Job ID = 9025477 sra ファイルのダウンロード中... Completed: 313556K bytes transferred in 5 seconds (433744K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 22318 0 22318 0 0 2414 0 --:--:-- 0:00:09 --:--:-- 8473 100 54318 0 54318 0 0 5220 0 --:--:-- 0:00:10 --:--:-- 14313 100 56377 0 56377 0 0 5417 0 --:--:-- 0:00:10 --:--:-- 14851 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... Written 12232138 spots for /home/okishinya/chipatlas/results/ce10/SRX1132919/SRR2144368.sra Written 12232138 spots total 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: 00:05:02 12232138 reads; of these: 12232138 (100.00%) were unpaired; of these: 1129988 (9.24%) aligned 0 times 9188717 (75.12%) aligned exactly 1 time 1913433 (15.64%) aligned >1 times 90.76% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 2923580 / 11102150 = 0.2633 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 @ Sat, 03 Jun 2017 04:10:14: # Command line: callpeak -t SRX1132919.bam -f BAM -g ce -n SRX1132919.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1132919.05 # format = BAM # ChIP-seq file = ['SRX1132919.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 INFO @ Sat, 03 Jun 2017 04:10:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:10:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:10:14: # Command line: callpeak -t SRX1132919.bam -f BAM -g ce -n SRX1132919.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1132919.10 # format = BAM # ChIP-seq file = ['SRX1132919.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 INFO @ Sat, 03 Jun 2017 04:10:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:10:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:10:14: # Command line: callpeak -t SRX1132919.bam -f BAM -g ce -n SRX1132919.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1132919.20 # format = BAM # ChIP-seq file = ['SRX1132919.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 INFO @ Sat, 03 Jun 2017 04:10:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:10:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:10:22: 1000000 INFO @ Sat, 03 Jun 2017 04:10:22: 1000000 INFO @ Sat, 03 Jun 2017 04:10:22: 1000000 INFO @ Sat, 03 Jun 2017 04:10:29: 2000000 INFO @ Sat, 03 Jun 2017 04:10:29: 2000000 INFO @ Sat, 03 Jun 2017 04:10:29: 2000000 INFO @ Sat, 03 Jun 2017 04:10:37: 3000000 INFO @ Sat, 03 Jun 2017 04:10:37: 3000000 INFO @ Sat, 03 Jun 2017 04:10:37: 3000000 INFO @ Sat, 03 Jun 2017 04:10:44: 4000000 INFO @ Sat, 03 Jun 2017 04:10:44: 4000000 INFO @ Sat, 03 Jun 2017 04:10:44: 4000000 INFO @ Sat, 03 Jun 2017 04:10:51: 5000000 INFO @ Sat, 03 Jun 2017 04:10:51: 5000000 INFO @ Sat, 03 Jun 2017 04:10:52: 5000000 INFO @ Sat, 03 Jun 2017 04:10:58: 6000000 INFO @ Sat, 03 Jun 2017 04:10:58: 6000000 INFO @ Sat, 03 Jun 2017 04:10:58: 6000000 INFO @ Sat, 03 Jun 2017 04:11:05: 7000000 INFO @ Sat, 03 Jun 2017 04:11:05: 7000000 INFO @ Sat, 03 Jun 2017 04:11:06: 7000000 INFO @ Sat, 03 Jun 2017 04:11:11: 8000000 INFO @ Sat, 03 Jun 2017 04:11:11: 8000000 INFO @ Sat, 03 Jun 2017 04:11:13: 8000000 INFO @ Sat, 03 Jun 2017 04:11:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:11:13: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:11:13: #1 total tags in treatment: 8178570 INFO @ Sat, 03 Jun 2017 04:11:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:11:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:11:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:11:13: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:11:13: #1 total tags in treatment: 8178570 INFO @ Sat, 03 Jun 2017 04:11:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:11:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:11:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:11:14: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:11:14: #1 total tags in treatment: 8178570 INFO @ Sat, 03 Jun 2017 04:11:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:11:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:11:14: #1 tags after filtering in treatment: 7967519 INFO @ Sat, 03 Jun 2017 04:11:14: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 03 Jun 2017 04:11:14: #1 finished! INFO @ Sat, 03 Jun 2017 04:11:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:11:14: #1 tags after filtering in treatment: 7967519 INFO @ Sat, 03 Jun 2017 