Job ID = 9025452 sra ファイルのダウンロード中... Completed: 1147350K bytes transferred in 11 seconds (838973K 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 --:--:-- 0 100 14324 0 14324 0 0 1691 0 --:--:-- 0:00:08 --:--:-- 7472 100 44726 0 44726 0 0 4645 0 --:--:-- 0:00:09 --:--:-- 14535 100 70835 0 70835 0 0 7111 0 --:--:-- 0:00:09 --:--:-- 20772 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 37064023 spots for /home/okishinya/chipatlas/results/ce10/SRX1007137/SRR1993097.sra Written 37064023 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: 00:06:16 37064023 reads; of these: 37064023 (100.00%) were unpaired; of these: 9961125 (26.88%) aligned 0 times 22932195 (61.87%) aligned exactly 1 time 4170703 (11.25%) aligned >1 times 73.12% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 5943649 / 27102898 = 0.2193 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 04:04:22: # Command line: callpeak -t SRX1007137.bam -f BAM -g ce -n SRX1007137.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1007137.05 # format = BAM # ChIP-seq file = ['SRX1007137.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 04:04:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:04:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:04:22: # Command line: callpeak -t SRX1007137.bam -f BAM -g ce -n SRX1007137.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1007137.10 # format = BAM # ChIP-seq file = ['SRX1007137.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 04:04:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:04:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:04:22: # Command line: callpeak -t SRX1007137.bam -f BAM -g ce -n SRX1007137.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1007137.20 # format = BAM # ChIP-seq file = ['SRX1007137.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 04:04:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:04:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:04:27: 1000000 INFO @ Sat, 03 Jun 2017 04:04:27: 1000000 INFO @ Sat, 03 Jun 2017 04:04:27: 1000000 INFO @ Sat, 03 Jun 2017 04:04:32: 2000000 INFO @ Sat, 03 Jun 2017 04:04:32: 2000000 INFO @ Sat, 03 Jun 2017 04:04:32: 2000000 INFO @ Sat, 03 Jun 2017 04:04:38: 3000000 INFO @ Sat, 03 Jun 2017 04:04:38: 3000000 INFO @ Sat, 03 Jun 2017 04:04:38: 3000000 INFO @ Sat, 03 Jun 2017 04:04:43: 4000000 INFO @ Sat, 03 Jun 2017 04:04:43: 4000000 INFO @ Sat, 03 Jun 2017 04:04:43: 4000000 INFO @ Sat, 03 Jun 2017 04:04:48: 5000000 INFO @ Sat, 03 Jun 2017 04:04:48: 5000000 INFO @ Sat, 03 Jun 2017 04:04:48: 5000000 INFO @ Sat, 03 Jun 2017 04:04:53: 6000000 INFO @ Sat, 03 Jun 2017 04:04:53: 6000000 INFO @ Sat, 03 Jun 2017 04:04:53: 6000000 INFO @ Sat, 03 Jun 2017 04:04:58: 7000000 INFO @ Sat, 03 Jun 2017 04:04:58: 7000000 INFO @ Sat, 03 Jun 2017 04:04:58: 7000000 INFO @ Sat, 03 Jun 2017 04:05:03: 8000000 INFO @ Sat, 03 Jun 2017 04:05:03: 8000000 INFO @ Sat, 03 Jun 2017 04:05:04: 8000000 INFO @ Sat, 03 Jun 2017 04:05:08: 9000000 INFO @ Sat, 03 Jun 2017 04:05:09: 9000000 INFO @ Sat, 03 Jun 2017 04:05:09: 9000000 INFO @ Sat, 03 Jun 2017 04:05:13: 10000000 INFO @ Sat, 03 Jun 2017 04:05:14: 10000000 INFO @ Sat, 03 Jun 2017 04:05:14: 10000000 INFO @ Sat, 03 Jun 2017 04:05:19: 11000000 INFO @ Sat, 03 Jun 2017 04:05:19: 11000000 INFO @ Sat, 03 Jun 2017 04:05:19: 11000000 INFO @ Sat, 03 Jun 2017 04:05:24: 12000000 INFO @ Sat, 03 Jun 2017 04:05:24: 12000000 INFO @ Sat, 03 Jun 2017 04:05:25: 12000000 INFO @ Sat, 03 Jun 2017 04:05:29: 13000000 INFO @ Sat, 03 Jun 2017 04:05:30: 13000000 INFO @ Sat, 03 Jun 2017 04:05:30: 13000000 INFO @ Sat, 03 Jun 2017 04:05:34: 14000000 INFO @ Sat, 03 Jun 2017 04:05:35: 14000000 INFO @ Sat, 03 Jun 2017 04:05:36: 14000000 INFO @ Sat, 03 Jun 2017 04:05:40: 15000000 INFO @ Sat, 03 Jun 2017 04:05:41: 15000000 INFO @ Sat, 03 Jun 2017 04:05:42: 15000000 INFO @ Sat, 03 Jun 2017 04:05:46: 16000000 INFO @ Sat, 03 Jun 2017 04:05:48: 16000000 INFO @ Sat, 03 Jun 2017 04:05:48: 16000000 INFO @ Sat, 03 Jun 2017 04:05:52: 17000000 INFO @ Sat, 03 Jun 2017 04:05:54: 17000000 INFO @ Sat, 03 Jun 2017 04:05:55: 17000000 INFO @ Sat, 03 Jun 2017 04:05:58: 18000000 INFO @ Sat, 03 Jun 2017 04:06:01: 18000000 INFO @ Sat, 03 Jun 2017 04:06:02: 18000000 INFO @ Sat, 03 Jun 2017 04:06:04: 19000000 INFO @ Sat, 03 Jun 2017 04:06:07: 19000000 INFO @ Sat, 03 Jun 2017 04:06:10: 19000000 INFO @ Sat, 03 Jun 2017 04:06:11: 20000000 INFO @ Sat, 03 Jun 2017 04:06:14: 20000000 INFO @ Sat, 03 Jun 2017 04:06:17: 20000000 INFO @ Sat, 03 Jun 2017 04:06:17: 21000000 INFO @ Sat, 03 Jun 2017 04:06:18: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:06:18: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:06:18: #1 total tags in treatment: 21159249 INFO @ Sat, 03 Jun 2017 04:06:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:06:18: #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 04:06:21: 21000000 INFO @ Sat, 03 Jun 2017 04:06:22: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:06:22: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:06:22: #1 total tags in treatment: 21159249 INFO @ Sat, 