Job ID = 1301168 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:41:03 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 : 20,835,457 reads read : 20,835,457 reads written : 20,835,457 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:51 20835457 reads; of these: 20835457 (100.00%) were unpaired; of these: 9126344 (43.80%) aligned 0 times 10108726 (48.52%) aligned exactly 1 time 1600387 (7.68%) aligned >1 times 56.20% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 8591893 / 11709113 = 0.7338 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 19:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.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 19:54:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:54:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.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 19:54:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:54:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.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 19:54:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:54:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:55:01: 1000000 INFO @ Mon, 03 Jun 2019 19:55:01: 1000000 INFO @ Mon, 03 Jun 2019 19:55:03: 1000000 INFO @ Mon, 03 Jun 2019 19:55:08: 2000000 INFO @ Mon, 03 Jun 2019 19:55:08: 2000000 INFO @ Mon, 03 Jun 2019 19:55:12: 2000000 INFO @ Mon, 03 Jun 2019 19:55:16: 3000000 INFO @ Mon, 03 Jun 2019 19:55:16: 3000000 INFO @ Mon, 03 Jun 2019 19:55:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:55:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:55:17: #1 total tags in treatment: 3117220 INFO @ Mon, 03 Jun 2019 19:55:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:55:17: #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 19:55:17: #1 tags after filtering in treatment: 3117220 INFO @ Mon, 03 Jun 2019 19:55:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:55:17: #1 finished! INFO @ Mon, 03 Jun 2019 19:55:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:55:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:55:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:55:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:55:17: #1 total tags in treatment: 3117220 INFO @ Mon, 03 Jun 2019 19:55:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:55:17: #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 19:55:17: #1 tags after filtering in treatment: 3117220 INFO @ Mon, 03 Jun 2019 19:55:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:55:17: #1 finished! INFO @ Mon, 03 Jun 2019 19:55:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:55:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:55:17: #2 number of paired peaks: 678 WARNING @ Mon, 03 Jun 2019 19:55:17: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Mon, 03 Jun 2019 19:55:17: start model_add_line... INFO @ Mon, 03 Jun 2019 19:55:17: start X-correlation... INFO @ Mon, 03 Jun 2019 19:55:17: end of X-cor INFO @ Mon, 03 Jun 2019 19:55:17: #2 finished! INFO @ Mon, 03 Jun 2019 19:55:17: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 19:55:17: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 19:55:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.05_model.r INFO @ Mon, 03 Jun 2019 19:55:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:55:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:55:17: #2 number of paired peaks: 678 WARNING @ Mon, 03 Jun 2019 19:55:17: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Mon, 03 Jun 2019 19:55:17: start model_add_line... INFO @ Mon, 03 Jun 2019 19:55:17: start X-correlation... INFO @ Mon, 03 Jun 2019 19:55:17: end of X-cor INFO @ Mon, 03 Jun 2019 19:55:17: #2 finished! INFO @ Mon, 03 Jun 2019 19:55:17: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 19:55:17: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 19:55:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.10_model.r INFO @ Mon, 03 Jun 2019 19:55:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:55:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:55:21: 3000000 INFO @ Mon, 03 Jun 2019 19:55:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:55:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:55:22: #1 total tags in treatment: 3117220 INFO @ Mon, 03 Jun 2019 19:55:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:55:22: #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 19:55:22: #1 tags after filtering in treatment: 3117220 INFO @ Mon, 03 Jun 2019 19:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:55:22: #1 finished! INFO @ Mon, 03 Jun 2019 19:55:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:55:22: #2 number of paired peaks: 678 WARNING @ Mon, 03 Jun 2019 19:55:22: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Mon, 03 Jun 2019 19:55:22: start model_add_line... INFO @ Mon, 03 Jun 2019 19:55:22: start X-correlation... INFO @ Mon, 03 Jun 2019 19:55:22: end of X-cor INFO @ Mon, 03 Jun 2019 19:55:22: #2 finished! INFO @ Mon, 03 Jun 2019 19:55:22: #2 predicted fragment length is 134 bps INFO @ Mon, 03 Jun 2019 19:55:22: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 03 Jun 2019 19:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.20_model.r INFO @ Mon, 03 Jun 2019 19:55:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:55:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:55:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:55:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:55:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.05_summits.bed INFO @ Mon, 03 Jun 2019 19:55:32: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1340 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:55:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:55:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:55:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.10_summits.bed INFO @ Mon, 03 Jun 2019 19:55:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:55:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:55:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:55:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:55:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485204/SRX485204.20_summits.bed INFO @ Mon, 03 Jun 2019 19:55:37: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (157 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。