Job ID = 1294474 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:12:32 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 ) 2019-06-02T23:12:32 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 : 11,258,758 reads read : 11,258,758 reads written : 11,258,758 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: 00:05:32 11258758 reads; of these: 11258758 (100.00%) were unpaired; of these: 550853 (4.89%) aligned 0 times 7134488 (63.37%) aligned exactly 1 time 3573417 (31.74%) aligned >1 times 95.11% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 1087000 / 10707905 = 0.1015 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 08:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.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 08:27:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:27:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.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 08:27:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:27:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.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 08:27:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:27:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:27:41: 1000000 INFO @ Mon, 03 Jun 2019 08:27:42: 1000000 INFO @ Mon, 03 Jun 2019 08:27:44: 1000000 INFO @ Mon, 03 Jun 2019 08:27:49: 2000000 INFO @ Mon, 03 Jun 2019 08:27:51: 2000000 INFO @ Mon, 03 Jun 2019 08:27:54: 2000000 INFO @ Mon, 03 Jun 2019 08:27:57: 3000000 INFO @ Mon, 03 Jun 2019 08:27:59: 3000000 INFO @ Mon, 03 Jun 2019 08:28:03: 3000000 INFO @ Mon, 03 Jun 2019 08:28:04: 4000000 INFO @ Mon, 03 Jun 2019 08:28:08: 4000000 INFO @ Mon, 03 Jun 2019 08:28:12: 5000000 INFO @ Mon, 03 Jun 2019 08:28:13: 4000000 INFO @ Mon, 03 Jun 2019 08:28:16: 5000000 INFO @ Mon, 03 Jun 2019 08:28:20: 6000000 INFO @ Mon, 03 Jun 2019 08:28:22: 5000000 INFO @ Mon, 03 Jun 2019 08:28:24: 6000000 INFO @ Mon, 03 Jun 2019 08:28:27: 7000000 INFO @ Mon, 03 Jun 2019 08:28:31: 6000000 INFO @ Mon, 03 Jun 2019 08:28:33: 7000000 INFO @ Mon, 03 Jun 2019 08:28:35: 8000000 INFO @ Mon, 03 Jun 2019 08:28:41: 7000000 INFO @ Mon, 03 Jun 2019 08:28:41: 8000000 INFO @ Mon, 03 Jun 2019 08:28:42: 9000000 INFO @ Mon, 03 Jun 2019 08:28:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:28:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:28:47: #1 total tags in treatment: 9620905 INFO @ Mon, 03 Jun 2019 08:28:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:28:47: #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 08:28:48: #1 tags after filtering in treatment: 9620905 INFO @ Mon, 03 Jun 2019 08:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:28:48: #1 finished! INFO @ Mon, 03 Jun 2019 08:28:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:28:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:28:48: #2 number of paired peaks: 397 WARNING @ Mon, 03 Jun 2019 08:28:48: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 03 Jun 2019 08:28:48: start model_add_line... INFO @ Mon, 03 Jun 2019 08:28:48: start X-correlation... INFO @ Mon, 03 Jun 2019 08:28:49: end of X-cor INFO @ Mon, 03 Jun 2019 08:28:49: #2 finished! INFO @ Mon, 03 Jun 2019 08:28:49: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:28:49: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.10_model.r WARNING @ Mon, 03 Jun 2019 08:28:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:28:49: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:28:49: #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 08:28:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:28:49: 9000000 INFO @ Mon, 03 Jun 2019 08:28:49: 8000000 INFO @ Mon, 03 Jun 2019 08:28:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:28:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:28:55: #1 total tags in treatment: 9620905 INFO @ Mon, 03 Jun 2019 08:28:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:28:55: #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 08:28:55: #1 tags after filtering in treatment: 9620905 INFO @ Mon, 03 Jun 2019 08:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:28:55: #1 finished! INFO @ Mon, 03 Jun 2019 08:28:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:28:56: #2 number of paired peaks: 397 WARNING @ Mon, 03 Jun 2019 08:28:56: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 03 Jun 2019 08:28:56: start model_add_line... INFO @ Mon, 03 Jun 2019 08:28:56: start X-correlation... INFO @ Mon, 03 Jun 2019 08:28:56: end of X-cor INFO @ Mon, 03 Jun 2019 08:28:56: #2 finished! INFO @ Mon, 03 Jun 2019 08:28:56: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:28:56: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.05_model.r WARNING @ Mon, 03 Jun 2019 08:28:56: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:28:56: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:28:56: #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 08:28:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:28:58: 9000000 INFO @ Mon, 03 Jun 2019 08:29:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:29:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:29:04: #1 total tags in treatment: 9620905 INFO @ Mon, 03 Jun 2019 08:29:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:29:04: #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 08:29:04: #1 tags after filtering in treatment: 9620905 INFO @ Mon, 03 Jun 2019 08:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:29:04: #1 finished! INFO @ Mon, 03 Jun 2019 08:29:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:29:05: #2 number of paired peaks: 397 WARNING @ Mon, 03 Jun 2019 08:29:05: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 03 Jun 2019 08:29:05: start model_add_line... INFO @ Mon, 03 Jun 2019 08:29:05: start X-correlation... INFO @ Mon, 03 Jun 2019 08:29:05: end of X-cor INFO @ Mon, 03 Jun 2019 08:29:05: #2 finished! INFO @ Mon, 03 Jun 2019 08:29:05: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:29:05: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.20_model.r WARNING @ Mon, 03 Jun 2019 08:29:05: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:29:05: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:29:05: #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 08:29:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:29:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:29:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:29:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:29:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:29:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.10_summits.bed INFO @ Mon, 03 Jun 2019 08:29:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1673 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:29:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.05_summits.bed INFO @ Mon, 03 Jun 2019 08:29:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1955 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:29:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:29:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:29:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287674/SRX287674.20_summits.bed INFO @ Mon, 03 Jun 2019 08:29:45: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1156 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。