04:11:14: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 03 Jun 2017 04:11:14: #1 finished! INFO @ Sat, 03 Jun 2017 04:11:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:11:15: #1 tags after filtering in treatment: 7967519 INFO @ Sat, 03 Jun 2017 04:11:15: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 03 Jun 2017 04:11:15: #1 finished! INFO @ Sat, 03 Jun 2017 04:11:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:11:15: #2 number of paired peaks: 242 WARNING @ Sat, 03 Jun 2017 04:11:15: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sat, 03 Jun 2017 04:11:15: start model_add_line... INFO @ Sat, 03 Jun 2017 04:11:15: #2 number of paired peaks: 242 WARNING @ Sat, 03 Jun 2017 04:11:15: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sat, 03 Jun 2017 04:11:15: start model_add_line... INFO @ Sat, 03 Jun 2017 04:11:16: #2 number of paired peaks: 242 WARNING @ Sat, 03 Jun 2017 04:11:16: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sat, 03 Jun 2017 04:11:16: start model_add_line... INFO @ Sat, 03 Jun 2017 04:11:18: start X-correlation... INFO @ Sat, 03 Jun 2017 04:11:18: end of X-cor INFO @ Sat, 03 Jun 2017 04:11:18: #2 finished! INFO @ Sat, 03 Jun 2017 04:11:18: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 04:11:18: #2 alternative fragment length(s) may be 3,21,51,54,59,475,550 bps INFO @ Sat, 03 Jun 2017 04:11:18: #2.2 Generate R script for model : SRX1132919.10_model.r WARNING @ Sat, 03 Jun 2017 04:11:18: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:11:18: #2 You may need to consider one of the other alternative d(s): 3,21,51,54,59,475,550 WARNING @ Sat, 03 Jun 2017 04:11:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:11:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:11:18: start X-correlation... INFO @ Sat, 03 Jun 2017 04:11:18: end of X-cor INFO @ Sat, 03 Jun 2017 04:11:18: #2 finished! INFO @ Sat, 03 Jun 2017 04:11:18: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 04:11:18: #2 alternative fragment length(s) may be 3,21,51,54,59,475,550 bps INFO @ Sat, 03 Jun 2017 04:11:18: #2.2 Generate R script for model : SRX1132919.20_model.r WARNING @ Sat, 03 Jun 2017 04:11:18: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:11:18: #2 You may need to consider one of the other alternative d(s): 3,21,51,54,59,475,550 WARNING @ Sat, 03 Jun 2017 04:11:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:11:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:11:19: start X-correlation... INFO @ Sat, 03 Jun 2017 04:11:19: end of X-cor INFO @ Sat, 03 Jun 2017 04:11:19: #2 finished! INFO @ Sat, 03 Jun 2017 04:11:19: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 04:11:19: #2 alternative fragment length(s) may be 3,21,51,54,59,475,550 bps INFO @ Sat, 03 Jun 2017 04:11:19: #2.2 Generate R script for model : SRX1132919.05_model.r WARNING @ Sat, 03 Jun 2017 04:11:19: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:11:19: #2 You may need to consider one of the other alternative d(s): 3,21,51,54,59,475,550 WARNING @ Sat, 03 Jun 2017 04:11:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:11:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:12:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:32: #4 Write output xls file... SRX1132919.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:32: #4 Write peak in narrowPeak format file... SRX1132919.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:32: #4 Write summits bed file... SRX1132919.10_summits.bed INFO @ Sat, 03 Jun 2017 04:12:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:12:35: #4 Write output xls file... SRX1132919.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:35: #4 Write peak in narrowPeak format file... SRX1132919.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:35: #4 Write summits bed file... SRX1132919.20_summits.bed INFO @ Sat, 03 Jun 2017 04:12:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:12:37: #4 Write output xls file... SRX1132919.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:37: #4 Write peak in narrowPeak format file... SRX1132919.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:37: #4 Write summits bed file... SRX1132919.05_summits.bed INFO @ Sat, 03 Jun 2017 04:12:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (768 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。