Job ID = 10714501 sra ファイルのダウンロード中... Completed: 1344748K bytes transferred in 15 seconds (690464K 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 21026682 spots for /home/okishinya/chipatlas/results/ce10/SRX4085418/SRR7167447.sra Written 21026682 spots for /home/okishinya/chipatlas/results/ce10/SRX4085418/SRR7167447.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: 00:16:29 21026682 reads; of these: 21026682 (100.00%) were paired; of these: 9194375 (43.73%) aligned concordantly 0 times 10036212 (47.73%) aligned concordantly exactly 1 time 1796095 (8.54%) aligned concordantly >1 times ---- 9194375 pairs aligned concordantly 0 times; of these: 347987 (3.78%) aligned discordantly 1 time ---- 8846388 pairs aligned 0 times concordantly or discordantly; of these: 17692776 mates make up the pairs; of these: 13787181 (77.93%) aligned 0 times 3385196 (19.13%) aligned exactly 1 time 520399 (2.94%) aligned >1 times 67.22% overall alignment rate Time searching: 00:16:29 Overall time: 00:16:29 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_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] 807796 / 12064354 = 0.0670 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 13:24:48: # Command line: callpeak -t SRX4085418.bam -f BAM -g ce -n SRX4085418.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085418.20 # format = BAM # ChIP-seq file = ['SRX4085418.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 13:24:48: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:24:48: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:24:48: # Command line: callpeak -t SRX4085418.bam -f BAM -g ce -n SRX4085418.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085418.10 # format = BAM # ChIP-seq file = ['SRX4085418.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 13:24:48: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:24:48: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:24:48: # Command line: callpeak -t SRX4085418.bam -f BAM -g ce -n SRX4085418.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085418.05 # format = BAM # ChIP-seq file = ['SRX4085418.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 13:24:48: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:24:48: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:24:54: 1000000 INFO @ Sun, 03 Jun 2018 13:24:54: 1000000 INFO @ Sun, 03 Jun 2018 13:24:54: 1000000 INFO @ Sun, 03 Jun 2018 13:24:59: 2000000 INFO @ Sun, 03 Jun 2018 13:25:00: 2000000 INFO @ Sun, 03 Jun 2018 13:25:00: 2000000 INFO @ Sun, 03 Jun 2018 13:25:05: 3000000 INFO @ Sun, 03 Jun 2018 13:25:06: 3000000 INFO @ Sun, 03 Jun 2018 13:25:06: 3000000 INFO @ Sun, 03 Jun 2018 13:25:10: 4000000 INFO @ Sun, 03 Jun 2018 13:25:11: 4000000 INFO @ Sun, 03 Jun 2018 13:25:12: 4000000 INFO @ Sun, 03 Jun 2018 13:25:16: 5000000 INFO @ Sun, 03 Jun 2018 13:25:17: 5000000 INFO @ Sun, 03 Jun 2018 13:25:19: 5000000 INFO @ Sun, 03 Jun 2018 13:25:21: 6000000 INFO @ Sun, 03 Jun 2018 13:25:23: 6000000 INFO @ Sun, 03 Jun 2018 13:25:25: 6000000 INFO @ Sun, 03 Jun 2018 13:25:26: 7000000 INFO @ Sun, 03 Jun 2018 13:25:29: 7000000 INFO @ Sun, 03 Jun 2018 13:25:31: 7000000 INFO @ Sun, 03 Jun 2018 13:25:32: 8000000 INFO @ Sun, 03 Jun 2018 13:25:35: 8000000 INFO @ Sun, 03 Jun 2018 13:25:37: 9000000 INFO @ Sun, 03 Jun 2018 13:25:37: 8000000 INFO @ Sun, 03 Jun 2018 13:25:41: 9000000 INFO @ Sun, 03 Jun 2018 13:25:43: 10000000 INFO @ Sun, 03 Jun 2018 13:25:43: 9000000 INFO @ Sun, 03 Jun 2018 13:25:47: 10000000 INFO @ Sun, 03 Jun 2018 13:25:48: 11000000 INFO @ Sun, 03 Jun 2018 13:25:50: 10000000 INFO @ Sun, 03 Jun 2018 13:25:53: 11000000 INFO @ Sun, 03 Jun 2018 13:25:53: 12000000 INFO @ Sun, 