Job ID = 10714483 sra ファイルのダウンロード中... Completed: 2230736K bytes transferred in 39 seconds (462358K 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 32931163 spots for /home/okishinya/chipatlas/results/ce10/SRX4085399/SRR7167428.sra Written 32931163 spots for /home/okishinya/chipatlas/results/ce10/SRX4085399/SRR7167428.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: 00:32:28 32931163 reads; of these: 32931163 (100.00%) were paired; of these: 1116528 (3.39%) aligned concordantly 0 times 28116479 (85.38%) aligned concordantly exactly 1 time 3698156 (11.23%) aligned concordantly >1 times ---- 1116528 pairs aligned concordantly 0 times; of these: 321303 (28.78%) aligned discordantly 1 time ---- 795225 pairs aligned 0 times concordantly or discordantly; of these: 1590450 mates make up the pairs; of these: 880712 (55.38%) aligned 0 times 519681 (32.68%) aligned exactly 1 time 190057 (11.95%) aligned >1 times 98.66% overall alignment rate Time searching: 00:32:28 Overall time: 00:32:28 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 28 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] 20145306 / 31916875 = 0.6312 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 13:35:44: # Command line: callpeak -t SRX4085399.bam -f BAM -g ce -n SRX4085399.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085399.05 # format = BAM # ChIP-seq file = ['SRX4085399.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 13:35:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:44: # Command line: callpeak -t SRX4085399.bam -f BAM -g ce -n SRX4085399.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085399.10 # format = BAM # ChIP-seq file = ['SRX4085399.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 13:35:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:44: # Command line: callpeak -t SRX4085399.bam -f BAM -g ce -n SRX4085399.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085399.20 # format = BAM # ChIP-seq file = ['SRX4085399.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 13:35:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:50: 1000000 INFO @ Sun, 03 Jun 2018 13:35:50: 1000000 INFO @ Sun, 03 Jun 2018 13:35:50: 1000000 INFO @ Sun, 03 Jun 2018 13:35:57: 2000000 INFO @ Sun, 03 Jun 2018 13:35:57: 2000000 INFO @ Sun, 03 Jun 2018 13:35:57: 2000000 INFO @ Sun, 03 Jun 2018 13:36:03: 3000000 INFO @ Sun, 03 Jun 2018 13:36:03: 3000000 INFO @ Sun, 03 Jun 2018 13:36:03: 3000000 INFO @ Sun, 03 Jun 2018 13:36:10: 4000000 INFO @ Sun, 03 Jun 2018 13:36:10: 4000000 INFO @ Sun, 03 Jun 2018 13:36:10: 4000000 INFO @ Sun, 03 Jun 2018 13:36:16: 5000000 INFO @ Sun, 03 Jun 2018 13:36:17: 5000000 INFO @ Sun, 03 Jun 2018 13:36:17: 5000000 INFO @ Sun, 03 Jun 2018 13:36:23: 6000000 INFO @ Sun, 03 Jun 2018 13:36:24: 6000000 INFO @ Sun, 03 Jun 2018 13:36:24: 6000000 INFO @ Sun, 03 Jun 2018 13:36:30: 7000000 INFO @ Sun, 03 Jun 2018 13:36:31: 7000000 INFO @ Sun, 03 Jun 2018 13:36:31: 7000000 INFO @ Sun, 03 Jun 2018 13:36:37: 8000000 INFO @ Sun, 03 Jun 2018 13:36:38: 8000000 INFO @ Sun, 03 Jun 2018 13:36:38: 8000000 INFO @ Sun, 03 Jun 2018 13:36:44: 9000000 INFO @ Sun, 03 Jun 2018 13:36:44: 9000000 INFO @ Sun, 03 Jun 2018 13:36:45: 9000000 INFO @ Sun, 03 Jun 2018 13:36:51: 10000000 INFO @ Sun, 03 Jun 2018 13:36:51: 10000000 INFO @ Sun, 03 Jun 2018 13:36:51: 10000000 INFO @ Sun, 03 Jun 2018 13:36:57: 11000000 INFO @ Sun, 03 Jun 2018 13:36:58: 11000000 INFO @ Sun, 03 Jun 2018 13:36:58: 11000000 INFO @ Sun, 03 Jun 2018 13:37:04: 12000000 INFO @ Sun, 03 Jun 2018 13:37:05: 12000000 INFO @ Sun, 03 Jun 2018 13:37:05: 12000000 INFO @ Sun, 03 Jun 2018 13:37:11: 13000000 INFO @ Sun, 03 Jun 2018 13:37:12: 13000000 INFO @ Sun, 03 Jun 2018 13:37:12: 13000000 INFO @ Sun, 03 Jun 2018 13:37:18: 14000000 INFO @ Sun, 03 Jun 2018 13:37:19: 14000000 INFO @ Sun, 03 Jun 2018 13:37:19: 14000000 INFO @ Sun, 03 Jun 2018 13:37:25: 15000000 INFO @ Sun, 03 Jun 2018 13:37:25: 15000000 INFO @ Sun, 03 Jun 2018 13:37:26: 15000000 INFO @ Sun, 03 Jun 2018 13:37:32: 16000000 INFO @ Sun, 03 Jun 2018 13:37:32: 16000000 INFO @ Sun, 03 Jun 2018 13:37:32: 16000000 INFO @ Sun, 03 Jun 2018 13:37:38: 17000000 INFO @ Sun, 03 Jun 2018 13:37:39: 17000000 INFO @ Sun, 03 Jun 2018 13:37:39: 17000000 INFO @ Sun, 03 Jun 2018 13:37:45: 18000000 INFO @ Sun, 03 Jun 2018 13:37:46: 18000000 INFO @ Sun, 03 Jun 2018 13:37:46: 18000000 INFO @ Sun, 03 Jun 2018 13:37:52: 19000000 INFO @ Sun, 03 Jun 2018 13:37:52: 19000000 INFO @ Sun, 03 Jun 2018 13:37:53: 19000000 INFO @ Sun, 03 Jun 2018 13:37:58: 20000000 INFO @ Sun, 03 Jun 2018 13:37:59: 20000000 INFO @ Sun, 03 Jun 2018 13:37:59: 20000000 INFO @ Sun, 03 Jun 2018 13:38:05: 21000000 INFO @ Sun, 03 Jun 2018 13:38:06: 21000000 INFO @ Sun, 03 Jun 2018 13:38:06: 21000000 INFO @ Sun, 03 Jun 2018 13:38:12: 22000000 INFO @ Sun, 03 Jun 2018 13:38:13: 22000000 INFO @ Sun, 03 Jun 2018 13:38:13: 22000000 INFO @ Sun, 03 Jun 2018 13:38:19: 23000000 INFO @ Sun, 03 Jun 2018 13:38:20: 23000000 INFO @ Sun, 03 Jun 2018 13:38:20: 23000000 INFO @ Sun, 03 Jun 2018 13:38:25: 24000000 INFO @ Sun, 03 Jun 2018 13:38:26: 24000000 INFO @ Sun, 03 Jun 2018 13:38:27: 24000000 INFO @ Sun, 03 Jun 2018 13:38:30: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:38:30: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:38:30: #1 total tags in treatment: 11723534 INFO @ Sun, 03 Jun 2018 13:38:30: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:38:30: #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 13:38:30: #1 tags after filtering in treatment: 10231810 INFO @ Sun, 03 Jun 2018 13:38:30: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:38:30: #1 finished! INFO @ Sun, 03 Jun 2018 13:38:30: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:38:31: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:38:31: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:38:31: #1 total tags in treatment: 11723534 INFO @ Sun, 03 Jun 2018 13:38:31: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:38:31: #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 13:38:31: #2 number of paired peaks: 324 WARNING @ Sun, 03 Jun 2018 13:38:31: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sun, 03 Jun 2018 13:38:31: start model_add_line... INFO @ Sun, 03 Jun 2018 13:38:31: start X-correlation... INFO @ Sun, 03 Jun 2018 13:38:31: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:38:31: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:38:31: #1 total tags in treatment: 11723534 INFO @ Sun, 03 Jun 2018 13:38:31: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:38:31: #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 13:38:31: end of X-cor INFO @ Sun, 03 Jun 2018 13:38:31: #2 finished! INFO @ Sun, 03 Jun 2018 13:38:31: #2 predicted fragment length is 117 bps INFO @ Sun, 03 Jun 2018 13:38:31: #2 alternative fragment length(s) may be 3,117 bps INFO @ Sun, 03 Jun 2018 13:38:31: #2.2 Generate R script for model : SRX4085399.10_model.r