Job ID = 1299971 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:43:23 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T09:43:23 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed : NET - Reading : NET - Reading information from the socket failed ) 2019-06-03T09:43:23 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed : NET - Reading : NET - Reading information from the socket failed ) 2019-06-03T09:44:20 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 ) 2019-06-03T09:46:24 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 ) 2019-06-03T09:46:31 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 ) 2019-06-03T09:51:12 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 : 19,545,165 reads read : 19,545,165 reads written : 19,545,165 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:40 19545165 reads; of these: 19545165 (100.00%) were unpaired; of these: 434540 (2.22%) aligned 0 times 13033341 (66.68%) aligned exactly 1 time 6077284 (31.09%) aligned >1 times 97.78% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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 8 files... [bam_rmdupse_core] 1958146 / 19110625 = 0.1025 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 19:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.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 19:12:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:12:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.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 19:12:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:12:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.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 19:12:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:12:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:12:23: 1000000 INFO @ Mon, 03 Jun 2019 19:12:24: 1000000 INFO @ Mon, 03 Jun 2019 19:12:26: 1000000 INFO @ Mon, 03 Jun 2019 19:12:31: 2000000 INFO @ Mon, 03 Jun 2019 19:12:33: 2000000 INFO @ Mon, 03 Jun 2019 19:12:37: 2000000 INFO @ Mon, 03 Jun 2019 19:12:38: 3000000 INFO @ Mon, 03 Jun 2019 19:12:41: 3000000 INFO @ Mon, 03 Jun 2019 19:12:46: 4000000 INFO @ Mon, 03 Jun 2019 19:12:47: 3000000 INFO @ Mon, 03 Jun 2019 19:12:50: 4000000 INFO @ Mon, 03 Jun 2019 19:12:53: 5000000 INFO @ Mon, 03 Jun 2019 19:12:57: 4000000 INFO @ Mon, 03 Jun 2019 19:12:58: 5000000 INFO @ Mon, 03 Jun 2019 19:13:01: 6000000 INFO @ Mon, 03 Jun 2019 19:13:06: 6000000 INFO @ Mon, 03 Jun 2019 19:13:07: 5000000 INFO @ Mon, 03 Jun 2019 19:13:08: 7000000 INFO @ Mon, 03 Jun 2019 19:13:15: 7000000 INFO @ Mon, 03 Jun 2019 19:13:16: 8000000 INFO @ Mon, 03 Jun 2019 19:13:18: 6000000 INFO @ Mon, 03 Jun 2019 19:13:23: 8000000 INFO @ Mon, 03 Jun 2019 19:13:23: 9000000 INFO @ Mon, 03 Jun 2019 19:13:27: 7000000 INFO @ Mon, 03 Jun 2019 19:13:31: 10000000 INFO @ Mon, 03 Jun 2019 19:13:31: 9000000 INFO @ Mon, 03 Jun 2019 19:13:37: 8000000 INFO @ Mon, 03 Jun 2019 19:13:38: 11000000 INFO @ Mon, 03 Jun 2019 19:13:40: 10000000 INFO @ Mon, 03 Jun 2019 19:13:46: 12000000 INFO @ Mon, 03 Jun 2019 19:13:48: 11000000 INFO @ Mon, 03 Jun 2019 19:13:48: 9000000 INFO @ Mon, 03 Jun 2019 19:13:53: 13000000 INFO @ Mon, 03 Jun 2019 19:13:56: 12000000 INFO @ Mon, 03 Jun 2019 19:13:58: 10000000 INFO @ Mon, 03 Jun 2019 19:14:01: 14000000 INFO @ Mon, 03 Jun 2019 19:14:05: 13000000 INFO @ Mon, 03 Jun 2019 19:14:08: 15000000 INFO @ Mon, 03 Jun 2019 19:14:09: 11000000 INFO @ Mon, 03 Jun 2019 19:14:14: 14000000 INFO @ Mon, 03 Jun 2019 19:14:16: 16000000 INFO @ Mon, 03 Jun 2019 19:14:19: 12000000 INFO @ Mon, 03 Jun 2019 19:14:24: 15000000 INFO @ Mon, 03 Jun 2019 19:14:24: 17000000 INFO @ Mon, 03 Jun 2019 19:14:25: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:14:25: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:14:25: #1 total tags in treatment: 17152479 INFO @ Mon, 03 Jun 2019 19:14:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:14:25: #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 19:14:26: #1 tags after filtering in treatment: 17152479 INFO @ Mon, 03 Jun 2019 19:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:14:26: #1 finished! INFO @ Mon, 03 Jun 2019 19:14:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:14:27: #2 number of paired peaks: 840 WARNING @ Mon, 03 Jun 2019 19:14:27: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Mon, 03 Jun 2019 19:14:27: start model_add_line... INFO @ Mon, 03 Jun 2019 19:14:28: start X-correlation... INFO @ Mon, 03 