Job ID = 11170833 sra ファイルのダウンロード中... Completed: 1947548K bytes transferred in 131 seconds (121618K 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 15591285 spots for /home/okishinya/chipatlas/results/ce10/SRX3058060/SRR5892351.sra Written 15591285 spots for /home/okishinya/chipatlas/results/ce10/SRX3058060/SRR5892351.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: 00:38:22 15591285 reads; of these: 15591285 (100.00%) were paired; of these: 1531681 (9.82%) aligned concordantly 0 times 12364930 (79.31%) aligned concordantly exactly 1 time 1694674 (10.87%) aligned concordantly >1 times ---- 1531681 pairs aligned concordantly 0 times; of these: 127775 (8.34%) aligned discordantly 1 time ---- 1403906 pairs aligned 0 times concordantly or discordantly; of these: 2807812 mates make up the pairs; of these: 2598190 (92.53%) aligned 0 times 142172 (5.06%) aligned exactly 1 time 67450 (2.40%) aligned >1 times 91.67% overall alignment rate Time searching: 00:38:22 Overall time: 00:38:22 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 24 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] 2175224 / 14167293 = 0.1535 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 12:20:37: # Command line: callpeak -t SRX3058060.bam -f BAM -g ce -n SRX3058060.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3058060.20 # format = BAM # ChIP-seq file = ['SRX3058060.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 12:20:37: # Command line: callpeak -t SRX3058060.bam -f BAM -g ce -n SRX3058060.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3058060.05 # format = BAM # ChIP-seq file = ['SRX3058060.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 12:20:37: # Command line: callpeak -t SRX3058060.bam -f BAM -g ce -n SRX3058060.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3058060.10 # format = BAM # ChIP-seq file = ['SRX3058060.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 12:20:37: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:20:37: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:20:37: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:20:37: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:20:37: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:20:37: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:20:45: 1000000 INFO @ Sat, 08 Sep 2018 12:20:45: 1000000 INFO @ Sat, 08 Sep 2018 12:20:45: 1000000 INFO @ Sat, 08 Sep 2018 12:20:54: 2000000 INFO @ Sat, 08 Sep 2018 12:20:54: 2000000 INFO @ Sat, 08 Sep 2018 12:20:54: 2000000 INFO @ Sat, 08 Sep 2018 12:21:03: 3000000 INFO @ Sat, 08 Sep 2018 12:21:03: 3000000 INFO @ Sat, 08 Sep 2018 12:21:03: 3000000 INFO @ Sat, 08 Sep 2018 12:21:11: 4000000 INFO @ Sat, 08 Sep 2018 12:21:12: 4000000 INFO @ Sat, 08 Sep 2018 12:21:12: 4000000 INFO @ Sat, 08 Sep 2018 12:21:20: 5000000 INFO @ Sat, 08 Sep 2018 12:21:21: 5000000 INFO @ Sat, 08 Sep 2018 12:21:21: 5000000 INFO @ Sat, 08 Sep 2018 12:21:28: 6000000 INFO @ Sat, 08 Sep 2018 12:21:29: 6000000 INFO @ Sat, 08 Sep 2018 12:21:30: 6000000 INFO @ Sat, 08 Sep 2018 12:21:37: 7000000 INFO @ Sat, 08 Sep 2018 12:21:38: 7000000 INFO @ Sat, 08 Sep 2018 12:21:39: 7000000 INFO @ Sat, 08 Sep 2018 12:21:45: 8000000 INFO @ Sat, 08 Sep 2018 12:21:48: 8000000 INFO @ Sat, 08 Sep 2018 12:21:48: 8000000 INFO @ Sat, 08 Sep 2018 12:21:54: 9000000 INFO @ Sat, 08 Sep 2018 12:21:57: 9000000 INFO @ Sat, 08 Sep 2018 12:21:58: 9000000 INFO @ Sat, 08 Sep 2018 12:22:02: 10000000 INFO @ Sat, 08 Sep 2018 12:22:06: 10000000 INFO @ Sat, 08 Sep 2018 12:22:07: 10000000 INFO @ Sat, 08 Sep 2018 12:22:11: 11000000 INFO @ Sat, 08 Sep 2018 12:22:16: 11000000 INFO @ Sat, 08 Sep 2018 12:22:17: 11000000 INFO @ Sat, 08 Sep 2018 12:22:19: 12000000 INFO @ Sat, 08 Sep 2018 12:22:25: 12000000 INFO @ Sat, 08 Sep 2018 12:22:26: 12000000 INFO @ Sat, 08 Sep 2018 12:22:28: 13000000 INFO @ Sat, 08 Sep 2018 12:22:35: 13000000 INFO @ Sat, 08 Sep 2018 12:22:36: 13000000 INFO @ Sat, 08 Sep 2018 12:22:36: 14000000 INFO @ Sat, 08 Sep 2018 12:22:44: 14000000 INFO @ Sat, 08 Sep 2018 12:22:45: 15000000 INFO @ Sat, 08 Sep 2018 12:22:45: 14000000 INFO @ Sat, 08 Sep 2018 12:22:53: 15000000 INFO @ Sat, 08 Sep 2018 12:22:53: 16000000 INFO @ Sat, 08 Sep 2018 12:22:55: 15000000 INFO @ Sat, 08 Sep 2018 12:23:02: 17000000 INFO @ Sat, 08 Sep 2018 12:23:03: 16000000 INFO @ Sat, 08 Sep 2018 12:23:04: 16000000 INFO @ Sat, 08 Sep 2018 12:23:10: 18000000 INFO @ Sat, 08 Sep 2018 12:23:12: 17000000 INFO @ Sat, 08 Sep 2018 12:23:14: 17000000 INFO @ Sat, 08 Sep 2018 12:23:19: 19000000 INFO @ Sat, 08 Sep 2018 12:23:22: 18000000 INFO @ Sat, 08 Sep 2018 12:23:23: 18000000 INFO @ Sat, 08 Sep 2018 12:23:27: 20000000 INFO @ Sat, 08 Sep 2018 12:23:31: 19000000 INFO @ Sat, 08 Sep 2018 12:23:33: 19000000 INFO @ Sat, 08 Sep 2018 12:23:36: 21000000 INFO @ Sat, 08 Sep 2018 12:23:40: 20000000 INFO @ Sat, 08 Sep 2018 12:23:42: 20000000 INFO @ Sat, 08 Sep 2018 12:23:44: 22000000 INFO @ Sat, 08 Sep 2018 12:23:50: 21000000 INFO @ Sat, 08 Sep 2018 12:23:52: 21000000 INFO @ Sat, 08 Sep 2018 12:23:53: 23000000 INFO @ Sat, 08 Sep 2018 12:23:59: 22000000 INFO @ Sat, 08 Sep 2018 12:24:01: 22000000 INFO @ Sat, 08 Sep 2018 12:24:01: 24000000 INFO @ Sat, 08 Sep 2018 12:24:03: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 12:24:03: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 12:24:03: #1 total tags in treatment: 11898449 INFO @ Sat, 08 Sep 2018 12:24:03: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:24:03: #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 12:24:04: #1 tags after filtering in treatment: 11061534 INFO @ Sat, 08 Sep 2018 12:24:04: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Sep 2018 12:24:04: #1 finished! INFO @ Sat, 08 Sep 2018 12:24:04: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:24:04: #2 number of paired peaks: 318 WARNING @ Sat, 08 Sep 2018 12:24:04: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Sat, 08 Sep 2018 12:24:04: start model_add_line... INFO @ Sat, 08 Sep 2018 12:24:04: start X-correlation... INFO @ Sat, 08 Sep 2018 12:24:04: end of X-cor INFO @ Sat, 08 Sep 2018 12:24:04: #2 finished! INFO @ Sat, 08 Sep 2018 12:24:04: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Sep 2018 12:24:04: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 08 Sep 2018 12:24:04: #2.2 Generate R script for model : SRX3058060.10_model.r WARNING @ Sat, 08 Sep 2018 12:24:04: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:24:04: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Sat, 08 Sep 2018 12:24:04: #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 12:24:04: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:24:08: 23000000 INFO @ Sat, 08 Sep 2018 12:24:10: 23000000 INFO @ Sat, 08 Sep 2018 12:24:18: 24000000 INFO @ Sat, 08 Sep 2018 12:24:20: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 12:24:20: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 12:24:20: #1 total tags in treatment: 11898449 INFO @ Sat, 08 Sep 2018 12:24:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:24:20: #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 12:24:20: 24000000 INFO @ Sat, 08 Sep 2018 12:24:20: #1 tags after filtering in treatment: 11061534 INFO @ Sat, 08 Sep 2018 12:24:20: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Sep 2018 12:24:20: #1 finished! INFO @ Sat, 08 Sep 2018 12:24:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:24:21: #2 number of paired peaks: 