Job ID = 9162292 sra ファイルのダウンロード中... Completed: 749490K bytes transferred in 10 seconds (608173K bits/sec), in 1 file, 2 directories. 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... Written 6174744 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872721/SRR3713194.sra Written 6174744 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: 00:07:45 6174744 reads; of these: 6174744 (100.00%) were paired; of these: 1657620 (26.85%) aligned concordantly 0 times 3876694 (62.78%) aligned concordantly exactly 1 time 640430 (10.37%) aligned concordantly >1 times ---- 1657620 pairs aligned concordantly 0 times; of these: 653165 (39.40%) aligned discordantly 1 time ---- 1004455 pairs aligned 0 times concordantly or discordantly; of these: 2008910 mates make up the pairs; of these: 1576636 (78.48%) aligned 0 times 166062 (8.27%) aligned exactly 1 time 266212 (13.25%) aligned >1 times 87.23% overall alignment rate Time searching: 00:07:45 Overall time: 00:07:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 88629 / 5095266 = 0.0174 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 @ Wed, 28 Jun 2017 07:27:19: # Command line: callpeak -t SRX1872721.bam -f BAM -g 12100000 -n SRX1872721.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872721.20 # format = BAM # ChIP-seq file = ['SRX1872721.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 07:27:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:27:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:27:19: # Command line: callpeak -t SRX1872721.bam -f BAM -g 12100000 -n SRX1872721.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872721.10 # format = BAM # ChIP-seq file = ['SRX1872721.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 07:27:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:27:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:27:19: # Command line: callpeak -t SRX1872721.bam -f BAM -g 12100000 -n SRX1872721.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872721.05 # format = BAM # ChIP-seq file = ['SRX1872721.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 07:27:19: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:27:19: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:27:27: 1000000 INFO @ Wed, 28 Jun 2017 07:27:29: 1000000 INFO @ Wed, 28 Jun 2017 07:27:29: 1000000 INFO @ Wed, 28 Jun 2017 07:27:35: 2000000 INFO @ Wed, 28 Jun 2017 07:27:38: 2000000 INFO @ Wed, 28 Jun 2017 07:27:38: 2000000 INFO @ Wed, 28 Jun 2017 07:27:42: 3000000 INFO @ Wed, 28 Jun 2017 07:27:47: 3000000 INFO @ Wed, 28 Jun 2017 07:27:47: 3000000 INFO @ Wed, 28 Jun 2017 07:27:49: 4000000 INFO @ Wed, 28 Jun 2017 07:27:56: 4000000 INFO @ Wed, 28 Jun 2017 07:27:56: 4000000 INFO @ Wed, 28 Jun 2017 07:27:57: 5000000 INFO @ Wed, 28 Jun 2017 07:28:05: 6000000 INFO @ Wed, 28 Jun 2017 07:28:05: 5000000 INFO @ Wed, 28 Jun 2017 07:28:05: 5000000 INFO @ Wed, 28 Jun 2017 07:28:12: 7000000 INFO @ Wed, 28 Jun 2017 07:28:14: 6000000 INFO @ Wed, 28 Jun 2017 07:28:14: 6000000 INFO @ Wed, 28 Jun 2017 07:28:19: 8000000 INFO @ Wed, 28 Jun 2017 07:28:23: 7000000 INFO @ Wed, 28 Jun 2017 07:28:23: 7000000 INFO @ Wed, 28 Jun 2017 07:28:27: 9000000 INFO @ Wed, 28 Jun 2017 07:28:32: 8000000 INFO @ Wed, 28 Jun 2017 07:28:32: 8000000 INFO @ Wed, 28 Jun 2017 07:28:34: 10000000 INFO @ Wed, 28 Jun 2017 07:28:39: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:28:39: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:28:39: #1 total tags in treatment: 4441304 INFO @ Wed, 28 Jun 2017 07:28:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:28:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:28:39: #1 tags after filtering in treatment: 3316304 INFO @ Wed, 28 Jun 2017 07:28:39: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 28 Jun 2017 07:28:39: #1 finished! INFO @ Wed, 28 Jun 2017 07:28:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:28:39: #2 number of paired peaks: 167 WARNING @ Wed, 28 Jun 2017 07:28:39: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Wed, 28 Jun 2017 07:28:39: start model_add_line... INFO @ Wed, 28 Jun 2017 07:28:39: start X-correlation... INFO @ Wed, 28 Jun 2017 07:28:39: end of X-cor INFO @ Wed, 28 Jun 2017 07:28:39: #2 finished! INFO @ Wed, 28 Jun 2017 07:28:39: #2 predicted fragment length is 95 bps INFO @ Wed, 28 Jun 2017 07:28:39: #2 alternative fragment length(s) may be 26,42,45,95,195,202,229,238,269,300,320,334,358,388,404,422,438,443,450,480,522,539,546,563,580 bps INFO @ Wed, 28 Jun 2017 07:28:39: #2.2 Generate R script for model : SRX1872721.20_model.r WARNING @ Wed, 28 Jun 2017 07:28:39: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:28:39: #2 You may need to consider one of the other alternative d(s): 26,42,45,95,195,202,229,238,269,300,320,334,358,388,404,422,438,443,450,480,522,539,546,563,580 WARNING @ Wed, 28 Jun 2017 07:28:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:28:39: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:28:41: 9000000 INFO @ Wed, 28 Jun 2017 07:28:41: 9000000 INFO @ Wed, 28 Jun 2017 07:28:45: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:28:47: #4 Write output xls file... SRX1872721.20_peaks.xls INFO @ Wed, 28 Jun 2017 07:28:47: #4 Write peak in narrowPeak format file... SRX1872721.