Jun 2019 19:14:28: end of X-cor INFO @ Mon, 03 Jun 2019 19:14:28: #2 finished! INFO @ Mon, 03 Jun 2019 19:14:28: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 19:14:28: #2 alternative fragment length(s) may be 3,67 bps INFO @ Mon, 03 Jun 2019 19:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.05_model.r WARNING @ Mon, 03 Jun 2019 19:14:28: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:14:28: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Mon, 03 Jun 2019 19:14:28: #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 19:14:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:14:30: 13000000 INFO @ Mon, 03 Jun 2019 19:14:33: 16000000 INFO @ Mon, 03 Jun 2019 19:14:40: 14000000 INFO @ Mon, 03 Jun 2019 19:14:41: 17000000 INFO @ Mon, 03 Jun 2019 19:14:43: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:14:43: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:14:43: #1 total tags in treatment: 17152479 INFO @ Mon, 03 Jun 2019 19:14:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:14:43: #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 19:14:43: #1 tags after filtering in treatment: 17152479 INFO @ Mon, 03 Jun 2019 19:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:14:43: #1 finished! INFO @ Mon, 03 Jun 2019 19:14:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:14:45: #2 number of paired peaks: 840 WARNING @ Mon, 03 Jun 2019 19:14:45: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Mon, 03 Jun 2019 19:14:45: start model_add_line... INFO @ Mon, 03 Jun 2019 19:14:45: start X-correlation... INFO @ Mon, 03 Jun 2019 19:14:45: end of X-cor INFO @ Mon, 03 Jun 2019 19:14:45: #2 finished! INFO @ Mon, 03 Jun 2019 19:14:45: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 19:14:45: #2 alternative fragment length(s) may be 3,67 bps INFO @ Mon, 03 Jun 2019 19:14:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.10_model.r WARNING @ Mon, 03 Jun 2019 19:14:45: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:14:45: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Mon, 03 Jun 2019 19:14:45: #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 19:14:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:14:49: 15000000 INFO @ Mon, 03 Jun 2019 19:15:00: 16000000 INFO @ Mon, 03 Jun 2019 19:15:10: 17000000 INFO @ Mon, 03 Jun 2019 19:15:12: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:12: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:12: #1 total tags in treatment: 17152479 INFO @ Mon, 03 Jun 2019 19:15:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:12: #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 19:15:12: #1 tags after filtering in treatment: 17152479 INFO @ Mon, 03 Jun 2019 19:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:12: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:15:14: #2 number of paired peaks: 840 WARNING @ Mon, 03 Jun 2019 19:15:14: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Mon, 03 Jun 2019 19:15:14: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:14: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:14: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:14: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:14: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 19:15:14: #2 alternative fragment length(s) may be 3,67 bps INFO @ Mon, 03 Jun 2019 19:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.20_model.r WARNING @ Mon, 03 Jun 2019 19:15:14: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:15:14: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Mon, 03 Jun 2019 19:15:14: #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 19:15:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:15:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.05_summits.bed INFO @ Mon, 03 Jun 2019 19:15:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3375 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:15:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:15:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:15:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.10_summits.bed INFO @ Mon, 03 Jun 2019 19:15:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1904 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:16:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801800/SRX4801800.20_summits.bed INFO @ Mon, 03 Jun 2019 19:16:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (884 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。