Job ID = 4178524 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:43:43 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 : 19,497,639 reads read : 19,497,639 reads written : 19,497,639 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:48 19497639 reads; of these: 19497639 (100.00%) were unpaired; of these: 1390097 (7.13%) aligned 0 times 14673506 (75.26%) aligned exactly 1 time 3434036 (17.61%) aligned >1 times 92.87% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 5368015 / 18107542 = 0.2965 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.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 12:56:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:55: 1000000 INFO @ Thu, 05 Dec 2019 12:57:06: 2000000 INFO @ Thu, 05 Dec 2019 12:57:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.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 12:57:14: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:57:14: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:57:17: 3000000 INFO @ Thu, 05 Dec 2019 12:57:24: 1000000 INFO @ Thu, 05 Dec 2019 12:57:29: 4000000 INFO @ Thu, 05 Dec 2019 12:57:34: 2000000 INFO @ Thu, 05 Dec 2019 12:57:41: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:57:44: 3000000 INFO @ Thu, 05 Dec 2019 12:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.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 12:57:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:57:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:57:52: 6000000 INFO @ Thu, 05 Dec 2019 12:57:53: 1000000 INFO @ Thu, 05 Dec 2019 12:57:54: 4000000 INFO @ Thu, 05 Dec 2019 12:58:01: 2000000 INFO @ Thu, 05 Dec 2019 12:58:04: 5000000 INFO @ Thu, 05 Dec 2019 12:58:04: 7000000 INFO @ Thu, 05 Dec 2019 12:58:10: 3000000 INFO @ Thu, 05 Dec 2019 12:58:13: 6000000 INFO @ Thu, 05 Dec 2019 12:58:16: 8000000 INFO @ Thu, 05 Dec 2019 12:58:19: 4000000 INFO @ Thu, 05 Dec 2019 12:58:23: 7000000 INFO @ Thu, 05 Dec 2019 12:58:29: 9000000 INFO @ Thu, 05 Dec 2019 12:58:31: 5000000 INFO @ Thu, 05 Dec 2019 12:58:32: 8000000 INFO @ Thu, 05 Dec 2019 12:58:40: 6000000 INFO @ Thu, 05 Dec 2019 12:58:41: 10000000 INFO @ Thu, 05 Dec 2019 12:58:42: 9000000 INFO @ Thu, 05 Dec 2019 12:58:51: 10000000 INFO @ Thu, 05 Dec 2019 12:58:52: 7000000 INFO @ Thu, 05 Dec 2019 12:58:53: 11000000 INFO @ Thu, 05 Dec 2019 12:59:01: 11000000 INFO @ Thu, 05 Dec 2019 12:59:01: 8000000 INFO @ Thu, 05 Dec 2019 12:59:05: 12000000 INFO @ Thu, 05 Dec 2019 12:59:10: 9000000 INFO @ Thu, 05 Dec 2019 12:59:10: 12000000 INFO @ Thu, 05 Dec 2019 12:59:13: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:13: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:13: #1 total tags in treatment: 12739527 INFO @ Thu, 05 Dec 2019 12:59:13: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:13: #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 12:59:14: #1 tags after filtering in treatment: 12739527 INFO @ Thu, 05 Dec 2019 12:59:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:14: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:14: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:15: #2 number of paired peaks: 303 WARNING @ Thu, 05 Dec 2019 12:59:15: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 05 Dec 2019 12:59:15: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:15: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:15: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:15: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:15: #2 predicted fragment length is 59 bps INFO @ Thu, 05 Dec 2019 12:59:15: #2 alternative fragment length(s) may be 30,59,81,97,125,149,240,318,389,428,468,496,522 bps INFO @ Thu, 05 Dec 2019 12:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.05_model.r WARNING @ Thu, 05 Dec 2019 12:59:15: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:15: #2 You may need to consider one of the other alternative d(s): 30,59,81,97,125,149,240,318,389,428,468,496,522 WARNING @ Thu, 05 Dec 2019 12:59:15: #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 12:59:15: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:17: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:17: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:17: #1 total tags in treatment: 12739527 INFO @ Thu, 05 Dec 2019 12:59:17: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:17: #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 12:59:18: #1 tags after filtering in treatment: 12739527 INFO @ Thu, 05 Dec 2019 12:59:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:18: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:18: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:18: 10000000 INFO @ Thu, 05 Dec 2019 12:59:19: #2 number of paired peaks: 303 WARNING @ Thu, 05 Dec 2019 12:59:19: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 05 Dec 2019 12:59:19: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:19: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:19: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:19: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:19: #2 predicted fragment length is 59 bps INFO @ Thu, 05 Dec 2019 12:59:19: #2 alternative fragment length(s) may be 30,59,81,97,125,149,240,318,389,428,468,496,522 bps INFO @ Thu, 05 Dec 2019 12:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.10_model.r WARNING @ Thu, 05 Dec 2019 12:59:19: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:19: #2 You may need to consider one of the other alternative d(s): 30,59,81,97,125,149,240,318,389,428,468,496,522 WARNING @ Thu, 05 Dec 2019 12:59:19: #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 12:59:19: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:26: 11000000 INFO @ Thu, 05 Dec 2019 12:59:35: 12000000 INFO @ Thu, 05 Dec 2019 12:59:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:41: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:41: #1 total tags in treatment: 12739527 INFO @ Thu, 05 Dec 2019 12:59:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:41: #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 12:59:41: #1 tags after filtering in treatment: 12739527 INFO @ Thu, 05 Dec 2019 12:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:41: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:42: #2 number of paired peaks: 303 WARNING @ Thu, 05 Dec 2019 12:59:42: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 05 Dec 2019 12:59:42: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:42: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:42: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:42: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:42: #2 predicted fragment length is 59 bps INFO @ Thu, 05 Dec 2019 12:59:42: #2 alternative fragment length(s) may be 30,59,81,97,125,149,240,318,389,428,468,496,522 bps INFO @ Thu, 05 Dec 2019 12:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.20_model.r WARNING @ Thu, 05 Dec 2019 12:59:42: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:42: #2 You may need to consider one of the other alternative d(s): 30,59,81,97,125,149,240,318,389,428,468,496,522 WARNING @ Thu, 05 Dec 2019 12:59:42: #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 12:59:42: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:59:53: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.05_summits.bed INFO @ Thu, 05 Dec 2019 13:00:08: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1367 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.10_summits.bed INFO @ Thu, 05 Dec 2019 13:00:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (571 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:00:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717043/SRX5717043.20_summits.bed INFO @ Thu, 05 Dec 2019 13:00:32: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。