Job ID = 11293646 sra ファイルのダウンロード中... Completed: 727657K bytes transferred in 20 seconds (284336K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 21752982 spots for /home/okishinya/chipatlas/results/ce10/SRX4344426/SRR7474953.sra Written 21752982 spots for /home/okishinya/chipatlas/results/ce10/SRX4344426/SRR7474953.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:05:29 21752982 reads; of these: 21752982 (100.00%) were unpaired; of these: 1049628 (4.83%) aligned 0 times 17892169 (82.25%) aligned exactly 1 time 2811185 (12.92%) aligned >1 times 95.17% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 2354942 / 20703354 = 0.1137 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, 04 Nov 2018 17:59:24: # Command line: callpeak -t SRX4344426.bam -f BAM -g ce -n SRX4344426.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4344426.20 # format = BAM # ChIP-seq file = ['SRX4344426.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, 04 Nov 2018 17:59:24: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:59:24: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:59:24: # Command line: callpeak -t SRX4344426.bam -f BAM -g ce -n SRX4344426.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4344426.10 # format = BAM # ChIP-seq file = ['SRX4344426.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, 04 Nov 2018 17:59:24: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:59:24: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:59:24: # Command line: callpeak -t SRX4344426.bam -f BAM -g ce -n SRX4344426.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4344426.05 # format = BAM # ChIP-seq file = ['SRX4344426.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, 04 Nov 2018 17:59:24: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:59:24: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:59:31: 1000000 INFO @ Sun, 04 Nov 2018 17:59:31: 1000000 INFO @ Sun, 04 Nov 2018 17:59:31: 1000000 INFO @ Sun, 04 Nov 2018 17:59:39: 2000000 INFO @ Sun, 04 Nov 2018 17:59:39: 2000000 INFO @ Sun, 04 Nov 2018 17:59:39: 2000000 INFO @ Sun, 04 Nov 2018 17:59:46: 3000000 INFO @ Sun, 04 Nov 2018 17:59:46: 3000000 INFO @ Sun, 04 Nov 2018 17:59:46: 3000000 INFO @ Sun, 04 Nov 2018 17:59:53: 4000000 INFO @ Sun, 04 Nov 2018 17:59:54: 4000000 INFO @ Sun, 04 Nov 2018 17:59:54: 4000000 INFO @ Sun, 04 Nov 2018 18:00:01: 5000000 INFO @ Sun, 04 Nov 2018 18:00:01: 5000000 INFO @ Sun, 04 Nov 2018 18:00:01: 5000000 INFO @ Sun, 04 Nov 2018 18:00:09: 6000000 INFO @ Sun, 04 Nov 2018 18:00:09: 6000000 INFO @ Sun, 04 Nov 2018 18:00:09: 6000000 INFO @ Sun, 04 Nov 2018 18:00:16: 7000000 INFO @ Sun, 04 Nov 2018 18:00:17: 7000000 INFO @ Sun, 04 Nov 2018 18:00:17: 7000000 INFO @ Sun, 04 Nov 2018 18:00:24: 8000000 INFO @ Sun, 04 Nov 2018 18:00:25: 8000000 INFO @ Sun, 04 Nov 2018 18:00:25: 8000000 INFO @ Sun, 04 Nov 2018 18:00:31: 9000000 INFO @ Sun, 04 Nov 2018 18:00:32: 9000000 INFO @ Sun, 04 Nov 2018 18:00:32: 9000000 INFO @ Sun, 04 Nov 2018 18:00:38: 10000000 INFO @ Sun, 04 Nov 2018 18:00:39: 10000000 INFO @ Sun, 04 Nov 2018 18:00:39: 10000000 INFO @ Sun, 04 Nov 2018 18:00:44: 11000000 INFO @ Sun, 04 Nov 2018 18:00:47: 11000000 INFO @ Sun, 04 Nov 2018 18:00:47: 11000000 INFO @ Sun, 04 Nov 2018 18:00:51: 12000000 INFO @ Sun, 04 Nov 2018 18:00:54: 12000000 INFO @ Sun, 04 Nov 2018 18:00:54: 12000000 INFO @ Sun, 04 Nov 2018 18:00:58: 13000000 INFO @ Sun, 04 Nov 2018 18:01:01: 13000000 INFO @ Sun, 04 Nov 2018 18:01:01: 13000000 INFO @ Sun, 04 Nov 2018 18:01:05: 14000000 INFO @ Sun, 04 Nov 2018 18:01:08: 14000000 INFO @ Sun, 04 Nov 2018 18:01:08: 14000000 INFO @ Sun, 04 Nov 2018 18:01:12: 15000000 INFO @ Sun, 04 Nov 2018 18:01:15: 15000000 INFO @ Sun, 04 Nov 2018 18:01:15: 15000000 INFO @ Sun, 04 Nov 2018 18:01:19: 16000000 INFO @ Sun, 04 Nov 2018 18:01:23: 16000000 INFO @ Sun, 04 Nov 2018 18:01:23: 16000000 INFO @ Sun, 04 Nov 2018 18:01:25: 17000000 INFO @ Sun, 04 Nov 2018 18:01:30: 17000000 INFO @ Sun, 04 Nov 2018 18:01:30: 17000000 INFO @ Sun, 04 Nov 2018 18:01:32: 18000000 INFO @ Sun, 04 Nov 2018 18:01:35: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 18:01:35: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 18:01:35: #1 total tags in treatment: 18348412 INFO @ Sun, 04 Nov 2018 18:01:35: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:01:35: #1 tags after filtering in treatment: 18348412 INFO @ Sun, 04 Nov 2018 18:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:01:35: #1 finished! INFO @ Sun, 04 Nov 2018 18:01:35: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:01:37: 18000000 INFO @ Sun, 04 Nov 2018 18:01:37: 18000000 INFO @ Sun, 04 Nov 2018 18:01:37: #2 number of paired peaks: 187 WARNING @ Sun, 04 Nov 2018 18:01:37: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 04 Nov 2018 18:01:37: start model_add_line... INFO @ Sun, 04 Nov 2018 18:01:37: start X-correlation... INFO @ Sun, 04 Nov 2018 18:01:37: end of X-cor INFO @ Sun, 04 Nov 2018 18:01:37: #2 finished! INFO @ Sun, 04 Nov 2018 18:01:37: #2 predicted fragment length is 52 bps INFO @ Sun, 04 Nov 2018 18:01:37: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 04 Nov 2018 18:01:37: #2.2 Generate R script for model : SRX4344426.10_model.r WARNING @ Sun, 04 Nov 2018 18:01:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 18:01:37: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 04 Nov 2018 18:01:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 18:01:37: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:01:39: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 18:01:39: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 18:01:39: #1 total tags in treatment: 18348412 INFO @ Sun, 04 Nov 2018 18:01:39: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:01:39: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 18:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:01:39: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 18:01:39: #1 total tags in treatment: 18348412 INFO @ Sun, 04 Nov 2018 18:01:39: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 18:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 18:01:40: #1 tags after filtering in treatment: 18348412 INFO @ Sun, 04 Nov 2018 18:01:40: #1 tags after filtering in treatment: 18348412 INFO @ Sun, 04 Nov 2018 18:01:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:01:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 18:01:40: #1 finished! INFO @ Sun, 04 Nov 2018 18:01:40: #1 finished! INFO @ Sun, 04 Nov 2018 18:01:40: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:01:40: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 18:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 18:01:41: #2 number of paired peaks: 187 WARNING @ Sun, 04 Nov 2018 18:01:41: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 04 Nov 2018 18:01:41: start model_add_line... INFO @ Sun, 04 Nov 2018 18:01:41: #2 number of paired peaks: 187 WARNING @ Sun, 04 Nov 2018 18:01:41: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 04 Nov 2018 18:01:41: start model_add_line... INFO @ Sun, 04 Nov 2018 18:01:41: start X-correlation... INFO @ Sun, 04 Nov 2018 18:01:41: end of X-cor INFO @ Sun, 04 Nov 2018 18:01:41: #2 finished! INFO @ Sun, 04 Nov 2018 18:01:41: #2 predicted fragment length is 52 bps INFO @ Sun, 04 Nov 2018 18:01:41: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 04 Nov 2018 18:01:41: #2.2 Generate R script for model : SRX4344426.05_model.r WARNING @ Sun, 04 Nov 2018 18:01:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 18:01:41: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 04 Nov 2018 18:01:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 18:01:41: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:01:41: start X-correlation... INFO @ Sun, 04 Nov 2018 18:01:41: end of X-cor INFO @ Sun, 04 Nov 2018 18:01:41: #2 finished! INFO @ Sun, 04 Nov 2018 18:01:41: #2 predicted fragment length is 52 bps INFO @ Sun, 04 Nov 2018 18:01:41: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 04 Nov 2018 18:01:41: #2.2 Generate R script for model : SRX4344426.20_model.r WARNING @ Sun, 04 Nov 2018 18:01:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 18:01:41: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 04 Nov 2018 18:01:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 18:01:41: #3 Call peaks... INFO @ Sun, 04 Nov 2018 18:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 18:02:13: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:02:17: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:02:18: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 18:02:30: #4 Write output xls file... SRX4344426.10_peaks.xls INFO @ Sun, 04 Nov 2018 18:02:30: #4 Write peak in narrowPeak format file... SRX4344426.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:02:30: #4 Write summits bed file... SRX4344426.10_summits.bed INFO @ Sun, 04 Nov 2018 18:02:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:02:36: #4 Write output xls file... SRX4344426.05_peaks.xls INFO @ Sun, 04 Nov 2018 18:02:36: #4 Write peak in narrowPeak format file... SRX4344426.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:02:36: #4 Write summits bed file... SRX4344426.05_summits.bed INFO @ Sun, 04 Nov 2018 18:02:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1014 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 18:02:37: #4 Write output xls file... SRX4344426.20_peaks.xls INFO @ Sun, 04 Nov 2018 18:02:37: #4 Write peak in narrowPeak format file... SRX4344426.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 18:02:37: #4 Write summits bed file... SRX4344426.20_summits.bed INFO @ Sun, 04 Nov 2018 18:02:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 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。