03 Jun 2018 13:25:56: 11000000 INFO @ Sun, 03 Jun 2018 13:25:58: 12000000 INFO @ Sun, 03 Jun 2018 13:25:59: 13000000 INFO @ Sun, 03 Jun 2018 13:26:02: 12000000 INFO @ Sun, 03 Jun 2018 13:26:04: 14000000 INFO @ Sun, 03 Jun 2018 13:26:04: 13000000 INFO @ Sun, 03 Jun 2018 13:26:08: 13000000 INFO @ Sun, 03 Jun 2018 13:26:10: 15000000 INFO @ Sun, 03 Jun 2018 13:26:10: 14000000 INFO @ Sun, 03 Jun 2018 13:26:14: 14000000 INFO @ Sun, 03 Jun 2018 13:26:15: 16000000 INFO @ Sun, 03 Jun 2018 13:26:16: 15000000 INFO @ Sun, 03 Jun 2018 13:26:20: 17000000 INFO @ Sun, 03 Jun 2018 13:26:20: 15000000 INFO @ Sun, 03 Jun 2018 13:26:22: 16000000 INFO @ Sun, 03 Jun 2018 13:26:26: 18000000 INFO @ Sun, 03 Jun 2018 13:26:26: 16000000 INFO @ Sun, 03 Jun 2018 13:26:28: 17000000 INFO @ Sun, 03 Jun 2018 13:26:31: 19000000 INFO @ Sun, 03 Jun 2018 13:26:33: 17000000 INFO @ Sun, 03 Jun 2018 13:26:33: 18000000 INFO @ Sun, 03 Jun 2018 13:26:36: 20000000 INFO @ Sun, 03 Jun 2018 13:26:39: 18000000 INFO @ Sun, 03 Jun 2018 13:26:39: 19000000 INFO @ Sun, 03 Jun 2018 13:26:42: 21000000 INFO @ Sun, 03 Jun 2018 13:26:45: 19000000 INFO @ Sun, 03 Jun 2018 13:26:45: 20000000 INFO @ Sun, 03 Jun 2018 13:26:47: 22000000 INFO @ Sun, 03 Jun 2018 13:26:51: 21000000 INFO @ Sun, 03 Jun 2018 13:26:51: 20000000 INFO @ Sun, 03 Jun 2018 13:26:52: 23000000 INFO @ Sun, 03 Jun 2018 13:26:57: 22000000 INFO @ Sun, 03 Jun 2018 13:26:58: 21000000 INFO @ Sun, 03 Jun 2018 13:26:58: 24000000 INFO @ Sun, 03 Jun 2018 13:27:03: 25000000 INFO @ Sun, 03 Jun 2018 13:27:03: 23000000 INFO @ Sun, 03 Jun 2018 13:27:04: 22000000 INFO @ Sun, 03 Jun 2018 13:27:08: 26000000 INFO @ Sun, 03 Jun 2018 13:27:09: 24000000 INFO @ Sun, 03 Jun 2018 13:27:10: 23000000 INFO @ Sun, 03 Jun 2018 13:27:12: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:27:12: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:27:12: #1 total tags in treatment: 11041953 INFO @ Sun, 03 Jun 2018 13:27:12: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:27:12: #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 13:27:12: #1 tags after filtering in treatment: 10091596 INFO @ Sun, 03 Jun 2018 13:27:12: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:27:12: #1 finished! INFO @ Sun, 03 Jun 2018 13:27:12: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:27:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:27:12: #2 number of paired peaks: 320 WARNING @ Sun, 03 Jun 2018 13:27:12: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sun, 03 Jun 2018 13:27:12: start model_add_line... INFO @ Sun, 03 Jun 2018 13:27:13: start X-correlation... INFO @ Sun, 03 Jun 2018 13:27:13: end of X-cor INFO @ Sun, 03 Jun 2018 13:27:13: #2 finished! INFO @ Sun, 03 Jun 2018 13:27:13: #2 predicted fragment length is 137 bps INFO @ Sun, 03 Jun 2018 13:27:13: #2 alternative fragment length(s) may be 4,137 bps INFO @ Sun, 03 Jun 2018 13:27:13: #2.2 Generate R script for model : SRX4085418.20_model.r INFO @ Sun, 03 Jun 2018 13:27:13: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:27:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:27:15: 25000000 INFO @ Sun, 03 Jun 2018 13:27:16: 24000000 INFO @ Sun, 03 Jun 2018 13:27:21: 26000000 INFO @ Sun, 03 Jun 2018 13:27:23: 25000000 INFO @ Sun, 03 Jun 2018 13:27:24: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:27:24: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:27:24: #1 total tags in treatment: 11041953 INFO @ Sun, 03 Jun 2018 13:27:24: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:27:24: #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 13:27:25: #1 tags after filtering in treatment: 10091596 INFO @ Sun, 03 Jun 2018 