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:28:47: #4 Write summits bed file... SRX1872721.20_summits.bed INFO @ Wed, 28 Jun 2017 07:28:47: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:28:50: 10000000 INFO @ Wed, 28 Jun 2017 07:28:50: 10000000 INFO @ Wed, 28 Jun 2017 07:28:56: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:28:56: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:28:56: #1 total tags in treatment: 4441304 INFO @ Wed, 28 Jun 2017 07:28:56: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:28:56: #1 tags after filtering in treatment: 3316304 INFO @ Wed, 28 Jun 2017 07:28:56: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 28 Jun 2017 07:28:56: #1 finished! INFO @ Wed, 28 Jun 2017 07:28:56: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:28:56: #2 number of paired peaks: 167 WARNING @ Wed, 28 Jun 2017 07:28:56: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Wed, 28 Jun 2017 07:28:56: start model_add_line... INFO @ Wed, 28 Jun 2017 07:28:56: start X-correlation... INFO @ Wed, 28 Jun 2017 07:28:56: end of X-cor INFO @ Wed, 28 Jun 2017 07:28:56: #2 finished! INFO @ Wed, 28 Jun 2017 07:28:56: #2 predicted fragment length is 95 bps INFO @ Wed, 28 Jun 2017 07:28:56: #2 alternative fragment length(s) may be 26,42,45,95,195,202,229,238,269,300,320,334,358,388,404,422,438,443,450,480,522,539,546,563,580 bps INFO @ Wed, 28 Jun 2017 07:28:56: #2.2 Generate R script for model : SRX1872721.05_model.r WARNING @ Wed, 28 Jun 2017 07:28:56: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:28:56: #2 You may need to consider one of the other alternative d(s): 26,42,45,95,195,202,229,238,269,300,320,334,358,388,404,422,438,443,450,480,522,539,546,563,580 WARNING @ Wed, 28 Jun 2017 07:28:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:28:56: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:28:57: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:28:57: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:28:57: #1 total tags in treatment: 4441304 INFO @ Wed, 28 Jun 2017 07:28:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:28:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:28:57: #1 tags after filtering in treatment: 3316304 INFO @ Wed, 28 Jun 2017 07:28:57: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 28 Jun 2017 07:28:57: #1 finished! INFO @ Wed, 28 Jun 2017 07:28:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:28:57: #2 number of paired peaks: 167 WARNING @ Wed, 28 Jun 2017 07:28:57: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Wed, 28 Jun 2017 07:28:57: start model_add_line... INFO @ Wed, 28 Jun 2017 07:28:57: start X-correlation... INFO @ Wed, 28 Jun 2017 07:28:57: end of X-cor INFO @ Wed, 28 Jun 2017 07:28:57: #2 finished! INFO @ Wed, 28 Jun 2017 07:28:57: #2 predicted fragment length is 95 bps INFO @ Wed, 28 Jun 2017 07:28:57: #2 alternative fragment length(s) may be 26,42,45,95,195,202,229,238,269,300,320,334,358,388,404,422,438,443,450,480,522,539,546,563,580 bps INFO @ Wed, 28 Jun 2017 07:28:57: #2.2 Generate R script for model : SRX1872721.10_model.r WARNING @ Wed, 28 Jun 2017 07:28:57: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:28:57: #2 You may need to consider one of the other alternative d(s): 26,42,45,95,195,202,229,238,269,300,320,334,358,388,404,422,438,443,450,480,522,539,546,563,580 WARNING @ Wed, 28 Jun 2017 07:28:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:28:57: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:29:02: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:29:03: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:29:05: #4 Write output xls file... SRX1872721.05_peaks.xls INFO @ Wed, 28 Jun 2017 07:29:05: #4 Write peak in narrowPeak format file... SRX1872721.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:29:05: #4 Write summits bed file... SRX1872721.05_summits.bed INFO @ Wed, 28 Jun 2017 07:29:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:29:05: #4 Write output xls file... SRX1872721.10_peaks.xls INFO @ Wed, 28 Jun 2017 07:29:05: #4 Write peak in narrowPeak format file... SRX1872721.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:29:05: #4 Write summits bed file... SRX1872721.10_summits.bed INFO @ Wed, 28 Jun 2017 07:29:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (17 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。