Job ID = 10845150 sra ファイルのダウンロード中... Completed: 1231155K bytes transferred in 85 seconds (118269K 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... Read 24188927 spots for /home/okishinya/chipatlas/results/ce10/SRX2973383/SRR5786986.sra Written 24188927 spots for /home/okishinya/chipatlas/results/ce10/SRX2973383/SRR5786986.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: 00:11:50 24188927 reads; of these: 24188927 (100.00%) were unpaired; of these: 1135667 (4.69%) aligned 0 times 19858388 (82.10%) aligned exactly 1 time 3194872 (13.21%) aligned >1 times 95.31% overall alignment rate Time searching: 00:11:50 Overall time: 00:11:50 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 12 files... [bam_rmdupse_core] 4341390 / 23053260 = 0.1883 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, 04 Jul 2018 09:48:05: # Command line: callpeak -t SRX2973383.bam -f BAM -g ce -n SRX2973383.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2973383.05 # format = BAM # ChIP-seq file = ['SRX2973383.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 @ Wed, 04 Jul 2018 09:48:05: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:48:05: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:48:05: # Command line: callpeak -t SRX2973383.bam -f BAM -g ce -n SRX2973383.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2973383.20 # format = BAM # ChIP-seq file = ['SRX2973383.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 @ Wed, 04 Jul 2018 09:48:05: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:48:05: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:48:05: # Command line: callpeak -t SRX2973383.bam -f BAM -g ce -n SRX2973383.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2973383.10 # format = BAM # ChIP-seq file = ['SRX2973383.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 @ Wed, 04 Jul 2018 09:48:05: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:48:05: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:48:13: 1000000 INFO @ Wed, 04 Jul 2018 09:48:13: 1000000 INFO @ Wed, 04 Jul 2018 09:48:14: 1000000 INFO @ Wed, 04 Jul 2018 09:48:21: 2000000 INFO @ Wed, 04 Jul 2018 09:48:21: 2000000 INFO @ Wed, 04 Jul 2018 09:48:23: 2000000 INFO @ Wed, 04 Jul 2018 09:48:29: 3000000 INFO @ Wed, 04 Jul 2018 09:48:30: 3000000 INFO @ Wed, 04 Jul 2018 09:48:31: 3000000 INFO @ Wed, 04 Jul 2018 09:48:37: 4000000 INFO @ Wed, 04 Jul 2018 09:48:38: 4000000 INFO @ Wed, 04 Jul 2018 09:48:40: 4000000 INFO @ Wed, 04 Jul 2018 09:48:46: 5000000 INFO @ Wed, 04 Jul 2018 09:48:46: 5000000 INFO @ Wed, 04 Jul 2018 09:48:49: 5000000 INFO @ Wed, 04 Jul 2018 09:48:54: 6000000 INFO @ Wed, 04 Jul 2018 09:48:55: 6000000 INFO @ Wed, 04 Jul 2018 09:48:57: 6000000 INFO @ Wed, 04 Jul 2018 09:49:02: 7000000 INFO @ Wed, 04 Jul 2018 09:49:03: 7000000 INFO @ Wed, 04 Jul 2018 09:49:06: 7000000 INFO @ Wed, 04 Jul 2018 09:49:11: 8000000 INFO @ Wed, 04 Jul 2018 09:49:12: 8000000 INFO @ Wed, 04 Jul 2018 09:49:15: 8000000 INFO @ Wed, 04 Jul 2018 09:49:19: 9000000 INFO @ Wed, 04 Jul 2018 09:49:20: 9000000 INFO @ Wed, 04 Jul 2018 09:49:24: 9000000 INFO @ Wed, 04 Jul 2018 09:49:28: 10000000 INFO @ Wed, 04 Jul 2018 09:49:29: 10000000 INFO @ Wed, 04 Jul 2018 09:49:34: 10000000 INFO @ Wed, 04 Jul 2018 09:49:36: 11000000 INFO @ Wed, 04 Jul 2018 09:49:38: 11000000 INFO @ Wed, 04 Jul 2018 09:49:44: 11000000 INFO @ Wed, 04 Jul 2018 09:49:45: 12000000 INFO @ Wed, 04 Jul 2018 09:49:47: 12000000 INFO @ Wed, 04 Jul 2018 09:49:53: 13000000 INFO @ Wed, 04 Jul 2018 09:49:54: 12000000 INFO @ Wed, 04 Jul 2018 09:49:56: 13000000 INFO @ Wed, 04 Jul 2018 09:50:02: 14000000 INFO @ Wed, 04 Jul 2018 09:50:03: 13000000 INFO @ Wed, 04 Jul 2018 09:50:04: 14000000 INFO @ Wed, 04 Jul 2018 09:50:11: 15000000 INFO @ Wed, 04 Jul 2018 09:50:13: 14000000 INFO @ Wed, 04 Jul 2018 09:50:13: 15000000 INFO @ Wed, 04 Jul 2018 09:50:19: 16000000 INFO @ Wed, 04 Jul 2018 09:50:22: 16000000 INFO @ Wed, 04 Jul 2018 09:50:22: 15000000 INFO @ Wed, 04 Jul 2018 09:50:28: 17000000 INFO @ Wed, 04 Jul 2018 09:50:31: 17000000 INFO @ Wed, 04 Jul 2018 09:50:32: 16000000 INFO @ Wed, 04 Jul 2018 09:50:37: 18000000 INFO @ Wed, 04 Jul 2018 09:50:40: 18000000 INFO @ Wed, 04 Jul 2018 09:50:42: 17000000 INFO @ Wed, 04 Jul 2018 09:50:43: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:50:43: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:50:43: #1 total tags in treatment: 18711870 INFO @ Wed, 04 Jul 2018 09:50:43: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:50:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:50:43: #1 tags after filtering in treatment: 18711870 INFO @ Wed, 04 Jul 2018 09:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:50:43: #1 finished! INFO @ Wed, 04 Jul 2018 09:50:43: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:50:45: #2 number of paired peaks: 1740 INFO @ Wed, 04 Jul 2018 09:50:45: start model_add_line... INFO @ Wed, 04 Jul 2018 09:50:45: start X-correlation... INFO @ Wed, 04 Jul 2018 09:50:45: end of X-cor INFO @ Wed, 04 Jul 2018 09:50:45: #2 finished! INFO @ Wed, 04 Jul 2018 09:50:45: #2 predicted fragment length is 167 bps INFO @ Wed, 04 Jul 2018 09:50:45: #2 alternative fragment length(s) may be 167 bps INFO @ Wed, 04 Jul 2018 09:50:45: #2.2 Generate R script for model : SRX2973383.05_model.r WARNING @ Wed, 04 Jul 2018 09:50:45: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:50:45: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Wed, 04 Jul 2018 09:50:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:50:45: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:50:46: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:50:46: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:50:46: #1 total tags in treatment: 18711870 INFO @ Wed, 04 Jul 2018 09:50:46: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:50:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:50:46: #1 tags after filtering in treatment: 18711870 INFO @ Wed, 04 Jul 2018 09:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:50:46: #1 finished! INFO @ Wed, 04 Jul 2018 09:50:46: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:50:48: #2 number of paired peaks: 1740 INFO @ Wed, 04 Jul 2018 09:50:48: start model_add_line... INFO @ Wed, 04 Jul 2018 09:50:48: start X-correlation... INFO @ Wed, 04 Jul 2018 09:50:48: end of X-cor INFO @ Wed, 04 Jul 2018 09:50:48: #2 finished! INFO @ Wed, 04 Jul 2018 09:50:48: #2 predicted fragment length is 167 bps INFO @ Wed, 04 Jul 2018 09:50:48: #2 alternative fragment length(s) may be 167 bps INFO @ Wed, 04 Jul 2018 09:50:48: #2.2 Generate R script for model : SRX2973383.20_model.r WARNING @ Wed, 04 Jul 2018 09:50:48: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:50:48: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Wed, 04 Jul 2018 09:50:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:50:48: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:50:51: 18000000 INFO @ Wed, 04 Jul 2018 09:50:58: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:50:58: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:50:58: #1 total tags in treatment: 18711870 INFO @ Wed, 04 Jul 2018 09:50:58: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:50:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:50:58: #1 tags after filtering in treatment: 18711870 INFO @ Wed, 04 Jul 2018 09:50:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:50:58: #1 finished! INFO @ Wed, 04 Jul 2018 09:50:58: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:51:00: #2 number of paired peaks: 1740 INFO @ Wed, 04 Jul 2018 09:51:00: start model_add_line... INFO @ Wed, 04 Jul 2018 09:51:00: start X-correlation... INFO @ Wed, 04 Jul 2018 09:51:00: end of X-cor INFO @ Wed, 04 Jul 2018 09:51:00: #2 finished! INFO @ Wed, 04 Jul 2018 09:51:00: #2 predicted fragment length is 167 bps INFO @ Wed, 04 Jul 2018 09:51:00: #2 alternative fragment length(s) may be 167 bps INFO @ Wed, 04 Jul 2018 09:51:00: #2.2 Generate R script for model : SRX2973383.10_model.r WARNING @ Wed, 04 Jul 2018 09:51:00: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:51:00: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Wed, 04 Jul 2018 09:51:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:51:00: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:51:30: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:51:33: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:51:46: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:51:50: #4 Write output xls file... SRX2973383.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:51:50: #4 Write peak in narrowPeak format file... SRX2973383.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:51:50: #4 Write summits bed file... SRX2973383.05_summits.bed INFO @ Wed, 04 Jul 2018 09:51:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5427 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:51:54: #4 Write output xls file... SRX2973383.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:51:54: #4 Write peak in narrowPeak format file... SRX2973383.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:51:54: #4 Write summits bed file... SRX2973383.20_summits.bed INFO @ Wed, 04 Jul 2018 09:51:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3125 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:52:06: #4 Write output xls file... SRX2973383.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:52:06: #4 Write peak in narrowPeak format file... SRX2973383.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:52:06: #4 Write summits bed file... SRX2973383.10_summits.bed INFO @ Wed, 04 Jul 2018 09:52:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4253 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。