13:27:25: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:27:25: #1 finished! INFO @ Sun, 03 Jun 2018 13:27:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:27:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:27:25: #2 number of paired peaks: 320 WARNING @ Sun, 03 Jun 2018 13:27:25: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sun, 03 Jun 2018 13:27:25: start model_add_line... INFO @ Sun, 03 Jun 2018 13:27:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:27:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:27:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:27:26: #2 predicted fragment length is 137 bps INFO @ Sun, 03 Jun 2018 13:27:26: #2 alternative fragment length(s) may be 4,137 bps INFO @ Sun, 03 Jun 2018 13:27:26: #2.2 Generate R script for model : SRX4085418.10_model.r INFO @ Sun, 03 Jun 2018 13:27:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:27:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:27:28: 26000000 INFO @ Sun, 03 Jun 2018 13:27:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:27:32: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:27:32: #1 total tags in treatment: 11041953 INFO @ Sun, 03 Jun 2018 13:27:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:27:32: #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 13:27:32: #1 tags after filtering in treatment: 10091596 INFO @ Sun, 03 Jun 2018 13:27:32: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:27:32: #1 finished! INFO @ Sun, 03 Jun 2018 13:27:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:27:33: #2 number of paired peaks: 320 WARNING @ Sun, 03 Jun 2018 13:27:33: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Sun, 03 Jun 2018 13:27:33: start model_add_line... INFO @ Sun, 03 Jun 2018 13:27:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:27:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:27:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:27:33: #2 predicted fragment length is 137 bps INFO @ Sun, 03 Jun 2018 13:27:33: #2 alternative fragment length(s) may be 4,137 bps INFO @ Sun, 03 Jun 2018 13:27:33: #2.2 Generate R script for model : SRX4085418.05_model.r INFO @ Sun, 03 Jun 2018 13:27:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:27:36: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:27:48: #4 Write output xls file... SRX4085418.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:27:48: #4 Write peak in narrowPeak format file... SRX4085418.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:27:48: #4 Write summits bed file... SRX4085418.20_summits.bed INFO @ Sun, 03 Jun 2018 13:27:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (287 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:27:48: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:27:54: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:27:59: #4 Write output xls file... SRX4085418.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:27:59: #4 Write peak in narrowPeak format file... SRX4085418.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:27:59: #4 Write summits bed file... SRX4085418.10_summits.bed INFO @ Sun, 03 Jun 2018 13:27:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (625 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:28:08: #4 Write output xls file... SRX4085418.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:28:08: #4 Write peak in narrowPeak format file... SRX4085418.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:28:08: #4 Write summits bed file... SRX4085418.05_summits.bed INFO @ Sun, 03 Jun 2018 13:28:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1093 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。