Job ID = 2589934 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:51:31 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 : 21,599,570 reads read : 43,199,140 reads written : 21,599,570 reads 0-length : 21,599,570 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: 00:08:05 21599570 reads; of these: 21599570 (100.00%) were unpaired; of these: 2840769 (13.15%) aligned 0 times 15608735 (72.26%) aligned exactly 1 time 3150066 (14.58%) aligned >1 times 86.85% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 3400057 / 18758801 = 0.1813 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 19:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.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 19:12:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:12:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:12:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.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 19:12:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:12:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:12:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.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 19:12:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:12:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:12:42: 1000000 INFO @ Mon, 12 Aug 2019 19:12:46: 1000000 INFO @ Mon, 12 Aug 2019 19:12:47: 1000000 INFO @ Mon, 12 Aug 2019 19:12:52: 2000000 INFO @ Mon, 12 Aug 2019 19:12:54: 2000000 INFO @ Mon, 12 Aug 2019 19:12:56: 2000000 INFO @ Mon, 12 Aug 2019 19:13:02: 3000000 INFO @ Mon, 12 Aug 2019 19:13:03: 3000000 INFO @ Mon, 12 Aug 2019 19:13:04: 3000000 INFO @ Mon, 12 Aug 2019 19:13:12: 4000000 INFO @ Mon, 12 Aug 2019 19:13:12: 4000000 INFO @ Mon, 12 Aug 2019 19:13:13: 4000000 INFO @ Mon, 12 Aug 2019 19:13:20: 5000000 INFO @ Mon, 12 Aug 2019 19:13:21: 5000000 INFO @ Mon, 12 Aug 2019 19:13:22: 5000000 INFO @ Mon, 12 Aug 2019 19:13:29: 6000000 INFO @ Mon, 12 Aug 2019 19:13:30: 6000000 INFO @ Mon, 12 Aug 2019 19:13:32: 6000000 INFO @ Mon, 12 Aug 2019 19:13:37: 7000000 INFO @ Mon, 12 Aug 2019 19:13:39: 7000000 INFO @ Mon, 12 Aug 2019 19:13:41: 7000000 INFO @ Mon, 12 Aug 2019 19:13:46: 8000000 INFO @ Mon, 12 Aug 2019 19:13:47: 8000000 INFO @ Mon, 12 Aug 2019 19:13:51: 8000000 INFO @ Mon, 12 Aug 2019 19:13:55: 9000000 INFO @ Mon, 12 Aug 2019 19:13:56: 9000000 INFO @ Mon, 12 Aug 2019 19:14:01: 9000000 INFO @ Mon, 12 Aug 2019 19:14:03: 10000000 INFO @ Mon, 12 Aug 2019 19:14:05: 10000000 INFO @ Mon, 12 Aug 2019 19:14:10: 10000000 INFO @ Mon, 12 Aug 2019 19:14:12: 11000000 INFO @ Mon, 12 Aug 2019 19:14:13: 11000000 INFO @ Mon, 12 Aug 2019 19:14:20: 11000000 INFO @ Mon, 12 Aug 2019 19:14:20: 12000000 INFO @ Mon, 12 Aug 2019 19:14:21: 12000000 INFO @ Mon, 12 Aug 2019 19:14:29: 12000000 INFO @ Mon, 12 Aug 2019 19:14:30: 13000000 INFO @ Mon, 12 Aug 2019 19:14:31: 13000000 INFO @ Mon, 12 Aug 2019 19:14:38: 13000000 INFO @ Mon, 12 Aug 2019 19:14:39: 14000000 INFO @ Mon, 12 Aug 2019 19:14:40: 14000000 INFO @ Mon, 12 Aug 2019 19:14:47: 15000000 INFO @ Mon, 12 Aug 2019 19:14:47: 14000000 INFO @ Mon, 12 Aug 2019 19:14:48: 15000000 INFO @ Mon, 12 Aug 2019 19:14:50: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:14:50: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:14:50: #1 total tags in treatment: 15358744 INFO @ Mon, 12 Aug 2019 19:14:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:14:50: #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 19:14:50: #1 tags after filtering in treatment: 15358744 INFO @ Mon, 12 Aug 2019 19:14:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:14:50: #1 finished! INFO @ Mon, 12 Aug 2019 19:14:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:14:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:14:51: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:14:51: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:14:51: #1 total tags in treatment: 15358744 INFO @ Mon, 12 Aug 2019 19:14:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:14:51: #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 19:14:51: #1 tags after filtering in treatment: 15358744 INFO @ Mon, 12 Aug 2019 