318 WARNING @ Sat, 08 Sep 2018 12:24:21: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Sat, 08 Sep 2018 12:24:21: start model_add_line... INFO @ Sat, 08 Sep 2018 12:24:21: start X-correlation... INFO @ Sat, 08 Sep 2018 12:24:21: end of X-cor INFO @ Sat, 08 Sep 2018 12:24:21: #2 finished! INFO @ Sat, 08 Sep 2018 12:24:21: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Sep 2018 12:24:21: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 08 Sep 2018 12:24:21: #2.2 Generate R script for model : SRX3058060.05_model.r INFO @ Sat, 08 Sep 2018 12:24:22: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 12:24:22: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 12:24:22: #1 total tags in treatment: 11898449 INFO @ Sat, 08 Sep 2018 12:24:22: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:24:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Sat, 08 Sep 2018 12:24:22: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:24:22: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Sat, 08 Sep 2018 12:24:22: #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 12:24:22: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:24:22: #1 tags after filtering in treatment: 11061534 INFO @ Sat, 08 Sep 2018 12:24:22: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Sep 2018 12:24:22: #1 finished! INFO @ Sat, 08 Sep 2018 12:24:22: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:24:23: #2 number of paired peaks: 318 WARNING @ Sat, 08 Sep 2018 12:24:23: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Sat, 08 Sep 2018 12:24:23: start model_add_line... INFO @ Sat, 08 Sep 2018 12:24:23: start X-correlation... INFO @ Sat, 08 Sep 2018 12:24:23: end of X-cor INFO @ Sat, 08 Sep 2018 12:24:23: #2 finished! INFO @ Sat, 08 Sep 2018 12:24:23: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Sep 2018 12:24:23: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 08 Sep 2018 12:24:23: #2.2 Generate R script for model : SRX3058060.20_model.r WARNING @ Sat, 08 Sep 2018 12:24:23: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:24:23: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Sat, 08 Sep 2018 12:24:23: #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 12:24:23: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:24:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:24:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:24:43: #4 Write output xls file... SRX3058060.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:24:43: #4 Write peak in narrowPeak format file... SRX3058060.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:24:43: #4 Write summits bed file... SRX3058060.10_summits.bed INFO @ Sat, 08 Sep 2018 12:24:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:24:46: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:24:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:24:58: #4 Write output xls file... SRX3058060.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:24:58: #4 Write peak in narrowPeak format file... SRX3058060.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:24:58: #4 Write summits bed file... SRX3058060.05_summits.bed INFO @ Sat, 08 Sep 2018 12:24:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (420 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:24:59: #4 Write output xls file... SRX3058060.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:24:59: #4 Write peak in narrowPeak format file... SRX3058060.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:24:59: #4 Write summits bed file... SRX3058060.20_summits.bed INFO @ Sat, 08 Sep 2018 12:24:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (235 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。