Job ID = 4178520 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:38:27 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 : 20,427,548 reads read : 20,427,548 reads written : 20,427,548 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: 00:07:38 20427548 reads; of these: 20427548 (100.00%) were unpaired; of these: 2608309 (12.77%) aligned 0 times 12205518 (59.75%) aligned exactly 1 time 5613721 (27.48%) aligned >1 times 87.23% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 3796366 / 17819239 = 0.2130 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.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 12:57:08: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:57:08: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:57:14: 1000000 INFO @ Thu, 05 Dec 2019 12:57:20: 2000000 INFO @ Thu, 05 Dec 2019 12:57:27: 3000000 INFO @ Thu, 05 Dec 2019 12:57:33: 4000000 INFO @ Thu, 05 Dec 2019 12:57:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.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 12:57:37: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:57:37: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:57:39: 5000000 INFO @ Thu, 05 Dec 2019 12:57:45: 1000000 INFO @ Thu, 05 Dec 2019 12:57:45: 6000000 INFO @ Thu, 05 Dec 2019 12:57:52: 2000000 INFO @ Thu, 05 Dec 2019 12:57:53: 7000000 INFO @ Thu, 05 Dec 2019 12:57:59: 3000000 INFO @ Thu, 05 Dec 2019 12:57:59: 8000000 INFO @ Thu, 05 Dec 2019 12:58:05: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:58:06: 9000000 INFO @ Thu, 05 Dec 2019 12:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.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 12:58:08: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:58:08: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:58:11: 5000000 INFO @ Thu, 05 Dec 2019 12:58:12: 10000000 INFO @ Thu, 05 Dec 2019 12:58:15: 1000000 INFO @ Thu, 05 Dec 2019 12:58:17: 6000000 INFO @ Thu, 05 Dec 2019 12:58:18: 11000000 INFO @ Thu, 05 Dec 2019 12:58:22: 2000000 INFO @ Thu, 05 Dec 2019 12:58:24: 7000000 INFO @ Thu, 05 Dec 2019 12:58:25: 12000000 INFO @ Thu, 05 Dec 2019 12:58:28: 3000000 INFO @ Thu, 05 Dec 2019 12:58:30: 8000000 INFO @ Thu, 05 Dec 2019 12:58:32: 13000000 INFO @ Thu, 05 Dec 2019 12:58:35: 4000000 INFO @ Thu, 05 Dec 2019 12:58:37: 9000000 INFO @ Thu, 05 Dec 2019 12:58:39: 14000000 INFO @ Thu, 05 Dec 2019 12:58:40: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:58:40: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:58:40: #1 total tags in treatment: 14022873 INFO @ Thu, 05 Dec 2019 12:58:40: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:58:40: #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 12:58:40: #1 tags after filtering in treatment: 14022873 INFO @ Thu, 05 Dec 2019 12:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:58:40: #1 finished! INFO @ Thu, 05 Dec 2019 12:58:40: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:58:41: #2 number of paired peaks: 122 WARNING @ Thu, 05 Dec 2019 12:58:41: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Thu, 05 Dec 2019 12:58:41: start model_add_line... INFO @ Thu, 05 Dec 2019 12:58:41: start X-correlation... INFO @ Thu, 05 Dec 2019 12:58:41: end of X-cor INFO @ Thu, 05 Dec 2019 12:58:41: #2 finished! INFO @ Thu, 05 Dec 2019 12:58:41: #2 predicted fragment length is 59 bps INFO @ Thu, 05 Dec 2019 12:58:41: #2 alternative fragment length(s) may be 26,45,59,78,145,151,233,256,308,340,416,451,489,525,589 bps INFO @ Thu, 05 Dec 2019 12:58:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.05_model.r WARNING @ Thu, 05 Dec 2019 12:58:41: #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 12:58:41: #2 You may need to consider one of the other alternative d(s): 26,45,59,78,145,151,233,256,308,340,416,451,489,525,589 WARNING @ Thu, 05 Dec 2019 12:58:41: #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 12:58:41: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:58:42: 5000000 INFO @ Thu, 05 Dec 2019 12:58:43: 10000000 INFO @ Thu, 05 Dec 2019 12:58:49: 6000000 INFO @ Thu, 05 Dec 2019 12:58:51: 11000000 INFO @ Thu, 05 Dec 2019 12:58:56: 7000000 INFO @ Thu, 05 Dec 2019 12:58:58: 12000000 INFO @ Thu, 05 Dec 2019 12:59:03: 8000000 INFO @ Thu, 05 Dec 2019 12:59:06: 13000000 INFO @ Thu, 05 Dec 2019 12:59:10: 9000000 INFO @ Thu, 05 Dec 2019 12:59:13: 14000000 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: 14022873 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: 14022873 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: 122 WARNING @ Thu, 05 Dec 2019 12:59:15: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 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 26,45,59,78,145,151,233,256,308,340,416,451,489,525,589 bps INFO @ Thu, 05 Dec 2019 12:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.10_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): 26,45,59,78,145,151,233,256,308,340,416,451,489,525,589 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: 10000000 INFO @ Thu, 05 Dec 2019 12:59:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:59:24: 11000000 INFO @ Thu, 05 Dec 2019 12:59:30: 12000000 INFO @ Thu, 05 Dec 2019 12:59:37: 13000000 INFO @ Thu, 05 Dec 2019 12:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.05_summits.bed INFO @ Thu, 05 Dec 2019 12:59:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1660 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:59:44: 14000000 INFO @ Thu, 05 Dec 2019 12:59:44: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:44: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:44: #1 total tags in treatment: 14022873 INFO @ Thu, 05 Dec 2019 12:59:44: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:44: #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 12:59:45: #1 tags after filtering in treatment: 14022873 INFO @ Thu, 05 Dec 2019 12:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:45: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:45: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:46: #2 number of paired peaks: 122 WARNING @ Thu, 05 Dec 2019 12:59:46: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Thu, 05 Dec 2019 12:59:46: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:46: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:46: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:46: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:46: #2 predicted fragment length is 59 bps INFO @ Thu, 05 Dec 2019 12:59:46: #2 alternative fragment length(s) may be 26,45,59,78,145,151,233,256,308,340,416,451,489,525,589 bps INFO @ Thu, 05 Dec 2019 12:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.20_model.r WARNING @ Thu, 05 Dec 2019 12:59:46: #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 12:59:46: #2 You may need to consider one of the other alternative d(s): 26,45,59,78,145,151,233,256,308,340,416,451,489,525,589 WARNING @ Thu, 05 Dec 2019 12:59:46: #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 12:59:46: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:53: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.10_summits.bed INFO @ Thu, 05 Dec 2019 13:00:11: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (689 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:00:23: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717040/SRX5717040.20_summits.bed INFO @ Thu, 05 Dec 2019 13:00:42: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (100 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。