Job ID = 1300674 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:28:47 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 ) 2019-06-03T10:28:47 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 ) 2019-06-03T10:28:47 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 ) 2019-06-03T10:34:03 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 ) 2019-06-03T10:34:03 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 : 47,019,076 reads read : 47,019,076 reads written : 47,019,076 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: 00:21:51 47019076 reads; of these: 47019076 (100.00%) were unpaired; of these: 9665125 (20.56%) aligned 0 times 14780382 (31.43%) aligned exactly 1 time 22573569 (48.01%) aligned >1 times 79.44% overall alignment rate Time searching: 00:21:51 Overall time: 00:21:51 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 16 files... [bam_rmdupse_core] 12021186 / 37353951 = 0.3218 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 20:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.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 20:05:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.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 20:05:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.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 20:05:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:05:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:05:19: 1000000 INFO @ Mon, 03 Jun 2019 20:05:19: 1000000 INFO @ Mon, 03 Jun 2019 20:05:20: 1000000 INFO @ Mon, 03 Jun 2019 20:05:27: 2000000 INFO @ Mon, 03 Jun 2019 20:05:27: 2000000 INFO @ Mon, 03 Jun 2019 20:05:28: 2000000 INFO @ Mon, 03 Jun 2019 20:05:34: 3000000 INFO @ Mon, 03 Jun 2019 20:05:35: 3000000 INFO @ Mon, 03 Jun 2019 20:05:36: 3000000 INFO @ Mon, 03 Jun 2019 20:05:41: 4000000 INFO @ Mon, 03 Jun 2019 20:05:42: 4000000 INFO @ Mon, 03 Jun 2019 20:05:44: 4000000 INFO @ Mon, 03 Jun 2019 20:05:48: 5000000 INFO @ Mon, 03 Jun 2019 20:05:49: 5000000 INFO @ Mon, 03 Jun 2019 20:05:52: 5000000 INFO @ Mon, 03 Jun 2019 20:05:55: 6000000 INFO @ Mon, 03 Jun 2019 20:05:57: 6000000 INFO @ Mon, 03 Jun 2019 20:05:59: 6000000 INFO @ Mon, 03 Jun 2019 20:06:02: 7000000 INFO @ Mon, 03 Jun 2019 20:06:04: 7000000 INFO @ Mon, 03 Jun 2019 20:06:07: 7000000 INFO @ Mon, 03 Jun 2019 20:06:09: 8000000 INFO @ Mon, 03 Jun 2019 20:06:12: 8000000 INFO @ Mon, 03 Jun 2019 20:06:15: 8000000 INFO @ Mon, 03 Jun 2019 20:06:16: 9000000 INFO @ Mon, 03 Jun 2019 20:06:19: 9000000 INFO @ Mon, 03 Jun 2019 20:06:23: 10000000 INFO @ Mon, 03 Jun 2019 20:06:23: 9000000 INFO @ Mon, 03 Jun 2019 20:06:26: 10000000 INFO @ Mon, 03 Jun 2019 20:06:30: 11000000 INFO @ Mon, 03 Jun 2019 20:06:31: 10000000 INFO @ Mon, 03 Jun 2019 20:06:34: 11000000 INFO @ Mon, 03 Jun 2019 20:06:37: 12000000 INFO @ Mon, 03 Jun 2019 20:06:38: 11000000 INFO @ Mon, 03 Jun 2019 20:06:41: 12000000 INFO @ Mon, 03 Jun 2019 20:06:44: 13000000 INFO @ Mon, 03 Jun 2019 20:06:46: 12000000 INFO @ Mon, 03 Jun 2019 20:06:49: 13000000 INFO @ Mon, 03 Jun 2019 20:06:51: 14000000 INFO @ Mon, 03 Jun 2019 20:06:53: 13000000 INFO @ Mon, 03 Jun 2019 20:06:56: 14000000 INFO @ Mon, 03 Jun 2019 20:06:58: 15000000 INFO @ Mon, 03 Jun 2019 20:07:01: 14000000 INFO @ Mon, 03 Jun 2019 20:07:03: 15000000 INFO @ Mon, 03 Jun 2019 20:07:06: 16000000 INFO @ Mon, 03 Jun 2019 20:07:08: 15000000 INFO @ Mon, 03 Jun 2019 20:07:11: 16000000 INFO @ Mon, 03 Jun 2019 20:07:14: 17000000 INFO @ Mon, 03 Jun 2019 20:07:15: 16000000 INFO @ Mon, 03 Jun 2019 20:07:18: 17000000 INFO @ Mon, 03 Jun 2019 20:07:22: 18000000 INFO @ Mon, 03 Jun 2019 20:07:23: 17000000 INFO @ Mon, 03 Jun 2019 20:07:25: 18000000 INFO @ Mon, 03 Jun 2019 20:07:29: 19000000 INFO @ Mon, 03 Jun 2019 20:07:30: 18000000 INFO @ Mon, 03 Jun 2019 20:07:33: 19000000 INFO @ Mon, 03 Jun 2019 20:07:37: 20000000 INFO @ Mon, 03 Jun 2019 20:07:38: 19000000 INFO @ Mon, 03 Jun 2019 20:07:40: 20000000 INFO @ Mon, 03 Jun 2019 20:07:45: 21000000 INFO @ Mon, 03 Jun 2019 20:07:45: 20000000 INFO @ Mon, 03 Jun 2019 20:07:47: 21000000 INFO @ Mon, 03 Jun 2019 20:07:53: 21000000 INFO @ Mon, 03 Jun 2019 20:07:53: 22000000 INFO @ Mon, 03 Jun 2019 20:07:55: 22000000 INFO @ Mon, 03 Jun 2019 20:08:00: 22000000 INFO @ Mon, 03 Jun 2019 20:08:01: 23000000 INFO @ Mon, 03 Jun 2019 20:08:02: 23000000 INFO @ Mon, 03 Jun 2019 20:08:08: 23000000 INFO @ Mon, 03 Jun 2019 20:08:09: 24000000 INFO @ Mon, 03 Jun 2019 20:08:10: 24000000 INFO @ Mon, 03 Jun 2019 20:08:16: 24000000 INFO @ Mon, 03 Jun 2019 20:08:17: 25000000 INFO @ Mon, 03 Jun 2019 20:08:17: 25000000 INFO @ Mon, 03 Jun 2019 20:08:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:08:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:08:20: #1 total tags in treatment: 25332765 