Job ID = 1292803 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T11:35:55 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 ) 2019-06-02T11:35:55 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 : 18,854,814 reads read : 18,854,814 reads written : 18,854,814 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: 00:04:16 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289133 (1.53%) aligned 0 times 14953826 (79.31%) aligned exactly 1 time 3611855 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 3522579 / 18565681 = 0.1897 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 20:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.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 20:48:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:48:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.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 20:48:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:48:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.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 20:48:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:48:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:48:49: 1000000 INFO @ Sun, 02 Jun 2019 20:48:50: 1000000 INFO @ Sun, 02 Jun 2019 20:48:50: 1000000 INFO @ Sun, 02 Jun 2019 20:48:57: 2000000 INFO @ Sun, 02 Jun 2019 20:48:58: 2000000 INFO @ Sun, 02 Jun 2019 20:48:58: 2000000 INFO @ Sun, 02 Jun 2019 20:49:04: 3000000 INFO @ Sun, 02 Jun 2019 20:49:07: 3000000 INFO @ Sun, 02 Jun 2019 20:49:07: 3000000 INFO @ Sun, 02 Jun 2019 20:49:12: 4000000 INFO @ Sun, 02 Jun 2019 20:49:16: 4000000 INFO @ Sun, 02 Jun 2019 20:49:16: 4000000 INFO @ Sun, 02 Jun 2019 20:49:19: 5000000 INFO @ Sun, 02 Jun 2019 20:49:23: 5000000 INFO @ Sun, 02 Jun 2019 20:49:24: 5000000 INFO @ Sun, 02 Jun 2019 20:49:26: 6000000 INFO @ Sun, 02 Jun 2019 20:49:31: 6000000 INFO @ Sun, 02 Jun 2019 20:49:31: 6000000 INFO @ Sun, 02 Jun 2019 20:49:33: 7000000 INFO @ Sun, 02 Jun 2019 20:49:39: 7000000 INFO @ Sun, 02 Jun 2019 20:49:40: 7000000 INFO @ Sun, 02 Jun 2019 20:49:41: 8000000 INFO @ Sun, 02 Jun 2019 20:49:47: 8000000 INFO @ Sun, 02 Jun 2019 20:49:48: 9000000 INFO @ Sun, 02 Jun 2019 20:49:48: 8000000 INFO @ Sun, 02 Jun 2019 20:49:54: 9000000 INFO @ Sun, 02 Jun 2019 20:49:55: 10000000 INFO @ Sun, 02 Jun 2019 20:49:56: 9000000 INFO @ Sun, 02 Jun 2019 20:50:02: 10000000 INFO @ Sun, 02 Jun 2019 20:50:03: 11000000 INFO @ Sun, 02 Jun 2019 20:50:04: 10000000 INFO @ Sun, 02 Jun 2019 20:50:10: 11000000 INFO @ Sun, 02 Jun 2019 20:50:10: 12000000 INFO @ Sun, 02 Jun 2019 20:50:12: 11000000 INFO @ Sun, 02 Jun 2019 20:50:18: 13000000 INFO @ Sun, 02 Jun 2019 20:50:19: 12000000 INFO @ Sun, 02 Jun 2019 20:50:20: 12000000 INFO @ Sun, 02 Jun 2019 20:50:25: 14000000 INFO @ Sun, 02 Jun 2019 20:50:27: 13000000 INFO @ Sun, 02 Jun 2019 20:50:28: 13000000 INFO @ Sun, 02 Jun 2019 20:50:33: 15000000 INFO @ Sun, 02 Jun 2019 20:50:33: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:50:33: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:50:33: #1 total tags in treatment: 15043102 INFO @ Sun, 02 Jun 2019 20:50:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:50:33: #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 20:50:33: #1 tags after filtering in treatment: 15043102 INFO @ Sun, 02 Jun 2019 20:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:50:33: #1 finished! INFO @ Sun, 02 Jun 2019 20:50:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:50:35: 14000000 INFO @ Sun, 02 Jun 2019 20:50:35: #2 number of paired peaks: 439 WARNING @ Sun, 02 Jun 2019 20:50:35: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sun, 02 Jun 2019 20:50:35: start model_add_line... INFO @ Sun, 02 Jun 2019 20:50:35: start X-correlation... INFO @ Sun, 02 Jun 2019 20:50:35: end of X-cor INFO @ Sun, 02 Jun 2019 20:50:35: #2 finished! INFO @ Sun, 02 Jun 2019 20:50:35: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 20:50:35: #2 alternative fragment length(s) may be 3,57,588 bps INFO @ Sun, 02 Jun 2019 20:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.20_model.r WARNING @ Sun, 02 