Job ID = 10714503 sra ファイルのダウンロード中... Completed: 1255424K bytes transferred in 16 seconds (606808K 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 19662544 spots for /home/okishinya/chipatlas/results/ce10/SRX4085420/SRR7167449.sra Written 19662544 spots for /home/okishinya/chipatlas/results/ce10/SRX4085420/SRR7167449.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: 00:15:59 19662544 reads; of these: 19662544 (100.00%) were paired; of these: 8586963 (43.67%) aligned concordantly 0 times 9372656 (47.67%) aligned concordantly exactly 1 time 1702925 (8.66%) aligned concordantly >1 times ---- 8586963 pairs aligned concordantly 0 times; of these: 415101 (4.83%) aligned discordantly 1 time ---- 8171862 pairs aligned 0 times concordantly or discordantly; of these: 16343724 mates make up the pairs; of these: 12414233 (75.96%) aligned 0 times 3390214 (20.74%) aligned exactly 1 time 539277 (3.30%) aligned >1 times 68.43% overall alignment rate Time searching: 00:15:59 Overall time: 00:15:59 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] 855346 / 11347073 = 0.0754 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 13:26:26: # Command line: callpeak -t SRX4085420.bam -f BAM -g ce -n SRX4085420.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085420.20 # format = BAM # ChIP-seq file = ['SRX4085420.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 13:26:26: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:26:26: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:26:26: # Command line: callpeak -t SRX4085420.bam -f BAM -g ce -n SRX4085420.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085420.05 # format = BAM # ChIP-seq file = ['SRX4085420.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 13:26:26: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:26:26: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:26:26: # Command line: callpeak -t SRX4085420.bam -f BAM -g ce -n SRX4085420.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085420.10 # format = BAM # ChIP-seq file = ['SRX4085420.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 13:26:26: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:26:26: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:26:32: 1000000 INFO @ Sun, 03 Jun 2018 13:26:32: 1000000 INFO @ Sun, 03 Jun 2018 13:26:32: 1000000 INFO @ Sun, 03 Jun 2018 13:26:37: 2000000 INFO @ Sun, 03 Jun 2018 13:26:39: 2000000 INFO @ Sun, 03 Jun 2018 13:26:39: 2000000 INFO @ Sun, 03 Jun 2018 13:26:43: 3000000 INFO @ Sun, 03 Jun 2018 13:26:45: 3000000 INFO @ Sun, 03 Jun 2018 13:26:45: 3000000 INFO @ Sun, 03 Jun 2018 13:26:49: 4000000 INFO @ Sun, 03 Jun 2018 13:26:51: 4000000 INFO @ Sun, 03 Jun 2018 13:26:51: 4000000 INFO @ Sun, 03 Jun 2018 13:26:54: 5000000 INFO @ Sun, 03 Jun 2018 13:26:58: 5000000 INFO @ Sun, 03 Jun 2018 13:26:58: 5000000 INFO @ Sun, 03 Jun 2018 13:27:00: 6000000 INFO @ Sun, 03 Jun 2018 13:27:04: 6000000 INFO @ Sun, 03 Jun 2018 13:27:04: 6000000 INFO @ Sun, 03 Jun 2018 13:27:06: 7000000 INFO @ Sun, 03 Jun 2018 13:27:11: 7000000 INFO @ Sun, 03 Jun 2018 13:27:11: 7000000 INFO @ Sun, 03 Jun 2018 13:27:12: 8000000 INFO @ Sun, 03 Jun 2018 13:27:17: 8000000 INFO @ Sun, 03 Jun 2018 13:27:17: 8000000 INFO @ Sun, 03 Jun 2018 13:27:17: 9000000 INFO @ Sun, 03 Jun 2018 13:27:23: 10000000 INFO @ Sun, 03 Jun 2018 13:27:23: 9000000 INFO @ Sun, 03 Jun 2018 13:27:23: 9000000 INFO @ Sun, 03 Jun 2018 13:27:29: 11000000 INFO @ Sun, 03 Jun 2018 13:27:30: 10000000 INFO @ Sun, 03 Jun 2018 13:27:30: 10000000 INFO @ Sun, 03 Jun 2018 13:27:34: 12000000 