Job ID = 2589933 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:52:23 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 : 17,983,911 reads read : 35,967,822 reads written : 17,983,911 reads 0-length : 17,983,911 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: 00:05:58 17983911 reads; of these: 17983911 (100.00%) were unpaired; of these: 5322469 (29.60%) aligned 0 times 10258722 (57.04%) aligned exactly 1 time 2402720 (13.36%) aligned >1 times 70.40% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1984576 / 12661442 = 0.1567 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 19:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.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 19:06:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:06:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.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 19:06:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:06:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:06:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.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 19:06:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:06:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:06:54: 1000000 INFO @ Mon, 12 Aug 2019 19:06:55: 1000000 INFO @ Mon, 12 Aug 2019 19:06:57: 1000000 INFO @ Mon, 12 Aug 2019 19:07:03: 2000000 INFO @ Mon, 12 Aug 2019 19:07:03: 2000000 INFO @ Mon, 12 Aug 2019 19:07:07: 2000000 INFO @ Mon, 12 Aug 2019 19:07:11: 3000000 INFO @ Mon, 12 Aug 2019 19:07:12: 3000000 INFO @ Mon, 12 Aug 2019 19:07:17: 3000000 INFO @ Mon, 12 Aug 2019 19:07:19: 4000000 INFO @ Mon, 12 Aug 2019 19:07:20: 4000000 INFO @ Mon, 12 Aug 2019 19:07:27: 4000000 INFO @ Mon, 12 Aug 2019 19:07:28: 5000000 INFO @ Mon, 12 Aug 2019 19:07:28: 5000000 INFO @ Mon, 12 Aug 2019 19:07:36: 6000000 INFO @ Mon, 12 Aug 2019 19:07:36: 5000000 INFO @ Mon, 12 Aug 2019 19:07:37: 6000000 INFO @ Mon, 12 Aug 2019 19:07:44: 7000000 INFO @ Mon, 12 Aug 2019 19:07:45: 7000000 INFO @ Mon, 12 Aug 2019 19:07:46: 6000000 INFO @ Mon, 12 Aug 2019 19:07:52: 8000000 INFO @ Mon, 12 Aug 2019 19:07:53: 8000000 INFO @ Mon, 12 Aug 2019 19:07:56: 7000000 INFO @ Mon, 12 Aug 2019 19:08:00: 9000000 INFO @ Mon, 12 Aug 2019 19:08:01: 9000000 INFO @ Mon, 12 Aug 2019 19:08:05: 8000000 INFO @ Mon, 12 Aug 2019 19:08:08: 10000000 INFO @ Mon, 12 Aug 2019 19:08:10: 10000000 INFO @ Mon, 12 Aug 2019 19:08:14: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:08:14: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:08:14: #1 total tags in treatment: 10676866 INFO @ Mon, 12 Aug 2019 19:08:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:08:14: #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 19:08:14: #1 tags after filtering in treatment: 10676866 INFO @ Mon, 12 Aug 2019 19:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:08:14: #1 finished! INFO @ Mon, 12 Aug 2019 19:08:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:08:15: 9000000 INFO @ Mon, 12 Aug 2019 19:08:15: #2 number of paired peaks: 271 WARNING @ Mon, 12 Aug 2019 19:08:15: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 12 Aug 2019 19:08:15: start model_add_line... INFO @ Mon, 12 Aug 2019 19:08:16: start X-correlation... INFO @ Mon, 12 Aug 2019 19:08:16: end of X-cor INFO @ Mon, 12 Aug 2019 19:08:16: #2 finished! INFO @ Mon, 12 Aug 2019 19:08:16: #2 predicted fragment length is 69 bps INFO @ Mon, 12 Aug 2019 19:08:16: #2 alternative fragment length(s) may be 4,69 bps INFO @ Mon, 12 Aug 2019 19:08:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.05_model.r WARNING @ Mon, 12 Aug 2019 19:08:16: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:08:16: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Mon, 12 Aug 2019 19:08:16: #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 19:08:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:08:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:08:16: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:08:16: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:08:16: #1 total tags in treatment: 10676866 INFO @ Mon, 12 Aug 2019 19:08:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:08:16: #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 19:08:16: #1 tags after filtering in treatment: 10676866 INFO @ Mon, 12 Aug 2019 19:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:08:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:08:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:08:17: #2 number of paired peaks: 271 WARNING @ Mon, 12 Aug 2019 19:08:17: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 12 Aug 2019 19:08:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:08:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:08:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:08:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:08:17: #2 predicted fragment length is 69 bps INFO @ Mon, 12 Aug 2019 19:08:17: #2 alternative fragment length(s) may be 4,69 bps INFO @ Mon, 12 Aug 2019 19:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.10_model.r WARNING @ Mon, 12 Aug 2019 19:08:17: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:08:17: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Mon, 12 Aug 2019 19:08:17: #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 19:08:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:08:24: 10000000 INFO @ Mon, 12 Aug 2019 19:08:30: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:08:30: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:08:30: #1 total tags in treatment: 10676866 INFO @ Mon, 12 Aug 2019 19:08:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:08:30: #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 19:08:31: #1 tags after filtering in treatment: 10676866 INFO @ Mon, 12 Aug 2019 19:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:08:31: #1 finished! INFO @ Mon, 12 Aug 2019 19:08:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:08:32: #2 number of paired peaks: 271 WARNING @ Mon, 12 Aug 2019 19:08:32: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 12 Aug 2019 19:08:32: start model_add_line... INFO @ Mon, 12 Aug 2019 19:08:32: start X-correlation... INFO @ Mon, 12 Aug 2019 19:08:32: end of X-cor INFO @ Mon, 12 Aug 2019 19:08:32: #2 finished! INFO @ Mon, 12 Aug 2019 19:08:32: #2 predicted fragment length is 69 bps INFO @ Mon, 12 Aug 2019 19:08:32: #2 alternative fragment length(s) may be 4,69 bps INFO @ Mon, 12 Aug 2019 19:08:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.20_model.r WARNING @ Mon, 12 Aug 2019 19:08:32: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:08:32: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Mon, 12 Aug 2019 19:08:32: #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 19:08:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:08:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:08:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:08:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.05_summits.bed INFO @ Mon, 12 Aug 2019 19:08:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.10_summits.bed INFO @ Mon, 12 Aug 2019 19:09:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (330 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:09:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:09:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:09:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862408/SRX3862408.20_summits.bed INFO @ Mon, 12 Aug 2019 19:09:15: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (191 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。