Job ID = 1292809 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T11:35:29 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 : 13,809,537 reads read : 13,809,537 reads written : 13,809,537 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: 00:03:41 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2269441 (16.43%) aligned 0 times 9709623 (70.31%) aligned exactly 1 time 1830473 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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_rmdupse_core] 1988200 / 11540096 = 0.1723 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 @ Sun, 02 Jun 2019 20:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.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 @ Sun, 02 Jun 2019 20:52:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:52:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.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 @ Sun, 02 Jun 2019 20:52:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:52:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.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 @ Sun, 02 Jun 2019 20:52:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:52:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:52:14: 1000000 INFO @ Sun, 02 Jun 2019 20:52:14: 1000000 INFO @ Sun, 02 Jun 2019 20:52:15: 1000000 INFO @ Sun, 02 Jun 2019 20:52:22: 2000000 INFO @ Sun, 02 Jun 2019 20:52:23: 2000000 INFO @ Sun, 02 Jun 2019 20:52:24: 2000000 INFO @ Sun, 02 Jun 2019 20:52:31: 3000000 INFO @ Sun, 02 Jun 2019 20:52:32: 3000000 INFO @ Sun, 02 Jun 2019 20:52:32: 3000000 INFO @ Sun, 02 Jun 2019 20:52:39: 4000000 INFO @ Sun, 02 Jun 2019 20:52:41: 4000000 INFO @ Sun, 02 Jun 2019 20:52:41: 4000000 INFO @ Sun, 02 Jun 2019 20:52:48: 5000000 INFO @ Sun, 02 Jun 2019 20:52:50: 5000000 INFO @ Sun, 02 Jun 2019 20:52:50: 5000000 INFO @ Sun, 02 Jun 2019 20:52:56: 6000000 INFO @ Sun, 02 Jun 2019 20:52:58: 6000000 INFO @ Sun, 02 Jun 2019 20:52:59: 6000000 INFO @ Sun, 02 Jun 2019 20:53:05: 7000000 INFO @ Sun, 02 Jun 2019 20:53:07: 7000000 INFO @ Sun, 02 Jun 2019 20:53:08: 7000000 INFO @ Sun, 02 Jun 2019 20:53:13: 8000000 INFO @ Sun, 02 Jun 2019 20:53:16: 8000000 INFO @ Sun, 02 Jun 2019 20:53:16: 8000000 INFO @ Sun, 02 Jun 2019 20:53:22: 9000000 INFO @ Sun, 02 Jun 2019 20:53:25: 9000000 INFO @ Sun, 02 Jun 2019 20:53:25: 9000000 INFO @ Sun, 02 Jun 2019 20:53:26: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:53:26: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:53:26: #1 total tags in treatment: 9551896 INFO @ Sun, 02 Jun 2019 20:53:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:53:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:53:27: #1 tags after filtering in treatment: 9551896 INFO @ Sun, 02 Jun 2019 20:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:53:27: #1 finished! INFO @ Sun, 02 Jun 2019 20:53:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:53:28: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 20:53:28: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 20:53:28: start model_add_line... INFO @ Sun, 02 Jun 2019 20:53:28: start X-correlation... INFO @ Sun, 02 Jun 2019 20:53:28: end of X-cor INFO @ Sun, 02 Jun 2019 20:53:28: #2 finished! INFO @ Sun, 02 Jun 2019 20:53:28: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 20:53:28: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 02 Jun 2019 20:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.20_model.r WARNING @ Sun, 02 Jun 2019 20:53:28: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:53:28: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 02 Jun 2019 20:53:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 20:53:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:53:30: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:53:30: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:53:30: #1 total tags in treatment: 9551896 INFO @ Sun, 02 Jun 2019 20:53:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:53:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:53:30: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:53:30: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:53:30: #1 total tags in treatment: 9551896 INFO @ Sun, 02 Jun 2019 20:53:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:53:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:53:30: #1 tags after filtering in treatment: 9551896 INFO @ Sun, 02 Jun 2019 20:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:53:30: #1 finished! INFO @ Sun, 02 Jun 2019 20:53:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:53:30: #1 tags after filtering in treatment: 9551896 INFO @ Sun, 02 Jun 2019 20:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:53:30: #1 finished! INFO @ Sun, 02 Jun 2019 20:53:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:53:31: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 20:53:31: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 20:53:31: start model_add_line... INFO @ Sun, 02 Jun 2019 20:53:31: start X-correlation... INFO @ Sun, 02 Jun 2019 20:53:31: end of X-cor INFO @ Sun, 02 Jun 2019 20:53:31: #2 finished! INFO @ Sun, 02 Jun 2019 20:53:31: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 20:53:31: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 02 Jun 2019 20:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.10_model.r WARNING @ Sun, 02 Jun 2019 20:53:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:53:31: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 02 Jun 2019 20:53:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 20:53:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:53:31: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 20:53:31: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 20:53:31: start model_add_line... INFO @ Sun, 02 Jun 2019 20:53:31: start X-correlation... INFO @ Sun, 02 Jun 2019 20:53:31: end of X-cor INFO @ Sun, 02 Jun 2019 20:53:31: #2 finished! INFO @ Sun, 02 Jun 2019 20:53:31: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 20:53:31: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 02 Jun 2019 20:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.05_model.r WARNING @ Sun, 02 Jun 2019 20:53:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:53:31: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 02 Jun 2019 20:53:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 20:53:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:53:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:54:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:54:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.20_summits.bed INFO @ Sun, 02 Jun 2019 20:54:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.05_summits.bed INFO @ Sun, 02 Jun 2019 20:54:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:54:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:54:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495054/SRX495054.10_summits.bed INFO @ Sun, 02 Jun 2019 20:54:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (308 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。