Jun 2019 20:50:35: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:50:35: #2 You may need to consider one of the other alternative d(s): 3,57,588 WARNING @ Sun, 02 Jun 2019 20:50:35: #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 20:50:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:50:36: 14000000 INFO @ Sun, 02 Jun 2019 20:50:42: 15000000 INFO @ Sun, 02 Jun 2019 20:50:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:50:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:50:43: #1 total tags in treatment: 15043102 INFO @ Sun, 02 Jun 2019 20:50:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:50:43: #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 20:50:43: #1 tags after filtering in treatment: 15043102 INFO @ Sun, 02 Jun 2019 20:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:50:43: #1 finished! INFO @ Sun, 02 Jun 2019 20:50:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:50:44: 15000000 INFO @ Sun, 02 Jun 2019 20:50:44: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:50:44: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:50:44: #1 total tags in treatment: 15043102 INFO @ Sun, 02 Jun 2019 20:50:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:50:44: #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 20:50:44: #1 tags after filtering in treatment: 15043102 INFO @ Sun, 02 Jun 2019 20:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:50:44: #1 finished! INFO @ Sun, 02 Jun 2019 20:50:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:50:45: #2 number of paired peaks: 439 WARNING @ Sun, 02 Jun 2019 20:50:45: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sun, 02 Jun 2019 20:50:45: start model_add_line... INFO @ Sun, 02 Jun 2019 20:50:45: start X-correlation... INFO @ Sun, 02 Jun 2019 20:50:45: end of X-cor INFO @ Sun, 02 Jun 2019 20:50:45: #2 finished! INFO @ Sun, 02 Jun 2019 20:50:45: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 20:50:45: #2 alternative fragment length(s) may be 3,57,588 bps INFO @ Sun, 02 Jun 2019 20:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.05_model.r WARNING @ Sun, 02 Jun 2019 20:50:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:50:45: #2 You may need to consider one of the other alternative d(s): 3,57,588 WARNING @ Sun, 02 Jun 2019 20:50:45: #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 20:50:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:50:46: #2 number of paired peaks: 439 WARNING @ Sun, 02 Jun 2019 20:50:46: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Sun, 02 Jun 2019 20:50:46: start model_add_line... INFO @ Sun, 02 Jun 2019 20:50:46: start X-correlation... INFO @ Sun, 02 Jun 2019 20:50:46: end of X-cor INFO @ Sun, 02 Jun 2019 20:50:46: #2 finished! INFO @ Sun, 02 Jun 2019 20:50:46: #2 predicted fragment length is 57 bps INFO @ Sun, 02 Jun 2019 20:50:46: #2 alternative fragment length(s) may be 3,57,588 bps INFO @ Sun, 02 Jun 2019 20:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.10_model.r WARNING @ Sun, 02 Jun 2019 20:50:46: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:50:46: #2 You may need to consider one of the other alternative d(s): 3,57,588 WARNING @ Sun, 02 Jun 2019 20:50:46: #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 20:50:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:50:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:51:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:51:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:51:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:51:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:51:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.20_summits.bed INFO @ Sun, 02 Jun 2019 20:51:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.10_summits.bed INFO @ Sun, 02 Jun 2019 20:51:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1313 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495049/SRX495049.05_summits.bed INFO @ Sun, 02 Jun 2019 20:51:43: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5625 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。