Job ID = 11170831 sra ファイルのダウンロード中... Completed: 2246287K bytes transferred in 149 seconds (123293K 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: PAIRED fastq に変換中... Read 17819829 spots for /home/okishinya/chipatlas/results/ce10/SRX3058058/SRR5892349.sra Written 17819829 spots for /home/okishinya/chipatlas/results/ce10/SRX3058058/SRR5892349.sra 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: 00:35:25 17819829 reads; of these: 17819829 (100.00%) were paired; of these: 5062342 (28.41%) aligned concordantly 0 times 11168844 (62.68%) aligned concordantly exactly 1 time 1588643 (8.92%) aligned concordantly >1 times ---- 5062342 pairs aligned concordantly 0 times; of these: 138993 (2.75%) aligned discordantly 1 time ---- 4923349 pairs aligned 0 times concordantly or discordantly; of these: 9846698 mates make up the pairs; of these: 9611746 (97.61%) aligned 0 times 160297 (1.63%) aligned exactly 1 time 74655 (0.76%) aligned >1 times 73.03% overall alignment rate Time searching: 00:35:26 Overall time: 00:35:26 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 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 6331596 / 12874555 = 0.4918 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, 08 Sep 2018 12:14:28: # Command line: callpeak -t SRX3058058.bam -f BAM -g ce -n SRX3058058.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3058058.20 # format = BAM # ChIP-seq file = ['SRX3058058.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 @ Sat, 08 Sep 2018 12:14:28: # Command line: callpeak -t SRX3058058.bam -f BAM -g ce -n SRX3058058.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3058058.05 # format = BAM # ChIP-seq file = ['SRX3058058.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 @ Sat, 08 Sep 2018 12:14:28: # Command line: callpeak -t SRX3058058.bam -f BAM -g ce -n SRX3058058.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3058058.10 # format = BAM # ChIP-seq file = ['SRX3058058.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 @ Sat, 08 Sep 2018 12:14:28: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:14:28: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:14:28: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:14:28: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:14:28: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:14:28: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:14:37: 1000000 INFO @ Sat, 08 Sep 2018 12:14:37: 1000000 INFO @ Sat, 08 Sep 2018 12:14:37: 1000000 INFO @ Sat, 08 Sep 2018 12:14:46: 2000000 INFO @ Sat, 08 Sep 2018 12:14:46: 2000000 INFO @ Sat, 08 Sep 2018 12:14:46: 2000000 INFO @ Sat, 08 Sep 2018 12:14:55: 3000000 INFO @ Sat, 08 Sep 2018 12:14:55: 3000000 INFO @ Sat, 08 Sep 2018 12:14:55: 3000000 INFO @ Sat, 08 Sep 2018 12:15:04: 4000000 INFO @ Sat, 08 Sep 2018 12:15:04: 4000000 INFO @ Sat, 08 Sep 2018 12:15:04: 4000000 INFO @ Sat, 08 Sep 2018 12:15:13: 5000000 INFO @ Sat, 08 Sep 2018 12:15:13: 5000000 INFO @ Sat, 08 Sep 2018 12:15:13: 5000000 INFO @ Sat, 08 Sep 2018 12:15:23: 6000000 INFO @ Sat, 08 Sep 2018 12:15:23: 6000000 INFO @ Sat, 08 Sep 2018 12:15:23: 6000000 INFO @ Sat, 08 Sep 2018 12:15:32: 7000000 INFO @ Sat, 08 Sep 2018 12:15:32: 7000000 INFO @ Sat, 08 Sep 2018 12:15:33: 7000000 INFO @ Sat, 08 Sep 2018 12:15:42: 8000000 INFO @ Sat, 08 Sep 2018 12:15:42: 8000000 INFO @ Sat, 08 Sep 2018 12:15:43: 8000000 INFO @ Sat, 08 Sep 2018 12:15:52: 9000000 INFO @ Sat, 08 Sep 2018 12:15:52: 9000000 INFO @ Sat, 08 Sep 2018 12:15:53: 9000000 INFO @ Sat, 08 Sep 2018 12:16:02: 10000000 INFO @ Sat, 08 Sep 2018 12:16:02: 10000000 INFO @ Sat, 08 Sep 2018 12:16:03: 10000000 INFO @ Sat, 08 Sep 2018 12:16:11: 11000000 INFO @ Sat, 08 Sep 2018 12:16:11: 11000000 INFO @ Sat, 08 Sep 2018 12:16:13: 11000000 INFO @ Sat, 08 Sep 2018 12:16:19: 12000000 INFO @ Sat, 08 Sep 2018 12:16:20: 12000000 INFO @ Sat, 08 Sep 2018 12:16:22: 12000000 INFO @ Sat, 08 Sep 2018 12:16:27: 13000000 INFO @ Sat, 08 Sep 2018 12:16:29: 13000000 INFO @ Sat, 08 Sep 2018 12:16:30: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 12:16:30: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 12:16:30: #1 total tags in treatment: 6462044 INFO @ Sat, 08 Sep 2018 12:16:30: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:16:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:16:31: #1 tags after filtering in treatment: 6068429 INFO @ Sat, 08 Sep 2018 12:16:31: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 12:16:31: #1 finished! INFO @ Sat, 08 Sep 2018 12:16:31: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:16:31: 13000000 INFO @ Sat, 08 Sep 2018 12:16:31: #2 number of paired peaks: 488 WARNING @ Sat, 08 Sep 2018 12:16:31: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Sat, 08 Sep 2018 12:16:31: start model_add_line... INFO @ Sat, 08 Sep 2018 12:16:31: start X-correlation... INFO @ Sat, 08 Sep 2018 12:16:31: end of X-cor INFO @ Sat, 08 Sep 2018 12:16:31: #2 