03 Jun 2017 04:06:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:06:22: #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 04:06:22: #1 tags after filtering in treatment: 21153631 INFO @ Sat, 03 Jun 2017 04:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:06:22: #1 finished! INFO @ Sat, 03 Jun 2017 04:06:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:06:23: 21000000 INFO @ Sat, 03 Jun 2017 04:06:24: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:06:24: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:06:24: #1 total tags in treatment: 21159249 INFO @ Sat, 03 Jun 2017 04:06:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:06:24: #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 04:06:25: #2 number of paired peaks: 538 WARNING @ Sat, 03 Jun 2017 04:06:25: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sat, 03 Jun 2017 04:06:25: start model_add_line... INFO @ Sat, 03 Jun 2017 04:06:26: #1 tags after filtering in treatment: 21153631 INFO @ Sat, 03 Jun 2017 04:06:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:06:26: #1 finished! INFO @ Sat, 03 Jun 2017 04:06:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:06:28: #1 tags after filtering in treatment: 21153631 INFO @ Sat, 03 Jun 2017 04:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:06:28: #1 finished! INFO @ Sat, 03 Jun 2017 04:06:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:06:30: #2 number of paired peaks: 538 WARNING @ Sat, 03 Jun 2017 04:06:30: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sat, 03 Jun 2017 04:06:30: start model_add_line... INFO @ Sat, 03 Jun 2017 04:06:31: #2 number of paired peaks: 538 WARNING @ Sat, 03 Jun 2017 04:06:31: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Sat, 03 Jun 2017 04:06:31: start model_add_line... INFO @ Sat, 03 Jun 2017 04:06:36: start X-correlation... INFO @ Sat, 03 Jun 2017 04:06:36: end of X-cor INFO @ Sat, 03 Jun 2017 04:06:36: #2 finished! INFO @ Sat, 03 Jun 2017 04:06:36: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:06:36: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sat, 03 Jun 2017 04:06:36: #2.2 Generate R script for model : SRX1007137.05_model.r WARNING @ Sat, 03 Jun 2017 04:06:36: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:06:36: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sat, 03 Jun 2017 04:06:36: #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 04:06:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:06:40: start X-correlation... INFO @ Sat, 03 Jun 2017 04:06:40: end of X-cor INFO @ Sat, 03 Jun 2017 04:06:40: #2 finished! INFO @ Sat, 03 Jun 2017 04:06:40: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:06:40: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sat, 03 Jun 2017 04:06:40: #2.2 Generate R script for model : SRX1007137.20_model.r WARNING @ Sat, 03 Jun 2017 04:06:40: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:06:40: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sat, 03 Jun 2017 04:06:40: #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 04:06:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:06:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:06:41: start X-correlation... INFO @ Sat, 03 Jun 2017 04:06:41: end of X-cor INFO @ Sat, 03 Jun 2017 04:06:41: #2 finished! INFO @ Sat, 03 Jun 2017 04:06:41: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:06:41: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sat, 03 Jun 2017 04:06:41: #2.2 Generate R script for model : SRX1007137.10_model.r WARNING @ Sat, 03 Jun 2017 04:06:41: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:06:41: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sat, 03 Jun 2017 04:06:41: #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 04:06:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:09:21: #4 Write output xls file... SRX1007137.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:09:21: #4 Write peak in narrowPeak format file... SRX1007137.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:09:21: #4 Write summits bed file... SRX1007137.20_summits.bed INFO @ Sat, 03 Jun 2017 04:09:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2438 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:09:24: #4 Write output xls file... SRX1007137.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:09:24: #4 Write peak in narrowPeak format file... SRX1007137.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:09:24: #4 Write summits bed file... SRX1007137.10_summits.bed INFO @ Sat, 03 Jun 2017 04:09:24: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5773 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:09:26: #4 Write output xls file... SRX1007137.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:09:26: #4 Write peak in narrowPeak format file... SRX1007137.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:09:26: #4 Write summits bed file... SRX1007137.05_summits.bed INFO @ Sat, 03 Jun 2017 04:09:26: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (11320 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。