INFO @ Sun, 03 Jun 2018 13:38:31: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:38:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:38:31: #1 tags after filtering in treatment: 10231810 INFO @ Sun, 03 Jun 2018 13:38:31: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:38:31: #1 finished! INFO @ Sun, 03 Jun 2018 13:38:31: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:38:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:38:31: #1 tags after filtering in treatment: 10231810 INFO @ Sun, 03 Jun 2018 13:38:31: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:38:31: #1 finished! INFO @ Sun, 03 Jun 2018 13:38:31: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:38:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:38:32: #2 number of paired peaks: 324 WARNING @ Sun, 03 Jun 2018 13:38:32: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sun, 03 Jun 2018 13:38:32: start model_add_line... INFO @ Sun, 03 Jun 2018 13:38:32: start X-correlation... INFO @ Sun, 03 Jun 2018 13:38:32: end of X-cor INFO @ Sun, 03 Jun 2018 13:38:32: #2 finished! INFO @ Sun, 03 Jun 2018 13:38:32: #2 predicted fragment length is 117 bps INFO @ Sun, 03 Jun 2018 13:38:32: #2 alternative fragment length(s) may be 3,117 bps INFO @ Sun, 03 Jun 2018 13:38:32: #2.2 Generate R script for model : SRX4085399.20_model.r INFO @ Sun, 03 Jun 2018 13:38:32: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:38:32: #2 number of paired peaks: 324 WARNING @ Sun, 03 Jun 2018 13:38:32: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sun, 03 Jun 2018 13:38:32: start model_add_line... INFO @ Sun, 03 Jun 2018 13:38:32: start X-correlation... INFO @ Sun, 03 Jun 2018 13:38:32: end of X-cor INFO @ Sun, 03 Jun 2018 13:38:32: #2 finished! INFO @ Sun, 03 Jun 2018 13:38:32: #2 predicted fragment length is 117 bps INFO @ Sun, 03 Jun 2018 13:38:32: #2 alternative fragment length(s) may be 3,117 bps INFO @ Sun, 03 Jun 2018 13:38:32: #2.2 Generate R script for model : SRX4085399.05_model.r INFO @ Sun, 03 Jun 2018 13:38:32: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:38:55: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:38:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:38:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:07: #4 Write output xls file... SRX4085399.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:39:07: #4 Write peak in narrowPeak format file... SRX4085399.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:39:07: #4 Write summits bed file... SRX4085399.10_summits.bed INFO @ Sun, 03 Jun 2018 13:39:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (749 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:39:07: #4 Write output xls file... SRX4085399.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:39:07: #4 Write peak in narrowPeak format file... SRX4085399.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:39:07: #4 Write summits bed file... SRX4085399.05_summits.bed INFO @ Sun, 03 Jun 2018 13:39:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2423 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:39:08: #4 Write output xls file... SRX4085399.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:39:08: #4 Write peak in narrowPeak format file... SRX4085399.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:39:08: #4 Write summits bed file... SRX4085399.20_summits.bed INFO @ Sun, 03 Jun 2018 13:39:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。