Job ID = 1292420 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,273,937 reads read : 12,547,874 reads written : 6,273,937 reads 0-length : 6,273,937 spots read : 6,126,991 reads read : 12,253,982 reads written : 6,126,991 reads 0-length : 6,126,991 spots read : 6,276,947 reads read : 12,553,894 reads written : 6,276,947 reads 0-length : 6,276,947 spots read : 6,072,531 reads read : 12,145,062 reads written : 6,072,531 reads 0-length : 6,072,531 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: 00:09:39 24750406 reads; of these: 24750406 (100.00%) were unpaired; of these: 691868 (2.80%) aligned 0 times 20583577 (83.16%) aligned exactly 1 time 3474961 (14.04%) aligned >1 times 97.20% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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 12 files... [bam_rmdupse_core] 5228499 / 24058538 = 0.2173 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 18:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.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 18:54:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:54:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.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 18:54:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:54:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.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 18:54:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:54:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:10: 1000000 INFO @ Sun, 02 Jun 2019 18:55:11: 1000000 INFO @ Sun, 02 Jun 2019 18:55:11: 1000000 INFO @ Sun, 02 Jun 2019 18:55:21: 2000000 INFO @ Sun, 02 Jun 2019 18:55:23: 2000000 INFO @ Sun, 02 Jun 2019 18:55:23: 2000000 INFO @ Sun, 02 Jun 2019 18:55:33: 3000000 INFO @ Sun, 02 Jun 2019 18:55:35: 3000000 INFO @ Sun, 02 Jun 2019 18:55:35: 3000000 INFO @ Sun, 02 Jun 2019 18:55:44: 4000000 INFO @ Sun, 02 Jun 2019 18:55:47: 4000000 INFO @ Sun, 02 Jun 2019 18:55:48: 4000000 INFO @ Sun, 02 Jun 2019 18:55:55: 5000000 INFO @ Sun, 02 Jun 2019 18:56:00: 5000000 INFO @ Sun, 02 Jun 2019 18:56:00: 5000000 INFO @ Sun, 02 Jun 2019 18:56:07: 6000000 INFO @ Sun, 02 Jun 2019 18:56:12: 6000000 INFO @ Sun, 02 Jun 2019 18:56:12: 6000000 INFO @ Sun, 02 Jun 2019 18:56:18: 7000000 INFO @ Sun, 02 Jun 2019 18:56:24: 7000000 INFO @ Sun, 02 Jun 2019 18:56:24: 7000000 INFO @ Sun, 02 Jun 2019 18:56:29: 8000000 INFO @ Sun, 02 Jun 2019 18:56:36: 8000000 INFO @ Sun, 02 Jun 2019 18:56:36: 8000000 INFO @ Sun, 02 Jun 2019 18:56:40: 9000000 INFO @ Sun, 02 Jun 2019 18:56:48: 9000000 INFO @ Sun, 02 Jun 2019 18:56:48: 9000000 INFO @ Sun, 02 Jun 2019 18:56:52: 10000000 INFO @ Sun, 02 Jun 2019 18:57:00: 10000000 INFO @ Sun, 02 Jun 2019 18:57:01: 10000000 INFO @ Sun, 02 Jun 2019 18:57:03: 11000000 INFO @ Sun, 02 Jun 2019 18:57:13: 11000000 INFO @ Sun, 02 Jun 2019 18:57:13: 11000000 INFO @ Sun, 02 Jun 2019 18:57:14: 12000000 INFO @ Sun, 02 Jun 2019 18:57:25: 12000000 INFO @ Sun, 02 Jun 2019 18:57:25: 12000000 INFO @ Sun, 02 Jun 2019 18:57:26: 13000000 INFO @ Sun, 02 Jun 2019 18:57:37: 14000000 INFO @ Sun, 02 Jun 2019 18:57:37: 13000000 INFO @ Sun, 02 Jun 2019 18:57:38: 13000000 INFO @ Sun, 02 Jun 2019 18:57:48: 15000000 INFO @ Sun, 02 Jun 2019 18:57:50: 14000000 INFO @ Sun, 02 Jun 2019 18:57:50: 14000000 INFO @ Sun, 02 Jun 2019 18:58:00: 16000000 INFO @ Sun, 02 Jun 2019 18:58:02: 15000000 INFO @ Sun, 02 Jun 2019 18:58:02: 15000000 INFO @ Sun, 02 Jun 2019 18:58:11: 17000000 INFO @ Sun, 02 Jun 2019 18:58:15: 16000000 INFO @ Sun, 02 Jun 2019 18:58:15: 16000000 INFO @ Sun, 02 Jun 2019 18:58:22: 18000000 INFO @ Sun, 02 Jun 2019 18:58:27: 17000000 INFO @ Sun, 02 Jun 2019 18:58:27: 17000000 INFO @ Sun, 02 Jun 2019 18:58:32: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:58:32: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:58:32: #1 total tags in treatment: 18830039 INFO @ Sun, 02 Jun 2019 18:58:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:32: #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 18:58:32: #1 tags after filtering in treatment: 18830039 INFO @ Sun, 02 Jun 2019 18:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:32: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:34: #2 number of paired peaks: 175 