finished! INFO @ Sat, 08 Sep 2018 12:16:31: #2 predicted fragment length is 216 bps INFO @ Sat, 08 Sep 2018 12:16:31: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 08 Sep 2018 12:16:31: #2.2 Generate R script for model : SRX3058058.20_model.r WARNING @ Sat, 08 Sep 2018 12:16:31: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:16:31: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sat, 08 Sep 2018 12:16:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:16:31: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:16:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:16:32: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 12:16:32: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 12:16:32: #1 total tags in treatment: 6462044 INFO @ Sat, 08 Sep 2018 12:16:32: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:16:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:16:32: #1 tags after filtering in treatment: 6068429 INFO @ Sat, 08 Sep 2018 12:16:32: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 12:16:32: #1 finished! INFO @ Sat, 08 Sep 2018 12:16:32: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:16:33: #2 number of paired peaks: 488 WARNING @ Sat, 08 Sep 2018 12:16:33: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Sat, 08 Sep 2018 12:16:33: start model_add_line... INFO @ Sat, 08 Sep 2018 12:16:33: start X-correlation... INFO @ Sat, 08 Sep 2018 12:16:33: end of X-cor INFO @ Sat, 08 Sep 2018 12:16:33: #2 finished! INFO @ Sat, 08 Sep 2018 12:16:33: #2 predicted fragment length is 216 bps INFO @ Sat, 08 Sep 2018 12:16:33: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 08 Sep 2018 12:16:33: #2.2 Generate R script for model : SRX3058058.10_model.r WARNING @ Sat, 08 Sep 2018 12:16:33: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:16:33: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sat, 08 Sep 2018 12:16:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:16:33: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:16:34: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 12:16:34: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 12:16:34: #1 total tags in treatment: 6462044 INFO @ Sat, 08 Sep 2018 12:16:34: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:16:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:16:34: #1 tags after filtering in treatment: 6068429 INFO @ Sat, 08 Sep 2018 12:16:34: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Sep 2018 12:16:34: #1 finished! INFO @ Sat, 08 Sep 2018 12:16:34: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:16:35: #2 number of paired peaks: 488 WARNING @ Sat, 08 Sep 2018 12:16:35: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Sat, 08 Sep 2018 12:16:35: start model_add_line... INFO @ Sat, 08 Sep 2018 12:16:35: start X-correlation... INFO @ Sat, 08 Sep 2018 12:16:35: end of X-cor INFO @ Sat, 08 Sep 2018 12:16:35: #2 finished! INFO @ Sat, 08 Sep 2018 12:16:35: #2 predicted fragment length is 216 bps INFO @ Sat, 08 Sep 2018 12:16:35: #2 alternative fragment length(s) may be 216 bps INFO @ Sat, 08 Sep 2018 12:16:35: #2.2 Generate R script for model : SRX3058058.05_model.r WARNING @ Sat, 08 Sep 2018 12:16:35: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:16:35: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sat, 08 Sep 2018 12:16:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 12:16:35: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:16:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:16:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:16:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:16:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:16:55: #4 Write output xls file... SRX3058058.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:16:55: #4 Write peak in narrowPeak format file... SRX3058058.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:16:55: #4 Write summits bed file... SRX3058058.20_summits.bed INFO @ Sat, 08 Sep 2018 12:16:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (749 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:16:57: #4 Write output xls file... SRX3058058.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:16:57: #4 Write peak in narrowPeak format file... SRX3058058.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:16:57: #4 Write summits bed file... SRX3058058.05_summits.bed INFO @ Sat, 08 Sep 2018 12:16:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3135 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:16:57: #4 Write output xls file... SRX3058058.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:16:57: #4 Write peak in narrowPeak format file... SRX3058058.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:16:57: #4 Write summits bed file... SRX3058058.10_summits.bed INFO @ Sat, 08 Sep 2018 12:16:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1793 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。