Job ID = 10194921 sra ファイルのダウンロード中... Completed: 117306K bytes transferred in 7 seconds (134641K bits/sec), in 1 file. Completed: 114642K bytes transferred in 5 seconds (157807K bits/sec), in 1 file. Completed: 192700K bytes transferred in 12 seconds (126694K bits/sec), in 1 file. Completed: 189351K bytes transferred in 15 seconds (99916K bits/sec), in 1 file. Completed: 189524K bytes transferred in 16 seconds (95371K bits/sec), in 1 file. Completed: 186955K bytes transferred in 12 seconds (123475K 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... Written 2681790 spots for /home/okishinya/chipatlas/results/rn6/SRX2202916/SRR4320041.sra Written 2681790 spots total Written 2755167 spots for /home/okishinya/chipatlas/results/rn6/SRX2202916/SRR4320040.sra Written 2755167 spots total Written 4121456 spots for /home/okishinya/chipatlas/results/rn6/SRX2202916/SRR4320044.sra Written 4121456 spots total Written 4072885 spots for /home/okishinya/chipatlas/results/rn6/SRX2202916/SRR4320045.sra Written 4072885 spots total Written 4090991 spots for /home/okishinya/chipatlas/results/rn6/SRX2202916/SRR4320043.sra Written 4090991 spots total Written 4189633 spots for /home/okishinya/chipatlas/results/rn6/SRX2202916/SRR4320042.sra Written 4189633 spots total 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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:45:45 21911922 reads; of these: 21911922 (100.00%) were unpaired; of these: 642199 (2.93%) aligned 0 times 14624454 (66.74%) aligned exactly 1 time 6645269 (30.33%) aligned >1 times 97.07% overall alignment rate Time searching: 00:45:49 Overall time: 00:45:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1422650 / 21269723 = 0.0669 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, 11 Nov 2017 00:04:38: # Command line: callpeak -t SRX2202916.bam -f BAM -g 2.15e9 -n SRX2202916.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202916.10 # format = BAM # ChIP-seq file = ['SRX2202916.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 00:04:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:38: # Command line: callpeak -t SRX2202916.bam -f BAM -g 2.15e9 -n SRX2202916.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202916.05 # format = BAM # ChIP-seq file = ['SRX2202916.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 00:04:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:38: # Command line: callpeak -t SRX2202916.bam -f BAM -g 2.15e9 -n SRX2202916.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202916.20 # format = BAM # ChIP-seq file = ['SRX2202916.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 00:04:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:51: 1000000 INFO @ Sat, 11 Nov 2017 00:04:53: 1000000 INFO @ Sat, 11 Nov 2017 00:04:55: 1000000 INFO @ Sat, 11 Nov 2017 00:05:04: 2000000 INFO @ Sat, 11 Nov 2017 00:05:10: 2000000 INFO @ Sat, 11 Nov 2017 00:05:12: 2000000 INFO @ Sat, 11 Nov 2017 00:05:17: 3000000 INFO @ Sat, 11 Nov 2017 00:05:26: 3000000 INFO @ Sat, 11 Nov 2017 00:05:29: 3000000 INFO @ Sat, 11 Nov 2017 00:05:30: 4000000 INFO @ Sat, 11 Nov 2017 00:05:43: 4000000 INFO @ Sat, 11 Nov 2017 00:05:43: 5000000 INFO @ Sat, 11 Nov 2017 00:05:46: 4000000 INFO @ Sat, 11 Nov 2017 00:05:57: 6000000 INFO @ Sat, 11 Nov 2017 00:05:59: 5000000 INFO @ Sat, 11 Nov 2017 00:06:02: 5000000 INFO @ Sat, 11 Nov 2017 00:06:10: 7000000 INFO @ Sat, 11 Nov 2017 00:06:16: 6000000 INFO @ Sat, 11 Nov 2017 00:06:17: 6000000 INFO @ Sat, 11 Nov 2017 00:06:24: 8000000 INFO @ Sat, 11 Nov 2017 00:06:32: 7000000 INFO @ Sat, 11 Nov 2017 00:06:34: 7000000 INFO @ Sat, 11 Nov 2017 00:06:41: 9000000 INFO @ Sat, 11 Nov 2017 00:06:47: 8000000 INFO @ Sat, 11 Nov 2017 00:06:51: 8000000 INFO @ Sat, 11 Nov 2017 00:06:58: 10000000 INFO @ Sat, 11 Nov 2017 00:07:03: 9000000 INFO @ Sat, 11 Nov 2017 00:07:09: 9000000 INFO @ Sat, 11 Nov 2017 00:07:13: 11000000 INFO @ Sat, 11 Nov 2017 00:07:18: 10000000 INFO @ Sat, 11 Nov 2017 00:07:26: 10000000 INFO @ Sat, 11 Nov 2017 00:07:27: 12000000 INFO @ Sat, 11 Nov 2017 00:07:32: 11000000 INFO @ Sat, 11 Nov 2017 00:07:40: 13000000 INFO @ Sat, 11 Nov 2017 00:07:43: 11000000 INFO @ Sat, 11 Nov 2017 00:07:44: 12000000 INFO @ Sat, 11 Nov 2017 00:07:52: 14000000 INFO @ Sat, 11 Nov 2017 00:07:56: 13000000 INFO @ Sat, 11 Nov 2017 00:08:00: 12000000 INFO @ Sat, 11 Nov 2017 00:08:03: 15000000 INFO @ Sat, 11 Nov 2017 00:08:10: 14000000 INFO @ Sat, 11 Nov 2017 00:08:13: 16000000 INFO @ Sat, 11 Nov 2017 00:08:18: 13000000 INFO @ Sat, 11 Nov 2017 00:08:24: 17000000 INFO @ Sat, 11 Nov 2017 00:08:25: 15000000 INFO @ Sat, 11 Nov 2017 00:08:34: 14000000 INFO @ Sat, 11 Nov 2017 00:08:36: 18000000 INFO @ Sat, 11 Nov 2017 00:08:40: 16000000 INFO @ Sat, 11 Nov 2017 00:08:49: 15000000 INFO @ Sat, 11 Nov 2017 00:08:54: 17000000 INFO @ Sat, 11 Nov 2017 00:08:58: 19000000 INFO @ Sat, 11 Nov 2017 00:09:03: 16000000 INFO @ Sat, 11 Nov 2017 00:09:06: 18000000 INFO @ Sat, 11 Nov 2017 00:09:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:09:16: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:09:16: #1 total tags in treatment: 19847073 INFO @ Sat, 11 Nov 2017 00:09:16: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:09:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:09:17: #1 tags after