WARNING @ Sun, 02 Jun 2019 18:58:34: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:34: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:34: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:34: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:34: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:34: #2 predicted fragment length is 67 bps INFO @ Sun, 02 Jun 2019 18:58:34: #2 alternative fragment length(s) may be 1,67,529,575 bps INFO @ Sun, 02 Jun 2019 18:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.20_model.r WARNING @ Sun, 02 Jun 2019 18:58:34: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:34: #2 You may need to consider one of the other alternative d(s): 1,67,529,575 WARNING @ Sun, 02 Jun 2019 18:58:34: #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 18:58:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:40: 18000000 INFO @ Sun, 02 Jun 2019 18:58:40: 18000000 INFO @ Sun, 02 Jun 2019 18:58:50: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:58:50: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:58:50: #1 total tags in treatment: 18830039 INFO @ Sun, 02 Jun 2019 18:58:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:50: #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 18:58:50: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:58:50: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:58:50: #1 total tags in treatment: 18830039 INFO @ Sun, 02 Jun 2019 18:58:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:50: #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 18:58:50: #1 tags after filtering in treatment: 18830039 INFO @ Sun, 02 Jun 2019 18:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:50: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:50: #1 tags after filtering in treatment: 18830039 INFO @ Sun, 02 Jun 2019 18:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:50: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:52: #2 number of paired peaks: 175 WARNING @ Sun, 02 Jun 2019 18:58:52: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:52: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:52: #2 number of paired peaks: 175 WARNING @ Sun, 02 Jun 2019 18:58:52: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:52: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:52: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:52: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:52: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:52: #2 predicted fragment length is 67 bps INFO @ Sun, 02 Jun 2019 18:58:52: #2 alternative fragment length(s) may be 1,67,529,575 bps INFO @ Sun, 02 Jun 2019 18:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.10_model.r WARNING @ Sun, 02 Jun 2019 18:58:52: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:52: #2 You may need to consider one of the other alternative d(s): 1,67,529,575 WARNING @ Sun, 02 Jun 2019 18:58:52: #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 18:58:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:52: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:52: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:52: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:52: #2 predicted fragment length is 67 bps INFO @ Sun, 02 Jun 2019 18:58:52: #2 alternative fragment length(s) may be 1,67,529,575 bps INFO @ Sun, 02 Jun 2019 18:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.05_model.r WARNING @ Sun, 02 Jun 2019 18:58:52: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:52: #2 You may need to consider one of the other alternative d(s): 1,67,529,575 WARNING @ Sun, 02 Jun 2019 18:58:52: #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 18:58:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:59:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.20_summits.bed INFO @ Sun, 02 Jun 2019 18:59:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.10_summits.bed INFO @ Sun, 02 Jun 2019 18:59:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (522 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194205/SRX4194205.05_summits.bed INFO @ Sun, 02 Jun 2019 18:59:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1398 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。