INFO @ Sun, 03 Jun 2018 13:27:36: 11000000 INFO @ Sun, 03 Jun 2018 13:27:36: 11000000 INFO @ Sun, 03 Jun 2018 13:27:40: 13000000 INFO @ Sun, 03 Jun 2018 13:27:42: 12000000 INFO @ Sun, 03 Jun 2018 13:27:42: 12000000 INFO @ Sun, 03 Jun 2018 13:27:46: 14000000 INFO @ Sun, 03 Jun 2018 13:27:48: 13000000 INFO @ Sun, 03 Jun 2018 13:27:48: 13000000 INFO @ Sun, 03 Jun 2018 13:27:52: 15000000 INFO @ Sun, 03 Jun 2018 13:27:55: 14000000 INFO @ Sun, 03 Jun 2018 13:27:55: 14000000 INFO @ Sun, 03 Jun 2018 13:27:57: 16000000 INFO @ Sun, 03 Jun 2018 13:28:01: 15000000 INFO @ Sun, 03 Jun 2018 13:28:01: 15000000 INFO @ Sun, 03 Jun 2018 13:28:03: 17000000 INFO @ Sun, 03 Jun 2018 13:28:07: 16000000 INFO @ Sun, 03 Jun 2018 13:28:07: 16000000 INFO @ Sun, 03 Jun 2018 13:28:09: 18000000 INFO @ Sun, 03 Jun 2018 13:28:14: 17000000 INFO @ Sun, 03 Jun 2018 13:28:14: 17000000 INFO @ Sun, 03 Jun 2018 13:28:14: 19000000 INFO @ Sun, 03 Jun 2018 13:28:20: 18000000 INFO @ Sun, 03 Jun 2018 13:28:20: 18000000 INFO @ Sun, 03 Jun 2018 13:28:20: 20000000 INFO @ Sun, 03 Jun 2018 13:28:26: 21000000 INFO @ Sun, 03 Jun 2018 13:28:26: 19000000 INFO @ Sun, 03 Jun 2018 13:28:26: 19000000 INFO @ Sun, 03 Jun 2018 13:28:32: 22000000 INFO @ Sun, 03 Jun 2018 13:28:33: 20000000 INFO @ Sun, 03 Jun 2018 13:28:33: 20000000 INFO @ Sun, 03 Jun 2018 13:28:37: 23000000 INFO @ Sun, 03 Jun 2018 13:28:39: 21000000 INFO @ Sun, 03 Jun 2018 13:28:39: 21000000 INFO @ Sun, 03 Jun 2018 13:28:43: 24000000 INFO @ Sun, 03 Jun 2018 13:28:45: 22000000 INFO @ Sun, 03 Jun 2018 13:28:45: 22000000 INFO @ Sun, 03 Jun 2018 13:28:49: 25000000 INFO @ Sun, 03 Jun 2018 13:28:50: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:28:50: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:28:50: #1 total tags in treatment: 10242966 INFO @ Sun, 03 Jun 2018 13:28:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:28:50: #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 13:28:50: #1 tags after filtering in treatment: 9140262 INFO @ Sun, 03 Jun 2018 13:28:50: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 13:28:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:28:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:28:51: #2 number of paired peaks: 361 WARNING @ Sun, 03 Jun 2018 13:28:51: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 03 Jun 2018 13:28:51: start model_add_line... INFO @ Sun, 03 Jun 2018 13:28:51: start X-correlation... INFO @ Sun, 03 Jun 2018 13:28:51: end of X-cor INFO @ Sun, 03 Jun 2018 13:28:51: #2 finished! INFO @ Sun, 03 Jun 2018 13:28:51: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:28:51: #2 alternative fragment length(s) may be 112,585,588,597 bps INFO @ Sun, 03 Jun 2018 13:28:51: #2.2 Generate R script for model : SRX4085420.10_model.r INFO @ Sun, 03 Jun 2018 13:28:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:28:51: 23000000 INFO @ Sun, 03 Jun 2018 13:28:51: 23000000 INFO @ Sun, 03 Jun 2018 13:28:57: 24000000 INFO @ Sun, 03 Jun 2018 13:28:57: 24000000 INFO @ Sun, 03 Jun 2018 13:29:03: 25000000 INFO @ Sun, 03 Jun 2018 13:29:03: 25000000 INFO @ Sun, 03 Jun 2018 13:29:04: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:29:04: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:29:04: #1 total tags in treatment: 10242966 INFO @ Sun, 03 Jun 2018 13:29:04: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:29:04: #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 13:29:04: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:29:04: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:29:04: #1 total