Job ID = 10714455 sra ファイルのダウンロード中... Completed: 947815K bytes transferred in 22 seconds (341414K 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 14631211 spots for /home/okishinya/chipatlas/results/ce10/SRX4085371/SRR7167400.sra Written 14631211 spots for /home/okishinya/chipatlas/results/ce10/SRX4085371/SRR7167400.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: 00:10:17 14631211 reads; of these: 14631211 (100.00%) were paired; of these: 7610075 (52.01%) aligned concordantly 0 times 6226982 (42.56%) aligned concordantly exactly 1 time 794154 (5.43%) aligned concordantly >1 times ---- 7610075 pairs aligned concordantly 0 times; of these: 198121 (2.60%) aligned discordantly 1 time ---- 7411954 pairs aligned 0 times concordantly or discordantly; of these: 14823908 mates make up the pairs; of these: 11488364 (77.50%) aligned 0 times 2962888 (19.99%) aligned exactly 1 time 372656 (2.51%) aligned >1 times 60.74% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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_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] 537429 / 7135069 = 0.0753 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 @ Sun, 03 Jun 2018 12:56:13: # Command line: callpeak -t SRX4085371.bam -f BAM -g ce -n SRX4085371.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085371.05 # format = BAM # ChIP-seq file = ['SRX4085371.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 @ Sun, 03 Jun 2018 12:56:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:56:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:56:13: # Command line: callpeak -t SRX4085371.bam -f BAM -g ce -n SRX4085371.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085371.20 # format = BAM # ChIP-seq file = ['SRX4085371.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 @ Sun, 03 Jun 2018 12:56:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:56:13: # Command line: callpeak -t SRX4085371.bam -f BAM -g ce -n SRX4085371.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085371.10 # format = BAM # ChIP-seq file = ['SRX4085371.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 @ Sun, 03 Jun 2018 12:56:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:56:13: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:56:13: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:56:19: 1000000 INFO @ Sun, 03 Jun 2018 12:56:20: 1000000 INFO @ Sun, 03 Jun 2018 12:56:20: 1000000 INFO @ Sun, 03 Jun 2018 12:56:25: 2000000 INFO @ Sun, 03 Jun 2018 12:56:28: 2000000 INFO @ Sun, 03 Jun 2018 12:56:28: 2000000 INFO @ Sun, 03 Jun 2018 12:56:31: 3000000 INFO @ Sun, 03 Jun 2018 12:56:35: 3000000 INFO @ Sun, 03 Jun 2018 12:56:35: 3000000 INFO @ Sun, 03 Jun 2018 12:56:37: 4000000 INFO @ Sun, 03 Jun 2018 12:56:42: 4000000 INFO @ Sun, 03 Jun 2018 12:56:42: 4000000 INFO @ Sun, 03 Jun 2018 12:56:43: 5000000 INFO @ Sun, 03 Jun 2018 12:56:49: 6000000 INFO @ Sun, 03 Jun 2018 12:56:49: 5000000 INFO @ Sun, 03 Jun 2018 12:56:49: 5000000 INFO @ Sun, 03 Jun 2018 12:56:54: 7000000 INFO @ Sun, 03 Jun 2018 12:56:56: 6000000 INFO @ Sun, 03 Jun 2018 12:56:56: 6000000 INFO @ Sun, 03 Jun 2018 12:57:00: 8000000 INFO @ Sun, 03 Jun 2018 12:57:03: 7000000 INFO @ Sun, 03 Jun 2018 12:57:03: 7000000 INFO @ Sun, 03 Jun 2018 12:57:06: 9000000 INFO @ Sun, 03 Jun 2018 12:57:11: 8000000 INFO @ Sun, 03 Jun 2018 12:57:11: 8000000 INFO @ Sun, 03 Jun 2018 12:57:12: 10000000 INFO @ Sun, 03 Jun 2018 12:57:18: 11000000 INFO @ Sun, 03 Jun 2018 12:57:18: 9000000 INFO @ Sun, 03 Jun 2018 12:57:18: 9000000 INFO @ Sun, 03 Jun 2018 12:57:24: 12000000 INFO @ Sun, 03 Jun 2018 12:57:25: 10000000 INFO @ Sun, 03 Jun 2018 12:57:25: 10000000 INFO @ Sun, 03 Jun 2018 12:57:29: 13000000 INFO @ Sun, 03 Jun 2018 12:57:32: 11000000 INFO @ Sun, 03 Jun 2018 12:57:32: 11000000 INFO @ Sun, 03 Jun 2018 12:57:35: 14000000 INFO @ Sun, 03 Jun 2018 12:57:39: 12000000 INFO @ Sun, 03 Jun 2018 12:57:39: 12000000 INFO @ Sun, 03 Jun 2018 12:57:40: 15000000 INFO @ Sun, 03 Jun 2018 12:57:45: 13000000 INFO @ Sun, 03 Jun 2018 12:57:45: 13000000 INFO @ Sun, 03 Jun 2018 12:57:45: 16000000 INFO @ Sun, 03 Jun 2018 12:57:49: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:57:49: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:57:49: #1 total tags in treatment: 6490468 INFO @ Sun, 03 Jun 2018 12:57:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:57:49: #1 tags after filtering in treatment: 5984768 INFO @ Sun, 03 Jun 2018 12:57:49: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 12:57:49: #1 finished! INFO @ Sun, 03 Jun 2018 12:57:49: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:57:50: #2 number of paired peaks: 202 WARNING @ Sun, 03 Jun 2018 12:57:50: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sun, 03 Jun 2018 12:57:50: start model_add_line... INFO @ Sun, 03 Jun 2018 12:57:50: start X-correlation... INFO @ Sun, 03 Jun 2018 12:57:50: end of X-cor INFO @ Sun, 03 Jun 2018 12:57:50: #2 finished! INFO @ Sun, 03 Jun 2018 