Job ID = 1294508 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:32:12 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 ) 2019-06-02T23:32:12 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 ) 2019-06-02T23:39:50 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 ) 2019-06-02T23:39:50 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 ) 2019-06-02T23:39:50 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 ) 2019-06-02T23:39:50 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 : 18,953,572 reads read : 18,953,572 reads written : 18,953,572 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: 00:09:39 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 973830 (5.14%) aligned 0 times 11627629 (61.35%) aligned exactly 1 time 6352113 (33.51%) aligned >1 times 94.86% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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] 3038462 / 17979742 = 0.1690 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 08:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.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 08:55:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.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 08:55:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.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 08:55:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:56:02: 1000000 INFO @ Mon, 03 Jun 2019 08:56:03: 1000000 INFO @ Mon, 03 Jun 2019 08:56:04: 1000000 INFO @ Mon, 03 Jun 2019 08:56:10: 2000000 INFO @ Mon, 03 Jun 2019 08:56:11: 2000000 INFO @ Mon, 03 Jun 2019 08:56:14: 2000000 INFO @ Mon, 03 Jun 2019 08:56:18: 3000000 INFO @ Mon, 03 Jun 2019 08:56:19: 3000000 INFO @ Mon, 03 Jun 2019 08:56:24: 3000000 INFO @ Mon, 03 Jun 2019 08:56:27: 4000000 INFO @ Mon, 03 Jun 2019 08:56:28: 4000000 INFO @ Mon, 03 Jun 2019 08:56:34: 4000000 INFO @ Mon, 03 Jun 2019 08:56:35: 5000000 INFO @ Mon, 03 Jun 2019 08:56:36: 5000000 INFO @ Mon, 03 Jun 2019 08:56:43: 6000000 INFO @ Mon, 03 Jun 2019 08:56:44: 6000000 INFO @ Mon, 03 Jun 2019 08:56:44: 5000000 INFO @ Mon, 03 Jun 2019 08:56:51: 7000000 INFO @ Mon, 03 Jun 2019 08:56:53: 7000000 INFO @ Mon, 03 Jun 2019 08:56:54: 6000000 INFO @ Mon, 03 Jun 2019 08:56:59: 8000000 INFO @ Mon, 03 Jun 2019 08:57:02: 8000000 INFO @ Mon, 03 Jun 2019 08:57:05: 7000000 INFO @ Mon, 03 Jun 2019 08:57:07: 9000000 INFO @ Mon, 03 Jun 2019 08:57:11: 9000000 INFO @ Mon, 03 Jun 2019 08:57:14: 10000000 INFO @ Mon, 03 Jun 2019 08:57:15: 8000000 INFO @ Mon, 03 Jun 2019 08:57:19: 10000000 INFO @ Mon, 03 Jun 2019 08:57:23: 11000000 INFO @ Mon, 03 Jun 2019 08:57:24: 9000000 INFO @ Mon, 03 Jun 2019 08:57:28: 11000000 INFO @ Mon, 03 Jun 2019 08:57:32: 12000000 INFO @ Mon, 03 Jun 2019 08:57:34: 10000000 INFO @ Mon, 03 Jun 2019 08:57:36: 12000000 INFO @ Mon, 03 Jun 2019 08:57:40: 13000000 INFO @ Mon, 03 Jun 2019 08:57:44: 11000000 INFO @ Mon, 03 Jun 2019 08:57:44: 13000000 INFO @ Mon, 03 Jun 2019 08:57:48: 14000000 INFO @ Mon, 03 Jun 2019 08:57:52: 14000000 INFO @ Mon, 03 Jun 2019 08:57:54: 12000000 INFO @ Mon, 03 Jun 2019 08:57:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:57:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:57:55: #1 total tags in treatment: 14941280 INFO @ Mon, 03 Jun 2019 08:57:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:57:55: #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 08:57:56: #1 tags after filtering in treatment: 14941280 INFO @ Mon, 03 Jun 2019 08:57:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:57:56: #1 finished! INFO @ Mon, 03 Jun 2019 08:57:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:57:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:57:57: #2 number of paired peaks: 431 WARNING @ Mon, 03 Jun 2019 08:57:57: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Mon, 03 Jun 2019 08:57:57: start model_add_line... INFO @ Mon, 03 Jun 2019 08:57:57: start X-correlation... INFO @ Mon, 03 Jun 2019 08:57:57: end of X-cor INFO @ Mon, 03 Jun 2019 08:57:57: #2 finished! INFO @ Mon, 03 Jun 2019 08:57:57: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 08:57:57: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 08:57:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.05_model.r WARNING @ Mon, 03 Jun 2019 08:57:57: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:57:57: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 08:57:57: #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 08:57:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:57:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:58:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:58:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:58:00: #1 total tags in treatment: 14941280 INFO @ Mon, 03 Jun 2019 08:58:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:58:00: #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 08:58:00: #1 tags after filtering in treatment: 14941280 INFO @ Mon, 03 Jun 2019 08:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:58:00: #1 finished! INFO @ Mon, 03 Jun 2019 08:58:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:58:02: #2 number of paired peaks: 431 WARNING @ Mon, 03 Jun 2019 08:58:02: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Mon, 03 Jun 2019 08:58:02: start model_add_line... INFO @ Mon, 03 Jun 2019 08:58:02: start X-correlation... INFO @ Mon, 03 Jun 2019 08:58:02: end of X-cor INFO @ Mon, 03 Jun 2019 08:58:02: #2 finished! INFO @ Mon, 03 Jun 2019 08:58:02: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 08:58:02: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 08:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.20_model.r WARNING @ Mon, 03 Jun 2019 08:58:02: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:58:02: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 08:58:02: #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 08:58:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:58:03: 13000000 INFO @ Mon, 03 Jun 2019 08:58:13: 14000000 INFO @ Mon, 03 Jun 2019 08:58:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:58:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:58:22: #1 total tags in treatment: 14941280 INFO @ Mon, 03 Jun 2019 08:58:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:58:22: #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 08:58:22: #1 tags after filtering in treatment: 14941280 INFO @ Mon, 03 Jun 2019 08:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:58:22: #1 finished! INFO @ Mon, 03 Jun 2019 08:58:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:58:24: #2 number of paired peaks: 431 WARNING @ Mon, 03 Jun 2019 08:58:24: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Mon, 03 Jun 2019 08:58:24: start model_add_line... INFO @ Mon, 03 Jun 2019 08:58:24: start X-correlation... INFO @ Mon, 03 Jun 2019 08:58:24: end of X-cor INFO @ Mon, 03 Jun 2019 08:58:24: #2 finished! INFO @ Mon, 03 Jun 2019 08:58:24: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 08:58:24: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 08:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.10_model.r WARNING @ Mon, 03 Jun 2019 08:58:24: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:58:24: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 08:58:24: #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 08:58:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:58:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:58:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:58:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.05_summits.bed INFO @ Mon, 03 Jun 2019 08:58:56: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2206 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.20_summits.bed INFO @ Mon, 03 Jun 2019 08:59:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1537 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:59:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287706/SRX287706.10_summits.bed INFO @ Mon, 03 Jun 2019 08:59:22: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1956 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。