Job ID = 9028873 sra ファイルのダウンロード中... Completed: 145395K bytes transferred in 14 seconds (81089K 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 --:--:-- 0 100 7663 0 7663 0 0 1095 0 --:--:-- 0:00:06 --:--:-- 12460 100 30318 0 30318 0 0 3872 0 --:--:-- 0:00:07 --:--:-- 20981 100 51703 0 51703 0 0 6335 0 --:--:-- 0:00:08 --:--:-- 29095 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 6243277 spots for /home/okishinya/chipatlas/results/ce10/SRX982088/SRR1956575.sra Written 6243277 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: 00:01:36 6243277 reads; of these: 6243277 (100.00%) were unpaired; of these: 325142 (5.21%) aligned 0 times 4926387 (78.91%) aligned exactly 1 time 991748 (15.89%) aligned >1 times 94.79% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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_rmdupse_core] 259480 / 5918135 = 0.0438 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 12:10:21: # Command line: callpeak -t SRX982088.bam -f BAM -g ce -n SRX982088.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982088.10 # format = BAM # ChIP-seq file = ['SRX982088.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 12:10:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:10:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:10:21: # Command line: callpeak -t SRX982088.bam -f BAM -g ce -n SRX982088.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982088.05 # format = BAM # ChIP-seq file = ['SRX982088.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 12:10:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:10:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:10:21: # Command line: callpeak -t SRX982088.bam -f BAM -g ce -n SRX982088.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982088.20 # format = BAM # ChIP-seq file = ['SRX982088.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 12:10:21: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:10:21: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:10:28: 1000000 INFO @ Sat, 03 Jun 2017 12:10:29: 1000000 INFO @ Sat, 03 Jun 2017 12:10:29: 1000000 INFO @ Sat, 03 Jun 2017 12:10:35: 2000000 INFO @ Sat, 03 Jun 2017 12:10:36: 2000000 INFO @ Sat, 03 Jun 2017 12:10:36: 2000000 INFO @ Sat, 03 Jun 2017 12:10:41: 3000000 INFO @ Sat, 03 Jun 2017 12:10:44: 3000000 INFO @ Sat, 03 Jun 2017 12:10:44: 3000000 INFO @ Sat, 03 Jun 2017 12:10:48: 4000000 INFO @ Sat, 03 Jun 2017 12:10:52: 4000000 INFO @ Sat, 03 Jun 2017 12:10:52: 4000000 INFO @ Sat, 03 Jun 2017 12:10:55: 5000000 INFO @ Sat, 03 Jun 2017 12:10:59: 5000000 INFO @ Sat, 03 Jun 2017 12:10:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:10:59: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:10:59: #1 total tags in treatment: 5658655 INFO @ Sat, 03 Jun 2017 12:10:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:10:59: #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 12:10:59: 5000000 INFO @ Sat, 03 Jun 2017 12:11:00: #1 tags after filtering in treatment: 5658123 INFO @ Sat, 03 Jun 2017 12:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:11:00: #1 finished! INFO @ Sat, 03 Jun 2017 12:11:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:11:01: #2 number of paired peaks: 329 WARNING @ Sat, 03 Jun 2017 12:11:01: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Sat, 03 Jun 2017 12:11:01: start model_add_line... INFO @ Sat, 03 Jun 2017 12:11:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:11:04: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:11:04: #1 total tags in treatment: 5658655 INFO @ Sat, 03 Jun 2017 12:11:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:11:04: #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 12:11:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:11:04: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:11:04: #1 total tags in treatment: 5658655 INFO @ Sat, 03 Jun 2017 12:11:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:11:04: #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 12:11:05: start X-correlation... INFO @ Sat, 03 Jun 2017 12:11:05: end of X-cor INFO @ Sat, 03 Jun 2017 12:11:05: #2 finished! INFO @ Sat, 03 Jun 2017 12:11:05: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 12:11:05: #2 alternative fragment length(s) may be 4,52,554 bps INFO @ Sat, 03 Jun 2017 12:11:05: #2.2 Generate R script for model : SRX982088.05_model.r WARNING @ Sat, 03 Jun 2017 12:11:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:11:05: #2 You may need to consider one of the other alternative d(s): 4,52,554 WARNING @ Sat, 03 Jun 2017 12:11:05: #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 12:11:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:11:05: #1 tags after filtering in treatment: 5658123 INFO @ Sat, 03 Jun 2017 12:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:11:05: #1 finished! INFO @ Sat, 03 Jun 2017 12:11:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:11:06: #1 tags after filtering in treatment: 5658123 INFO @ Sat, 03 Jun 2017 12:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:11:06: #1 finished! INFO @ Sat, 03 Jun 2017 12:11:06: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:11:06: #2 number of paired peaks: 329 WARNING @ Sat, 03 Jun 2017 12:11:06: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Sat, 03 Jun 2017 12:11:06: start model_add_line... INFO @ Sat, 03 Jun 2017 12:11:07: #2 number of paired peaks: 329 WARNING @ Sat, 03 Jun 2017 12:11:07: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Sat, 03 Jun 2017 12:11:07: start model_add_line... INFO @ Sat, 03 Jun 2017 12:11:09: start X-correlation... INFO @ Sat, 03 Jun 2017 12:11:09: end of X-cor INFO @ Sat, 03 Jun 2017 12:11:09: #2 finished! INFO @ Sat, 03 Jun 2017 12:11:09: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 12:11:09: #2 alternative fragment length(s) may be 4,52,554 bps INFO @ Sat, 03 Jun 2017 12:11:09: #2.2 Generate R script for model : SRX982088.10_model.r WARNING @ Sat, 03 Jun 2017 12:11:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:11:09: #2 You may need to consider one of the other alternative d(s): 4,52,554 WARNING @ Sat, 03 Jun 2017 12:11:09: #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 12:11:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:11:10: start X-correlation... INFO @ Sat, 03 Jun 2017 12:11:10: end of X-cor INFO @ Sat, 03 Jun 2017 12:11:10: #2 finished! INFO @ Sat, 03 Jun 2017 12:11:10: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Jun 2017 12:11:10: #2 alternative fragment length(s) may be 4,52,554 bps INFO @ Sat, 03 Jun 2017 12:11:10: #2.2 Generate R script for model : SRX982088.20_model.r WARNING @ Sat, 03 Jun 2017 12:11:10: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:11:10: #2 You may need to consider one of the other alternative d(s): 4,52,554 WARNING @ Sat, 03 Jun 2017 12:11:10: #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 12:11:10: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:11:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:11:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:12:02: #4 Write output xls file... SRX982088.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:12:02: #4 Write peak in narrowPeak format file... SRX982088.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:12:02: #4 Write summits bed file... SRX982088.05_summits.bed INFO @ Sat, 03 Jun 2017 12:12:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:12:07: #4 Write output xls file... SRX982088.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:12:07: #4 Write peak in narrowPeak format file... SRX982088.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:12:07: #4 Write summits bed file... SRX982088.10_summits.bed INFO @ Sat, 03 Jun 2017 12:12:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:12:07: #4 Write output xls file... SRX982088.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:12:07: #4 Write peak in narrowPeak format file... SRX982088.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:12:07: #4 Write summits bed file... SRX982088.20_summits.bed INFO @ Sat, 03 Jun 2017 12:12:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (117 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。