Job ID = 4178469 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:29:04 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 : 48,005,801 reads read : 96,011,602 reads written : 48,005,801 reads 0-length : 48,005,801 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: 00:11:28 48005801 reads; of these: 48005801 (100.00%) were unpaired; of these: 721916 (1.50%) aligned 0 times 38964319 (81.17%) aligned exactly 1 time 8319566 (17.33%) aligned >1 times 98.50% overall alignment rate Time searching: 00:11:28 Overall time: 00:11:28 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 20 files... [bam_rmdupse_core] 27206075 / 47283885 = 0.5754 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.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 12:55:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:55:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:55:50: 1000000 INFO @ Thu, 05 Dec 2019 12:55:56: 2000000 INFO @ Thu, 05 Dec 2019 12:56:03: 3000000 INFO @ Thu, 05 Dec 2019 12:56:09: 4000000 INFO @ Thu, 05 Dec 2019 12:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.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 12:56:14: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:14: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:15: 5000000 INFO @ Thu, 05 Dec 2019 12:56:22: 1000000 INFO @ Thu, 05 Dec 2019 12:56:23: 6000000 INFO @ Thu, 05 Dec 2019 12:56:29: 7000000 INFO @ Thu, 05 Dec 2019 12:56:29: 2000000 INFO @ Thu, 05 Dec 2019 12:56:35: 8000000 INFO @ Thu, 05 Dec 2019 12:56:36: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:56:42: 9000000 INFO @ Thu, 05 Dec 2019 12:56:44: 4000000 INFO @ Thu, 05 Dec 2019 12:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.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 12:56:44: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:44: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:49: 10000000 INFO @ Thu, 05 Dec 2019 12:56:52: 5000000 INFO @ Thu, 05 Dec 2019 12:56:52: 1000000 INFO @ Thu, 05 Dec 2019 12:56:55: 11000000 INFO @ Thu, 05 Dec 2019 12:57:00: 6000000 INFO @ Thu, 05 Dec 2019 12:57:01: 2000000 INFO @ Thu, 05 Dec 2019 12:57:01: 12000000 INFO @ Thu, 05 Dec 2019 12:57:08: 13000000 INFO @ Thu, 05 Dec 2019 12:57:09: 7000000 INFO @ Thu, 05 Dec 2019 12:57:09: 3000000 INFO @ Thu, 05 Dec 2019 12:57:14: 14000000 INFO @ Thu, 05 Dec 2019 12:57:17: 8000000 INFO @ Thu, 05 Dec 2019 12:57:17: 4000000 INFO @ Thu, 05 Dec 2019 12:57:21: 15000000 INFO @ Thu, 05 Dec 2019 12:57:25: 9000000 INFO @ Thu, 05 Dec 2019 12:57:25: 5000000 INFO @ Thu, 05 Dec 2019 12:57:27: 16000000 INFO @ Thu, 05 Dec 2019 12:57:33: 10000000 INFO @ Thu, 05 Dec 2019 12:57:33: 6000000 INFO @ Thu, 05 Dec 2019 12:57:34: 17000000 INFO @ Thu, 05 Dec 2019 12:57:41: 18000000 INFO @ Thu, 05 Dec 2019 12:57:41: 11000000 INFO @ Thu, 05 Dec 2019 12:57:41: 7000000 INFO @ Thu, 05 Dec 2019 12:57:47: 19000000 INFO @ Thu, 05 Dec 2019 12:57:49: 12000000 INFO @ Thu, 05 Dec 2019 12:57:49: 8000000 INFO @ Thu, 05 Dec 2019 12:57:53: 20000000 INFO @ Thu, 05 Dec 2019 12:57:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:57:54: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:57:54: #1 total tags in treatment: 20077810 INFO @ Thu, 05 Dec 2019 12:57:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:57:54: #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 12:57:54: #1 tags after filtering in treatment: 20077810 INFO @ Thu, 05 Dec 2019 12:57:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:57:54: #1 finished! INFO @ Thu, 05 Dec 2019 12:57:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:57:56: #2 number of paired peaks: 301 WARNING @ Thu, 05 Dec 2019 12:57:56: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Thu, 05 Dec 2019 12:57:56: start model_add_line... INFO @ Thu, 05 Dec 2019 12:57:56: start X-correlation... INFO @ Thu, 05 Dec 2019 12:57:56: end of X-cor INFO @ Thu, 05 Dec 2019 12:57:56: #2 finished! INFO @ Thu, 05 Dec 2019 12:57:56: #2 predicted fragment length is 30 bps INFO @ Thu, 05 Dec 2019 12:57:56: #2 alternative fragment length(s) may be 16,30,52,76,91,171,384,531,565,590 bps INFO @ Thu, 05 Dec 2019 12:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.05_model.r WARNING @ Thu, 05 Dec 2019 12:57:56: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:57:56: #2 You may need to consider one of the other alternative d(s): 16,30,52,76,91,171,384,531,565,590 WARNING @ Thu, 05 Dec 2019 12:57:56: #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 12:57:56: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:57:57: 13000000 INFO @ Thu, 