tags in treatment: 10242966 INFO @ Sun, 03 Jun 2018 13:29:04: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:29:04: #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 13:29:04: #1 tags after filtering in treatment: 9140262 INFO @ Sun, 03 Jun 2018 13:29:04: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 13:29:04: #1 finished! INFO @ Sun, 03 Jun 2018 13:29:04: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:29:04: #1 tags after filtering in treatment: 9140262 INFO @ Sun, 03 Jun 2018 13:29:04: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 13:29:04: #1 finished! INFO @ Sun, 03 Jun 2018 13:29:04: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:29:05: #2 number of paired peaks: 361 WARNING @ Sun, 03 Jun 2018 13:29:05: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 03 Jun 2018 13:29:05: start model_add_line... INFO @ Sun, 03 Jun 2018 13:29:05: #2 number of paired peaks: 361 WARNING @ Sun, 03 Jun 2018 13:29:05: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 03 Jun 2018 13:29:05: start model_add_line... INFO @ Sun, 03 Jun 2018 13:29:05: start X-correlation... INFO @ Sun, 03 Jun 2018 13:29:05: end of X-cor INFO @ Sun, 03 Jun 2018 13:29:05: #2 finished! INFO @ Sun, 03 Jun 2018 13:29:05: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:29:05: #2 alternative fragment length(s) may be 112,585,588,597 bps INFO @ Sun, 03 Jun 2018 13:29:05: #2.2 Generate R script for model : SRX4085420.20_model.r INFO @ Sun, 03 Jun 2018 13:29:05: start X-correlation... INFO @ Sun, 03 Jun 2018 13:29:05: end of X-cor INFO @ Sun, 03 Jun 2018 13:29:05: #2 finished! INFO @ Sun, 03 Jun 2018 13:29:05: #2 predicted fragment length is 112 bps INFO @ Sun, 03 Jun 2018 13:29:05: #2 alternative fragment length(s) may be 112,585,588,597 bps INFO @ Sun, 03 Jun 2018 13:29:05: #2.2 Generate R script for model : SRX4085420.05_model.r INFO @ Sun, 03 Jun 2018 13:29:05: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:29:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:29:05: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:29:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:29:10: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:29:20: #4 Write output xls file... SRX4085420.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:29:20: #4 Write peak in narrowPeak format file... SRX4085420.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:29:20: #4 Write summits bed file... SRX4085420.10_summits.bed INFO @ Sun, 03 Jun 2018 13:29:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1430 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:29:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:29:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:29:36: #4 Write output xls file... SRX4085420.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:29:36: #4 Write peak in narrowPeak format file... SRX4085420.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:29:36: #4 Write summits bed file... SRX4085420.20_summits.bed INFO @ Sun, 03 Jun 2018 13:29:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (671 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:29:37: #4 Write output xls file... SRX4085420.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:29:37: #4 Write peak in narrowPeak format file... SRX4085420.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:29:37: #4 Write summits bed file... SRX4085420.05_summits.bed INFO @ Sun, 03 Jun 2018 13:29:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2481 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。