Job ID = 2008017 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:12:31 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 1900-01-00T00:00:00 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 1,655,800 reads read : 3,311,600 reads written : 3,311,600 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: 00:01:58 1655800 reads; of these: 1655800 (100.00%) were paired; of these: 114478 (6.91%) aligned concordantly 0 times 1427358 (86.20%) aligned concordantly exactly 1 time 113964 (6.88%) aligned concordantly >1 times ---- 114478 pairs aligned concordantly 0 times; of these: 58225 (50.86%) aligned discordantly 1 time ---- 56253 pairs aligned 0 times concordantly or discordantly; of these: 112506 mates make up the pairs; of these: 81260 (72.23%) aligned 0 times 19367 (17.21%) aligned exactly 1 time 11879 (10.56%) aligned >1 times 97.55% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 27270 / 1593449 = 0.0171 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 @ Fri, 05 Jul 2019 17:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 17:19:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 17:19:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 17:19:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:19:18: 1000000 INFO @ Fri, 05 Jul 2019 17:19:19: 1000000 INFO @ Fri, 05 Jul 2019 17:19:21: 1000000 INFO @ Fri, 05 Jul 2019 17:19:30: 2000000 INFO @ Fri, 05 Jul 2019 17:19:32: 2000000 INFO @ Fri, 05 Jul 2019 17:19:35: 2000000 INFO @ Fri, 05 Jul 2019 17:19:42: 3000000 INFO @ Fri, 05 Jul 2019 17:19:44: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:19:44: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:19:44: #1 total tags in treatment: 1514552 INFO @ Fri, 05 Jul 2019 17:19:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:19:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:19:44: #1 tags after filtering in treatment: 1401058 INFO @ Fri, 05 Jul 2019 17:19:44: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:19:44: #1 finished! INFO @ Fri, 05 Jul 2019 17:19:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:19:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:19:45: 3000000 INFO @ Fri, 05 Jul 2019 17:19:45: #2 number of paired peaks: 189 WARNING @ Fri, 05 Jul 2019 17:19:45: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 05 Jul 2019 17:19:45: start model_add_line... INFO @ Fri, 05 Jul 2019 17:19:45: start X-correlation... INFO @ Fri, 05 Jul 2019 17:19:45: end of X-cor INFO @ Fri, 05 Jul 2019 17:19:45: #2 finished! INFO @ Fri, 05 Jul 2019 17:19:45: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 17:19:45: #2 alternative fragment length(s) may be 174,179 bps INFO @ Fri, 05 Jul 2019 17:19:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.05_model.r WARNING @ Fri, 05 Jul 2019 17:19:45: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:19:45: #2 You may need to consider one of the other alternative d(s): 174,179 WARNING @ Fri, 05 Jul 2019 17:19:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:19:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:19:47: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:19:47: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:19:47: #1 total tags in treatment: 1514552 INFO @ Fri, 05 Jul 2019 17:19:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:19:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:19:47: #1 tags after filtering in treatment: 1401058 INFO @ Fri, 05 Jul 2019 17:19:47: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:19:47: #1 finished! INFO @ Fri, 05 Jul 2019 17:19:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:19:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:19:47: #2 number of paired peaks: 189 WARNING @ Fri, 05 Jul 2019 17:19:47: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 05 Jul 2019 17:19:47: start model_add_line... INFO @ Fri, 05 Jul 2019 17:19:47: start X-correlation... INFO @ Fri, 05 Jul 2019 17:19:47: end of X-cor INFO @ Fri, 05 Jul 2019 17:19:47: #2 finished! INFO @ Fri, 05 Jul 2019 17:19:47: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 17:19:47: #2 alternative fragment length(s) may be 174,179 bps INFO @ Fri, 05 Jul 2019 17:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.10_model.r WARNING @ Fri, 05 Jul 2019 17:19:47: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:19:47: #2 You may need to consider one of the other alternative d(s): 174,179 WARNING @ Fri, 05 Jul 2019 17:19:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:19:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:19:47: 3000000 INFO @ Fri, 05 Jul 2019 17:19:49: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:19:49: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:19:49: #1 total tags in treatment: 1514552 INFO @ Fri, 05 Jul 2019 17:19:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:19:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:19:49: #1 tags after filtering in treatment: 1401058 INFO @ Fri, 05 Jul 2019 17:19:49: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:19:49: #1 finished! INFO @ Fri, 05 Jul 2019 17:19:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:19:49: #2 number of paired peaks: 189 WARNING @ Fri, 05 Jul 2019 17:19:49: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 05 Jul 2019 17:19:49: start model_add_line... INFO @ Fri, 05 Jul 2019 17:19:49: start X-correlation... INFO @ Fri, 05 Jul 2019 17:19:49: end of X-cor INFO @ Fri, 05 Jul 2019 17:19:49: #2 finished! INFO @ Fri, 05 Jul 2019 17:19:49: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 17:19:49: #2 alternative fragment length(s) may be 174,179 bps INFO @ Fri, 05 Jul 2019 17:19:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.20_model.r WARNING @ Fri, 05 Jul 2019 17:19:49: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:19:49: #2 You may need to consider one of the other alternative d(s): 174,179 WARNING @ Fri, 05 Jul 2019 17:19:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:19:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:19:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:19:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:19:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:19:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:19:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.05_summits.bed INFO @ Fri, 05 Jul 2019 17:19:52: Done! INFO @ Fri, 05 Jul 2019 17:19:52: #3 Call peaks for each chromosome... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (739 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.10_summits.bed INFO @ Fri, 05 Jul 2019 17:19:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:19:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471805/ERX471805.20_summits.bed INFO @ Fri, 05 Jul 2019 17:19:56: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。