Job ID = 2589943 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:51:51 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 : 27,395,908 reads read : 54,791,816 reads written : 27,395,908 reads 0-length : 27,395,908 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: 00:07:06 27395908 reads; of these: 27395908 (100.00%) were unpaired; of these: 12421116 (45.34%) aligned 0 times 12748535 (46.53%) aligned exactly 1 time 2226257 (8.13%) aligned >1 times 54.66% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 14546326 / 14974792 = 0.9714 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, 12 Aug 2019 19:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 19:11:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:11:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 19:11:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:11:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 19:11:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:11:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:11:32: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:11:32: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:11:32: #1 total tags in treatment: 428466 INFO @ Mon, 12 Aug 2019 19:11:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:11:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:11:32: #1 tags after filtering in treatment: 428466 INFO @ Mon, 12 Aug 2019 19:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:11:32: #1 finished! INFO @ Mon, 12 Aug 2019 19:11:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:11:33: #2 number of paired peaks: 1541 INFO @ Mon, 12 Aug 2019 19:11:33: start model_add_line... INFO @ Mon, 12 Aug 2019 19:11:33: start X-correlation... INFO @ Mon, 12 Aug 2019 19:11:33: end of X-cor INFO @ Mon, 12 Aug 2019 19:11:33: #2 finished! INFO @ Mon, 12 Aug 2019 19:11:33: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:11:33: #2 alternative fragment length(s) may be 71,583 bps INFO @ Mon, 12 Aug 2019 19:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.05_model.r WARNING @ Mon, 12 Aug 2019 19:11:33: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:11:33: #2 You may need to consider one of the other alternative d(s): 71,583 WARNING @ Mon, 12 Aug 2019 19:11:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:11:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:11:33: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:11:33: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:11:33: #1 total tags in treatment: 428466 INFO @ Mon, 12 Aug 2019 19:11:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:11:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:11:33: #1 tags after filtering in treatment: 428466 INFO @ Mon, 12 Aug 2019 19:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:11:33: #1 finished! INFO @ Mon, 12 Aug 2019 19:11:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:11:34: #2 number of paired peaks: 1541 INFO @ Mon, 12 Aug 2019 19:11:34: start model_add_line... INFO @ Mon, 12 Aug 2019 19:11:34: start X-correlation... INFO @ Mon, 12 Aug 2019 19:11:34: end of X-cor INFO @ Mon, 12 Aug 2019 19:11:34: #2 finished! INFO @ Mon, 12 Aug 2019 19:11:34: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:11:34: #2 alternative fragment length(s) may be 71,583 bps INFO @ Mon, 12 Aug 2019 19:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.10_model.r WARNING @ Mon, 12 Aug 2019 19:11:34: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:11:34: #2 You may need to consider one of the other alternative d(s): 71,583 WARNING @ Mon, 12 Aug 2019 19:11:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:11:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:11:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:11:34: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:11:34: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:11:34: #1 total tags in treatment: 428466 INFO @ Mon, 12 Aug 2019 19:11:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:11:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:11:34: #1 tags after filtering in treatment: 428466 INFO @ Mon, 12 Aug 2019 19:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:11:34: #1 finished! INFO @ Mon, 12 Aug 2019 19:11:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:11:34: #2 number of paired peaks: 1541 INFO @ Mon, 12 Aug 2019 19:11:34: start model_add_line... INFO @ Mon, 12 Aug 2019 19:11:34: start X-correlation... INFO @ Mon, 12 Aug 2019 19:11:34: end of X-cor INFO @ Mon, 12 Aug 2019 19:11:34: #2 finished! INFO @ Mon, 12 Aug 2019 19:11:34: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:11:34: #2 alternative fragment length(s) may be 71,583 bps INFO @ Mon, 12 Aug 2019 19:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.20_model.r WARNING @ Mon, 12 Aug 2019 19:11:34: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:11:34: #2 You may need to consider one of the other alternative d(s): 71,583 WARNING @ Mon, 12 Aug 2019 19:11:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:11:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:11:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.05_summits.bed INFO @ Mon, 12 Aug 2019 19:11:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (454 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:11:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 19:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.10_summits.bed INFO @ Mon, 12 Aug 2019 19:11:36: Done! INFO @ Mon, 12 Aug 2019 19:11:36: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862418/SRX3862418.20_summits.bed INFO @ Mon, 12 Aug 2019 19:11:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。