12:57:50: #2 predicted fragment length is 99 bps INFO @ Sun, 03 Jun 2018 12:57:50: #2 alternative fragment length(s) may be 4,99 bps INFO @ Sun, 03 Jun 2018 12:57:50: #2.2 Generate R script for model : SRX4085371.05_model.r WARNING @ Sun, 03 Jun 2018 12:57:50: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:57:50: #2 You may need to consider one of the other alternative d(s): 4,99 WARNING @ Sun, 03 Jun 2018 12:57:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:57:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:57:51: 14000000 INFO @ Sun, 03 Jun 2018 12:57:51: 14000000 INFO @ Sun, 03 Jun 2018 12:57:56: 15000000 INFO @ Sun, 03 Jun 2018 12:57:56: 15000000 INFO @ Sun, 03 Jun 2018 12:58:02: 16000000 INFO @ Sun, 03 Jun 2018 12:58:02: 16000000 INFO @ Sun, 03 Jun 2018 12:58:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:58:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:58:06: #1 total tags in treatment: 6490468 INFO @ Sun, 03 Jun 2018 12:58:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:58:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:58:06: #1 tags after filtering in treatment: 5984768 INFO @ Sun, 03 Jun 2018 12:58:06: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 12:58:06: #1 finished! INFO @ Sun, 03 Jun 2018 12:58:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:58:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:58:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:58:06: #1 total tags in treatment: 6490468 INFO @ Sun, 03 Jun 2018 12:58:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:58:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:58:06: #2 number of paired peaks: 202 WARNING @ Sun, 03 Jun 2018 12:58:06: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sun, 03 Jun 2018 12:58:06: start model_add_line... INFO @ Sun, 03 Jun 2018 12:58:06: #1 tags after filtering in treatment: 5984768 INFO @ Sun, 03 Jun 2018 12:58:06: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 12:58:06: #1 finished! INFO @ Sun, 03 Jun 2018 12:58:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:58:06: start X-correlation... INFO @ Sun, 03 Jun 2018 12:58:06: end of X-cor INFO @ Sun, 03 Jun 2018 12:58:06: #2 finished! INFO @ Sun, 03 Jun 2018 12:58:06: #2 predicted fragment length is 99 bps INFO @ Sun, 03 Jun 2018 12:58:06: #2 alternative fragment length(s) may be 4,99 bps INFO @ Sun, 03 Jun 2018 12:58:06: #2.2 Generate R script for model : SRX4085371.20_model.r WARNING @ Sun, 03 Jun 2018 12:58:06: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:58:06: #2 You may need to consider one of the other alternative d(s): 4,99 WARNING @ Sun, 03 Jun 2018 12:58:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:58:06: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:58:07: #2 number of paired peaks: 202 WARNING @ Sun, 03 Jun 2018 12:58:07: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sun, 03 Jun 2018 12:58:07: start model_add_line... INFO @ Sun, 03 Jun 2018 12:58:07: start X-correlation... INFO @ Sun, 03 Jun 2018 12:58:07: end of X-cor INFO @ Sun, 03 Jun 2018 12:58:07: #2 finished! INFO @ Sun, 03 Jun 2018 12:58:07: #2 predicted fragment length is 99 bps INFO @ Sun, 03 Jun 2018 12:58:07: #2 alternative fragment length(s) may be 4,99 bps INFO @ Sun, 03 Jun 2018 12:58:07: #2.2 Generate R script for model : SRX4085371.10_model.r WARNING @ Sun, 03 Jun 2018 12:58:07: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:58:07: #2 You may need to consider one of the other alternative d(s): 4,99 WARNING @ Sun, 03 Jun 2018 12:58:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:58:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:58:10: #4 Write output xls file... SRX4085371.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:10: #4 Write peak in narrowPeak format file... SRX4085371.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:10: #4 Write summits bed file... SRX4085371.05_summits.bed INFO @ Sun, 03 Jun 2018 12:58:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1283 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:58:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:21: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:58:28: #4 Write output xls file... SRX4085371.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:28: #4 Write peak in narrowPeak format file... SRX4085371.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:28: #4 Write summits bed file... SRX4085371.20_summits.bed INFO @ Sun, 03 Jun 2018 12:58:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:58:28: #4 Write output xls file... SRX4085371.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:58:28: #4 Write peak in narrowPeak format file... SRX4085371.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:58:28: #4 Write summits bed file... SRX4085371.10_summits.bed INFO @ Sun, 03 Jun 2018 12:58:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (296 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。