Job ID = 4178482 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:27:44 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 : NET - Reading information from the socket failed ) 2019-12-05T03:27:44 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 : NET - Reading information from the socket failed ) spots read : 20,652,004 reads read : 20,652,004 reads written : 20,652,004 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: 00:09:30 20652004 reads; of these: 20652004 (100.00%) were unpaired; of these: 662255 (3.21%) aligned 0 times 12789062 (61.93%) aligned exactly 1 time 7200687 (34.87%) aligned >1 times 96.79% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:31 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 12 files... [bam_rmdupse_core] 5088586 / 19989749 = 0.2546 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.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 @ Thu, 05 Dec 2019 12:48:15: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:48:15: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:48:22: 1000000 INFO @ Thu, 05 Dec 2019 12:48:30: 2000000 INFO @ Thu, 05 Dec 2019 12:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.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 @ Thu, 05 Dec 2019 12:48:35: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:48:35: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:48:38: 3000000 INFO @ Thu, 05 Dec 2019 12:48:44: 1000000 INFO @ Thu, 05 Dec 2019 12:48:46: 4000000 INFO @ Thu, 05 Dec 2019 12:48:53: 2000000 INFO @ Thu, 05 Dec 2019 12:48:56: 5000000 INFO @ Thu, 05 Dec 2019 12:49:02: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:49:04: 6000000 INFO @ Thu, 05 Dec 2019 12:49:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.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 @ Thu, 05 Dec 2019 12:49:05: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:49:05: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:49:11: 4000000 INFO @ Thu, 05 Dec 2019 12:49:13: 1000000 INFO @ Thu, 05 Dec 2019 12:49:13: 7000000 INFO @ Thu, 05 Dec 2019 12:49:20: 2000000 INFO @ Thu, 05 Dec 2019 12:49:21: 5000000 INFO @ Thu, 05 Dec 2019 12:49:22: 8000000 INFO @ Thu, 05 Dec 2019 12:49:29: 3000000 INFO @ Thu, 05 Dec 2019 12:49:31: 9000000 INFO @ Thu, 05 Dec 2019 12:49:31: 6000000 INFO @ Thu, 05 Dec 2019 12:49:36: 4000000 INFO @ Thu, 05 Dec 2019 12:49:39: 10000000 INFO @ Thu, 05 Dec 2019 12:49:40: 7000000 INFO @ Thu, 05 Dec 2019 12:49:43: 5000000 INFO @ Thu, 05 Dec 2019 12:49:48: 11000000 INFO @ Thu, 05 Dec 2019 12:49:49: 8000000 INFO @ Thu, 05 Dec 2019 12:49:50: 6000000 INFO @ Thu, 05 Dec 2019 12:49:56: 12000000 INFO @ Thu, 05 Dec 2019 12:49:58: 7000000 INFO @ Thu, 05 Dec 2019 12:49:58: 9000000 INFO @ Thu, 05 Dec 2019 12:50:08: 10000000 INFO @ Thu, 05 Dec 2019 12:50:08: 8000000 INFO @ Thu, 05 Dec 2019 12:50:11: 13000000 INFO @ Thu, 05 Dec 2019 12:50:23: 11000000 INFO @ Thu, 05 Dec 2019 12:50:24: 9000000 INFO @ Thu, 05 Dec 2019 12:50:27: 14000000 INFO @ Thu, 05 Dec 2019 12:50:34: 12000000 INFO @ Thu, 05 Dec 2019 12:50:35: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:50:35: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:50:35: #1 total tags in treatment: 14901163 INFO @ Thu, 05 Dec 2019 12:50:35: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:50:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:50:35: #1 tags after filtering in treatment: 14901163 INFO @ Thu, 05 Dec 2019 12:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:50:35: #1 finished! INFO @ Thu, 05 Dec 2019 12:50:35: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:50:35: 10000000 INFO @ Thu, 05 Dec 2019 12:50:36: #2 number of paired peaks: 158 WARNING @ Thu, 05 Dec 2019 12:50:36: 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 @ Thu, 05 Dec 2019 12:50:36: start model_add_line... INFO @ Thu, 05 Dec 2019 12:50:37: start X-correlation... INFO @ Thu, 05 Dec 2019 12:50:37: end of X-cor INFO @ Thu, 05 Dec 2019 12:50:37: #2 finished! INFO @ Thu, 05 Dec 2019 12:50:37: #2 predicted fragment length is 40 bps INFO @ Thu, 05 Dec 2019 12:50:37: #2 alternative fragment length(s) may be 1,40,57,253,469,496,572,580,587 bps INFO @ Thu, 05 Dec 2019 12:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.05_model.r WARNING @ Thu, 05 Dec 2019 12:50:37: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:50:37: #2 You may need to consider one of the other alternative d(s): 1,40,57,253,469,496,572,580,587 WARNING @ Thu, 05 Dec 2019 12:50:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:50:37: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:50:44: 13000000 INFO @ Thu, 05 Dec 2019 12:50:45: 11000000 INFO @ Thu, 05 Dec 2019 12:50:55: 14000000 INFO @ Thu, 05 Dec 2019 12:50:55: 12000000 INFO @ Thu, 05 Dec 2019 12:51:04: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:51:04: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:51:04: #1 total tags in treatment: 14901163 INFO @ Thu, 05 Dec 2019 12:51:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:51:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:51:05: #1 tags after filtering in treatment: 14901163 INFO @ Thu, 05 Dec 2019 12:51:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:51:05: #1 finished! INFO @ Thu, 05 Dec 2019 12:51:05: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:51:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:51:05: 13000000 INFO @ Thu, 05 Dec 2019 12:51:06: #2 number of paired peaks: 158 WARNING @ Thu, 05 Dec 2019 12:51:06: 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 @ Thu, 05 Dec 2019 12:51:06: start model_add_line... INFO @ Thu, 05 Dec 2019 12:51:06: start X-correlation... INFO @ Thu, 05 Dec 2019 12:51:06: end of X-cor INFO @ Thu, 05 Dec 2019 12:51:06: #2 finished! INFO @ Thu, 05 Dec 2019 12:51:06: #2 predicted fragment length is 40 bps INFO @ Thu, 05 Dec 2019 12:51:06: #2 alternative fragment length(s) may be 1,40,57,253,469,496,572,580,587 bps INFO @ Thu, 05 Dec 2019 12:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.10_model.r WARNING @ Thu, 05 Dec 2019 12:51:06: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:51:06: #2 You may need to consider one of the other alternative d(s): 1,40,57,253,469,496,572,580,587 WARNING @ Thu, 05 Dec 2019 12:51:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:51:06: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:51:14: 14000000 INFO @ Thu, 05 Dec 2019 12:51:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:51:23: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:51:23: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:51:23: #1 total tags in treatment: 14901163 INFO @ Thu, 05 Dec 2019 12:51:23: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:51:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:51:23: #1 tags after filtering in treatment: 14901163 INFO @ Thu, 05 Dec 2019 12:51:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:51:23: #1 finished! INFO @ Thu, 05 Dec 2019 12:51:23: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:51:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:51:25: #2 number of paired peaks: 158 WARNING @ Thu, 05 Dec 2019 12:51:25: 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 @ Thu, 05 Dec 2019 12:51:25: start model_add_line... INFO @ Thu, 05 Dec 2019 12:51:25: start X-correlation... INFO @ Thu, 05 Dec 2019 12:51:25: end of X-cor INFO @ Thu, 05 Dec 2019 12:51:25: #2 finished! INFO @ Thu, 05 Dec 2019 12:51:25: #2 predicted fragment length is 40 bps INFO @ Thu, 05 Dec 2019 12:51:25: #2 alternative fragment length(s) may be 1,40,57,253,469,496,572,580,587 bps INFO @ Thu, 05 Dec 2019 12:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.20_model.r WARNING @ Thu, 05 Dec 2019 12:51:25: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:51:25: #2 You may need to consider one of the other alternative d(s): 1,40,57,253,469,496,572,580,587 WARNING @ Thu, 05 Dec 2019 12:51:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:51:25: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:51:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:51:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.05_summits.bed INFO @ Thu, 05 Dec 2019 12:51:38: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (1915 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:51:46: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:52:04: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.10_summits.bed INFO @ Thu, 05 Dec 2019 12:52:07: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (645 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535384/SRX5535384.20_summits.bed INFO @ Thu, 05 Dec 2019 12:52:23: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。