 2019 17:17:49: 8000000 INFO @ Sun, 02 Jun 2019 17:17:52: 11000000 INFO @ Sun, 02 Jun 2019 17:17:58: 9000000 INFO @ Sun, 02 Jun 2019 17:17:59: 12000000 INFO @ Sun, 02 Jun 2019 17:17:59: 9000000 INFO @ Sun, 02 Jun 2019 17:18:06: 13000000 INFO @ Sun, 02 Jun 2019 17:18:08: 10000000 INFO @ Sun, 02 Jun 2019 17:18:09: 10000000 INFO @ Sun, 02 Jun 2019 17:18:13: 14000000 INFO @ Sun, 02 Jun 2019 17:18:17: 11000000 INFO @ Sun, 02 Jun 2019 17:18:18: 11000000 INFO @ Sun, 02 Jun 2019 17:18:20: 15000000 INFO @ Sun, 02 Jun 2019 17:18:27: 12000000 INFO @ Sun, 02 Jun 2019 17:18:27: 16000000 INFO @ Sun, 02 Jun 2019 17:18:27: 12000000 INFO @ Sun, 02 Jun 2019 17:18:34: 17000000 INFO @ Sun, 02 Jun 2019 17:18:36: 13000000 INFO @ Sun, 02 Jun 2019 17:18:37: 13000000 INFO @ Sun, 02 Jun 2019 17:18:41: 18000000 INFO @ Sun, 02 Jun 2019 17:18:45: 14000000 INFO @ Sun, 02 Jun 2019 17:18:46: 14000000 INFO @ Sun, 02 Jun 2019 17:18:48: 19000000 INFO @ Sun, 02 Jun 2019 17:18:54: 15000000 INFO @ Sun, 02 Jun 2019 17:18:55: 20000000 INFO @ Sun, 02 Jun 2019 17:18:55: 15000000 INFO @ Sun, 02 Jun 2019 17:19:02: 21000000 INFO @ Sun, 02 Jun 2019 17:19:03: 16000000 INFO @ Sun, 02 Jun 2019 17:19:04: 16000000 INFO @ Sun, 02 Jun 2019 17:19:09: 22000000 INFO @ Sun, 02 Jun 2019 17:19:12: 17000000 INFO @ Sun, 02 Jun 2019 17:19:13: 17000000 INFO @ Sun, 02 Jun 2019 17:19:16: 23000000 INFO @ Sun, 02 Jun 2019 17:19:21: 18000000 INFO @ Sun, 02 Jun 2019 17:19:22: 18000000 INFO @ Sun, 02 Jun 2019 17:19:23: 24000000 INFO @ Sun, 02 Jun 2019 17:19:25: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:19:25: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:19:25: #1 total tags in treatment: 24111306 INFO @ Sun, 02 Jun 2019 17:19:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:19:25: #1 tags after filtering in treatment: 24111306 INFO @ Sun, 02 Jun 2019 17:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:25: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:27: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 17:19:27: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 17:19:27: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:27: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:27: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:27: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:27: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:19:27: #2 alternative fragment length(s) may be 1,46,511 bps INFO @ Sun, 02 Jun 2019 17:19:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.20_model.r WARNING @ Sun, 02 Jun 2019 17:19:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:19:27: #2 You may need to consider one of the other alternative d(s): 1,46,511 WARNING @ Sun, 02 Jun 2019 17:19:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:19:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:30: 19000000 INFO @ Sun, 02 Jun 2019 17:19:31: 19000000 INFO @ Sun, 02 Jun 2019 17:19:39: 20000000 INFO @ Sun, 02 Jun 2019 17:19:40: 20000000 INFO @ Sun, 02 Jun 2019 17:19:47: 21000000 INFO @ Sun, 02 Jun 2019 17:19:49: 21000000 INFO @ Sun, 02 Jun 2019 17:19:56: 22000000 INFO @ Sun, 02 Jun 2019 17:19:58: 22000000 INFO @ Sun, 02 Jun 2019 17:20:05: 23000000 INFO @ Sun, 02 Jun 2019 17:20:06: 23000000 INFO @ Sun, 02 Jun 2019 17:20:13: 24000000 INFO @ Sun, 02 Jun 2019 17:20:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:20:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:20:14: #1 total tags in treatment: 24111306 INFO @ Sun, 02 Jun 2019 17:20:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:20:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:20:15: #1 tags after filtering in treatment: 24111306 INFO @ Sun, 02 Jun 2019 17:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:20:15: #1 finished! INFO @ Sun, 02 Jun 2019 17:20:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:20:15: 24000000 INFO @ Sun, 02 Jun 2019 17:20:16: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:20:16: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:20:16: #1 total tags in treatment: 24111306 INFO @ Sun, 02 Jun 2019 17:20:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:20:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:20:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:20:17: #1 tags after filtering in treatment: 24111306 INFO @ Sun, 02 Jun 2019 17:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:20:17: #1 finished! INFO @ Sun, 02 Jun 2019 17:20:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:20:17: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 17:20:17: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 17:20:17: start model_add_line... INFO @ Sun, 02 Jun 2019 17:20:17: start X-correlation... INFO @ Sun, 02 Jun 2019 17:20:17: end of X-cor INFO @ Sun, 02 Jun 2019 17:20:17: #2 finished! INFO @ Sun, 02 Jun 2019 17:20:17: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:20:17: #2 alternative fragment length(s) may be 1,46,511 bps INFO @ Sun, 02 Jun 2019 17:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.10_model.r WARNING @ Sun, 02 Jun 2019 17:20:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:20:17: #2 You may need to consider one of the other alternative d(s): 1,46,511 WARNING @ Sun, 02 Jun 2019 17:20:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:20:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:20:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:20:19: #2 number of paired peaks: 158 WARNING @ Sun, 02 Jun 2019 17:20:19: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sun, 02 Jun 2019 17:20:19: start model_add_line... INFO @ Sun, 02 Jun 2019 17:20:19: start X-correlation... INFO @ Sun, 02 Jun 2019 17:20:19: end of X-cor INFO @ Sun, 02 Jun 2019 17:20:19: #2 finished! INFO @ Sun, 02 Jun 2019 17:20:19: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:20:19: #2 alternative fragment length(s) may be 1,46,511 bps INFO @ Sun, 02 Jun 2019 17:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.05_model.r WARNING @ Sun, 02 Jun 2019 17:20:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:20:19: #2 You may need to consider one of the other alternative d(s): 1,46,511 WARNING @ Sun, 02 Jun 2019 17:20:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:20:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:20:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:20:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:20:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:20:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.20_summits.bed INFO @ Sun, 02 Jun 2019 17:20:38: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:21:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:21:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.10_summits.bed INFO @ Sun, 02 Jun 2019 17:21:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257708/SRX257708.05_summits.bed INFO @ Sun, 02 Jun 2019 17:21:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。