INFO @ Mon, 03 Jun 2019 20:08:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:08:20: #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 20:08:20: #1 tags after filtering in treatment: 25332765 INFO @ Mon, 03 Jun 2019 20:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:08:20: #1 finished! INFO @ Mon, 03 Jun 2019 20:08:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:08:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:08:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:08:20: #1 total tags in treatment: 25332765 INFO @ Mon, 03 Jun 2019 20:08:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:08:20: #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 20:08:21: #1 tags after filtering in treatment: 25332765 INFO @ Mon, 03 Jun 2019 20:08:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:08:21: #1 finished! INFO @ Mon, 03 Jun 2019 20:08:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:08:23: #2 number of paired peaks: 551 WARNING @ Mon, 03 Jun 2019 20:08:23: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Mon, 03 Jun 2019 20:08:23: start model_add_line... INFO @ Mon, 03 Jun 2019 20:08:23: start X-correlation... INFO @ Mon, 03 Jun 2019 20:08:23: end of X-cor INFO @ Mon, 03 Jun 2019 20:08:23: #2 finished! INFO @ Mon, 03 Jun 2019 20:08:23: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:08:23: #2 alternative fragment length(s) may be 2,29,548 bps INFO @ Mon, 03 Jun 2019 20:08:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.20_model.r WARNING @ Mon, 03 Jun 2019 20:08:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:08:23: #2 You may need to consider one of the other alternative d(s): 2,29,548 WARNING @ Mon, 03 Jun 2019 20:08:23: #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 20:08:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:08:23: #2 number of paired peaks: 551 WARNING @ Mon, 03 Jun 2019 20:08:23: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Mon, 03 Jun 2019 20:08:23: start model_add_line... INFO @ Mon, 03 Jun 2019 20:08:23: start X-correlation... INFO @ Mon, 03 Jun 2019 20:08:23: end of X-cor INFO @ Mon, 03 Jun 2019 20:08:23: #2 finished! INFO @ Mon, 03 Jun 2019 20:08:23: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:08:23: #2 alternative fragment length(s) may be 2,29,548 bps INFO @ Mon, 03 Jun 2019 20:08:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.05_model.r WARNING @ Mon, 03 Jun 2019 20:08:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:08:23: #2 You may need to consider one of the other alternative d(s): 2,29,548 WARNING @ Mon, 03 Jun 2019 20:08:23: #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 20:08:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:08:25: 25000000 INFO @ Mon, 03 Jun 2019 20:08:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:08:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:08:28: #1 total tags in treatment: 25332765 INFO @ Mon, 03 Jun 2019 20:08:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:08:28: #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 20:08:28: #1 tags after filtering in treatment: 25332765 INFO @ Mon, 03 Jun 2019 20:08:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:08:28: #1 finished! INFO @ Mon, 03 Jun 2019 20:08:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:08:30: #2 number of paired peaks: 551 WARNING @ Mon, 03 Jun 2019 20:08:30: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Mon, 03 Jun 2019 20:08:30: start model_add_line... INFO @ Mon, 03 Jun 2019 20:08:31: start X-correlation... INFO @ Mon, 03 Jun 2019 20:08:31: end of X-cor INFO @ Mon, 03 Jun 2019 20:08:31: #2 finished! INFO @ Mon, 03 Jun 2019 20:08:31: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:08:31: #2 alternative fragment length(s) may be 2,29,548 bps INFO @ Mon, 03 Jun 2019 20:08:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.10_model.r WARNING @ Mon, 03 Jun 2019 20:08:31: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:08:31: #2 You may need to consider one of the other alternative d(s): 2,29,548 WARNING @ Mon, 03 Jun 2019 20:08:31: #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 20:08:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:08:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:09:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:09:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:09:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.05_summits.bed INFO @ Mon, 03 Jun 2019 20:09:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.20_summits.bed INFO @ Mon, 03 Jun 2019 20:09:47: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823789/SRX4823789.10_summits.bed INFO @ Mon, 03 Jun 2019 20:09:53: 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。