19:14:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:14:51: #1 finished! INFO @ Mon, 12 Aug 2019 19:14:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:14:51: #2 number of paired peaks: 184 WARNING @ Mon, 12 Aug 2019 19:14:51: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 12 Aug 2019 19:14:51: start model_add_line... INFO @ Mon, 12 Aug 2019 19:14:52: start X-correlation... INFO @ Mon, 12 Aug 2019 19:14:52: end of X-cor INFO @ Mon, 12 Aug 2019 19:14:52: #2 finished! INFO @ Mon, 12 Aug 2019 19:14:52: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 19:14:52: #2 alternative fragment length(s) may be 2,54,536,597 bps INFO @ Mon, 12 Aug 2019 19:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.10_model.r WARNING @ Mon, 12 Aug 2019 19:14:52: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:14:52: #2 You may need to consider one of the other alternative d(s): 2,54,536,597 WARNING @ Mon, 12 Aug 2019 19:14:52: #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 19:14:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:14:53: #2 number of paired peaks: 184 WARNING @ Mon, 12 Aug 2019 19:14:53: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 12 Aug 2019 19:14:53: start model_add_line... INFO @ Mon, 12 Aug 2019 19:14:53: start X-correlation... INFO @ Mon, 12 Aug 2019 19:14:53: end of X-cor INFO @ Mon, 12 Aug 2019 19:14:53: #2 finished! INFO @ Mon, 12 Aug 2019 19:14:53: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 19:14:53: #2 alternative fragment length(s) may be 2,54,536,597 bps INFO @ Mon, 12 Aug 2019 19:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.20_model.r WARNING @ Mon, 12 Aug 2019 19:14:53: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:14:53: #2 You may need to consider one of the other alternative d(s): 2,54,536,597 WARNING @ Mon, 12 Aug 2019 19:14:53: #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 19:14:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:14:56: 15000000 INFO @ Mon, 12 Aug 2019 19:15:00: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:15:00: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:15:00: #1 total tags in treatment: 15358744 INFO @ Mon, 12 Aug 2019 19:15:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:15:00: #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 19:15:00: #1 tags after filtering in treatment: 15358744 INFO @ Mon, 12 Aug 2019 19:15:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:15:00: #1 finished! INFO @ Mon, 12 Aug 2019 19:15:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:15:01: #2 number of paired peaks: 184 WARNING @ Mon, 12 Aug 2019 19:15:01: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Mon, 12 Aug 2019 19:15:01: start model_add_line... INFO @ Mon, 12 Aug 2019 19:15:02: start X-correlation... INFO @ Mon, 12 Aug 2019 19:15:02: end of X-cor INFO @ Mon, 12 Aug 2019 19:15:02: #2 finished! INFO @ Mon, 12 Aug 2019 19:15:02: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 19:15:02: #2 alternative fragment length(s) may be 2,54,536,597 bps INFO @ Mon, 12 Aug 2019 19:15:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.05_model.r WARNING @ Mon, 12 Aug 2019 19:15:02: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:15:02: #2 You may need to consider one of the other alternative d(s): 2,54,536,597 WARNING @ Mon, 12 Aug 2019 19:15:02: #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 19:15:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:15:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:15:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:15:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:15:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.10_summits.bed INFO @ Mon, 12 Aug 2019 19:15:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.20_summits.bed INFO @ Mon, 12 Aug 2019 19:15:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:15:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:15:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:15:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862409/SRX3862409.05_summits.bed INFO @ Mon, 12 Aug 2019 19:15:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。