filtering in treatment: 19846964 INFO @ Sat, 11 Nov 2017 00:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:09:17: #1 finished! INFO @ Sat, 11 Nov 2017 00:09:17: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:09:18: 19000000 INFO @ Sat, 11 Nov 2017 00:09:18: 17000000 INFO @ Sat, 11 Nov 2017 00:09:20: #2 number of paired peaks: 16224 INFO @ Sat, 11 Nov 2017 00:09:20: start model_add_line... INFO @ Sat, 11 Nov 2017 00:09:21: start X-correlation... INFO @ Sat, 11 Nov 2017 00:09:21: end of X-cor INFO @ Sat, 11 Nov 2017 00:09:21: #2 finished! INFO @ Sat, 11 Nov 2017 00:09:21: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Nov 2017 00:09:21: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Nov 2017 00:09:21: #2.2 Generate R script for model : SRX2202916.05_model.r WARNING @ Sat, 11 Nov 2017 00:09:21: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:09:21: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Nov 2017 00:09:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:09:21: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:09:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:09:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:09:28: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:09:28: #1 total tags in treatment: 19847073 INFO @ Sat, 11 Nov 2017 00:09:28: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:09:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:09:29: #1 tags after filtering in treatment: 19846964 INFO @ Sat, 11 Nov 2017 00:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:09:29: #1 finished! INFO @ Sat, 11 Nov 2017 00:09:29: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:09:32: #2 number of paired peaks: 16224 INFO @ Sat, 11 Nov 2017 00:09:32: start model_add_line... INFO @ Sat, 11 Nov 2017 00:09:32: start X-correlation... INFO @ Sat, 11 Nov 2017 00:09:32: end of X-cor INFO @ Sat, 11 Nov 2017 00:09:32: #2 finished! INFO @ Sat, 11 Nov 2017 00:09:32: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Nov 2017 00:09:32: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Nov 2017 00:09:32: #2.2 Generate R script for model : SRX2202916.10_model.r WARNING @ Sat, 11 Nov 2017 00:09:32: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:09:32: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Nov 2017 00:09:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:09:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:09:34: 18000000 INFO @ Sat, 11 Nov 2017 00:09:50: 19000000 INFO @ Sat, 11 Nov 2017 00:10:03: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:10:03: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:10:03: #1 total tags in treatment: 19847073 INFO @ Sat, 11 Nov 2017 00:10:03: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:10:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:10:04: #1 tags after filtering in treatment: 19846964 INFO @ Sat, 11 Nov 2017 00:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:10:04: #1 finished! INFO @ Sat, 11 Nov 2017 00:10:04: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:10:08: #2 number of paired peaks: 16224 INFO @ Sat, 11 Nov 2017 00:10:08: start model_add_line... INFO @ Sat, 11 Nov 2017 00:10:08: start X-correlation... INFO @ Sat, 11 Nov 2017 00:10:08: end of X-cor INFO @ Sat, 11 Nov 2017 00:10:08: #2 finished! INFO @ Sat, 11 Nov 2017 00:10:08: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Nov 2017 00:10:08: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Nov 2017 00:10:08: #2.2 Generate R script for model : SRX2202916.20_model.r WARNING @ Sat, 11 Nov 2017 00:10:08: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:10:08: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Nov 2017 00:10:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:10:08: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:10:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:10:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:11:00: #4 Write output xls file... SRX2202916.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:11:00: #4 Write peak in narrowPeak format file... SRX2202916.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:11:00: #4 Write summits bed file... SRX2202916.05_summits.bed INFO @ Sat, 11 Nov 2017 00:11:00: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (2092 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:11:08: #4 Write output xls file... SRX2202916.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:11:08: #4 Write peak in narrowPeak format file... SRX2202916.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:11:08: #4 Write summits bed file... SRX2202916.10_summits.bed INFO @ Sat, 11 Nov 2017 00:11:08: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1010 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:11:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:11:45: #4 Write output xls file... SRX2202916.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:11:46: #4 Write peak in narrowPeak format file... SRX2202916.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:11:46: #4 Write summits bed file... SRX2202916.20_summits.bed INFO @ Sat, 11 Nov 2017 00:11:46: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (511 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。