05 Dec 2019 12:57:58: 9000000 INFO @ Thu, 05 Dec 2019 12:58:05: 14000000 INFO @ Thu, 05 Dec 2019 12:58:06: 10000000 INFO @ Thu, 05 Dec 2019 12:58:13: 15000000 INFO @ Thu, 05 Dec 2019 12:58:14: 11000000 INFO @ Thu, 05 Dec 2019 12:58:21: 16000000 INFO @ Thu, 05 Dec 2019 12:58:22: 12000000 INFO @ Thu, 05 Dec 2019 12:58:28: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:58:29: 17000000 INFO @ Thu, 05 Dec 2019 12:58:30: 13000000 INFO @ Thu, 05 Dec 2019 12:58:38: 18000000 INFO @ Thu, 05 Dec 2019 12:58:38: 14000000 INFO @ Thu, 05 Dec 2019 12:58:46: 19000000 INFO @ Thu, 05 Dec 2019 12:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.05_summits.bed INFO @ Thu, 05 Dec 2019 12:58:46: Done! INFO @ Thu, 05 Dec 2019 12:58:46: 15000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2231 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:58:53: 20000000 INFO @ Thu, 05 Dec 2019 12:58:54: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:58:54: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:58:54: #1 total tags in treatment: 20077810 INFO @ Thu, 05 Dec 2019 12:58:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:58:54: #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 12:58:54: 16000000 INFO @ Thu, 05 Dec 2019 12:58:54: #1 tags after filtering in treatment: 20077810 INFO @ Thu, 05 Dec 2019 12:58:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:58:54: #1 finished! INFO @ Thu, 05 Dec 2019 12:58:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:58:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:58:56: #2 number of paired peaks: 301 WARNING @ Thu, 05 Dec 2019 12:58:56: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Thu, 05 Dec 2019 12:58:56: start model_add_line... INFO @ Thu, 05 Dec 2019 12:58:56: start X-correlation... INFO @ Thu, 05 Dec 2019 12:58:56: end of X-cor INFO @ Thu, 05 Dec 2019 12:58:56: #2 finished! INFO @ Thu, 05 Dec 2019 12:58:56: #2 predicted fragment length is 30 bps INFO @ Thu, 05 Dec 2019 12:58:56: #2 alternative fragment length(s) may be 16,30,52,76,91,171,384,531,565,590 bps INFO @ Thu, 05 Dec 2019 12:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.10_model.r WARNING @ Thu, 05 Dec 2019 12:58:56: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:58:56: #2 You may need to consider one of the other alternative d(s): 16,30,52,76,91,171,384,531,565,590 WARNING @ Thu, 05 Dec 2019 12:58:56: #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 12:58:56: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:01: 17000000 INFO @ Thu, 05 Dec 2019 12:59:09: 18000000 INFO @ Thu, 05 Dec 2019 12:59:16: 19000000 INFO @ Thu, 05 Dec 2019 12:59:23: 20000000 INFO @ Thu, 05 Dec 2019 12:59:23: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:23: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:23: #1 total tags in treatment: 20077810 INFO @ Thu, 05 Dec 2019 12:59:23: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:23: #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 12:59:24: #1 tags after filtering in treatment: 20077810 INFO @ Thu, 05 Dec 2019 12:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:24: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:24: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:25: #2 number of paired peaks: 301 WARNING @ Thu, 05 Dec 2019 12:59:25: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Thu, 05 Dec 2019 12:59:25: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:25: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:25: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:25: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:25: #2 predicted fragment length is 30 bps INFO @ Thu, 05 Dec 2019 12:59:25: #2 alternative fragment length(s) may be 16,30,52,76,91,171,384,531,565,590 bps INFO @ Thu, 05 Dec 2019 12:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.20_model.r WARNING @ Thu, 05 Dec 2019 12:59:25: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:25: #2 You may need to consider one of the other alternative d(s): 16,30,52,76,91,171,384,531,565,590 WARNING @ Thu, 05 Dec 2019 12:59:25: #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 12:59:25: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.10_summits.bed INFO @ Thu, 05 Dec 2019 12:59:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:59:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535370/SRX5535370.20_summits.bed INFO @ Thu, 05 Dec 2019 13:00:17: Done! pass1 - making usageList (2 chroms): 2 millis pass2 - checking and writing primary data (30 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。