Job ID = 10201956 sra ファイルのダウンロード中... Completed: 347107K bytes transferred in 11 seconds (252961K 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 19452610 spots for /home/okishinya/chipatlas/results/ce10/SRX2576625/SRR5272582.sra Written 19452610 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 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: 00:04:43 19452610 reads; of these: 19452610 (100.00%) were unpaired; of these: 3497021 (17.98%) aligned 0 times 13051462 (67.09%) aligned exactly 1 time 2904127 (14.93%) aligned >1 times 82.02% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:44 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] 7222225 / 15955589 = 0.4526 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 @ Mon, 13 Nov 2017 13:16:24: # Command line: callpeak -t SRX2576625.bam -f BAM -g ce -n SRX2576625.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576625.10 # format = BAM # ChIP-seq file = ['SRX2576625.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 @ Mon, 13 Nov 2017 13:16:24: # Command line: callpeak -t SRX2576625.bam -f BAM -g ce -n SRX2576625.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576625.20 # format = BAM # ChIP-seq file = ['SRX2576625.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 @ Mon, 13 Nov 2017 13:16:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:24: # Command line: callpeak -t SRX2576625.bam -f BAM -g ce -n SRX2576625.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576625.05 # format = BAM # ChIP-seq file = ['SRX2576625.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 @ Mon, 13 Nov 2017 13:16:24: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:16:24: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:16:30: 1000000 INFO @ Mon, 13 Nov 2017 13:16:31: 1000000 INFO @ Mon, 13 Nov 2017 13:16:31: 1000000 INFO @ Mon, 13 Nov 2017 13:16:37: 2000000 INFO @ Mon, 13 Nov 2017 13:16:37: 2000000 INFO @ Mon, 13 Nov 2017 13:16:37: 2000000 INFO @ Mon, 13 Nov 2017 13:16:44: 3000000 INFO @ Mon, 13 Nov 2017 13:16:44: 3000000 INFO @ Mon, 13 Nov 2017 13:16:44: 3000000 INFO @ Mon, 13 Nov 2017 13:16:50: 4000000 INFO @ Mon, 13 Nov 2017 13:16:50: 4000000 INFO @ Mon, 13 Nov 2017 13:16:51: 4000000 INFO @ Mon, 13 Nov 2017 13:16:57: 5000000 INFO @ Mon, 13 Nov 2017 13:16:57: 5000000 INFO @ Mon, 13 Nov 2017 13:16:58: 5000000 INFO @ Mon, 13 Nov 2017 13:17:03: 6000000 INFO @ Mon, 13 Nov 2017 13:17:04: 6000000 INFO @ Mon, 13 Nov 2017 13:17:05: 6000000 INFO @ Mon, 13 Nov 2017 13:17:10: 7000000 INFO @ Mon, 13 Nov 2017 13:17:11: 7000000 INFO @ Mon, 13 Nov 2017 13:17:13: 7000000 INFO @ Mon, 13 Nov 2017 13:17:16: 8000000 INFO @ Mon, 13 Nov 2017 13:17:18: 8000000 INFO @ Mon, 13 Nov 2017 13:17:20: 8000000 INFO @ Mon, 13 Nov 2017 13:17:21: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:17:21: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:17:21: #1 total tags in treatment: 8733364 INFO @ Mon, 13 Nov 2017 13:17:21: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:21: #1 tags after filtering in treatment: 8733364 INFO @ Mon, 13 Nov 2017 13:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:21: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:21: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:21: #2 number of paired peaks: 476 WARNING @ Mon, 13 Nov 2017 13:17:21: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:21: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:22: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:22: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:22: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:22: #2 predicted fragment length is 80 bps INFO @ Mon, 13 Nov 2017 13:17:22: #2 alternative fragment length(s) may be 4,80 bps INFO @ Mon, 13 Nov 2017 13:17:22: #2.2 Generate R script for model : SRX2576625.05_model.r WARNING @ Mon, 13 Nov 2017 13:17:22: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:17:22: #2 You may need to consider one of the other alternative d(s): 4,80 WARNING @ Mon, 13 Nov 2017 13:17:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:17:22: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:23: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:17:23: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:17:23: #1 total tags in treatment: 8733364 INFO @ Mon, 13 Nov 2017 13:17:23: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:23: #1 tags after filtering in treatment: 8733364 INFO @ Mon, 13 Nov 2017 13:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:23: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:23: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:23: #2 number of paired peaks: 476 WARNING @ Mon, 13 Nov 2017 13:17:23: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:23: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:24: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:24: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:24: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:24: #2 predicted fragment length is 80 bps INFO @ Mon, 13 Nov 2017 13:17:24: #2 alternative fragment length(s) may be 4,80 bps INFO @ Mon, 13 Nov 2017 13:17:24: #2.2 Generate R script for model : SRX2576625.20_model.r WARNING @ Mon, 13 Nov 2017 13:17:24: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:17:24: #2 You may need to consider one of the other alternative d(s): 4,80 WARNING @ Mon, 13 Nov 2017 13:17:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:17:24: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:25: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:17:25: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:17:25: #1 total tags in treatment: 8733364 INFO @ Mon, 13 Nov 2017 13:17:25: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:25: #1 tags after filtering in treatment: 8733364 INFO @ Mon, 13 Nov 2017 13:17:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:25: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:25: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:26: #2 number of paired peaks: 476 WARNING @ Mon, 13 Nov 2017 13:17:26: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:26: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:26: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:26: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:26: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:26: #2 predicted fragment length is 80 bps INFO @ Mon, 13 Nov 2017 13:17:26: #2 alternative fragment length(s) may be 4,80 bps INFO @ Mon, 13 Nov 2017 13:17:26: #2.2 Generate R script for model : SRX2576625.10_model.r WARNING @ Mon, 13 Nov 2017 13:17:26: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:17:26: #2 You may need to consider one of the other alternative d(s): 4,80 WARNING @ Mon, 13 Nov 2017 13:17:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:17:26: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:40: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:44: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:46: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:50: #4 Write output xls file... SRX2576625.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:50: #4 Write peak in narrowPeak format file... SRX2576625.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:50: #4 Write summits bed file... SRX2576625.05_summits.bed INFO @ Mon, 13 Nov 2017 13:17:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1235 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:17:54: #4 Write output xls file... SRX2576625.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:54: #4 Write peak in narrowPeak format file... SRX2576625.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:54: #4 Write summits bed file... SRX2576625.20_summits.bed INFO @ Mon, 13 Nov 2017 13:17:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (452 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:17:56: #4 Write output xls file... SRX2576625.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:17:56: #4 Write peak in narrowPeak format file... SRX2576625.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:17:56: #4 Write summits bed file... SRX2576625.10_summits.bed INFO @ Mon, 13 Nov 2017 13:17:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (840 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。