Job ID = 11158468 sra ファイルのダウンロード中... Completed: 1779087K bytes transferred in 18 seconds (799914K 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 27766032 spots for /home/okishinya/chipatlas/results/ce10/SRX4029334/SRR7100994.sra Written 27766032 spots for /home/okishinya/chipatlas/results/ce10/SRX4029334/SRR7100994.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:44:12 27766032 reads; of these: 27766032 (100.00%) were paired; of these: 6614387 (23.82%) aligned concordantly 0 times 18726381 (67.44%) aligned concordantly exactly 1 time 2425264 (8.73%) aligned concordantly >1 times ---- 6614387 pairs aligned concordantly 0 times; of these: 2808919 (42.47%) aligned discordantly 1 time ---- 3805468 pairs aligned 0 times concordantly or discordantly; of these: 7610936 mates make up the pairs; of these: 5696244 (74.84%) aligned 0 times 1210964 (15.91%) aligned exactly 1 time 703728 (9.25%) aligned >1 times 89.74% overall alignment rate Time searching: 00:44:14 Overall time: 00:44:14 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 24 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] 7497483 / 23938559 = 0.3132 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 @ Tue, 04 Sep 2018 10:39:09: # Command line: callpeak -t SRX4029334.bam -f BAM -g ce -n SRX4029334.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4029334.20 # format = BAM # ChIP-seq file = ['SRX4029334.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 @ Tue, 04 Sep 2018 10:39:09: # Command line: callpeak -t SRX4029334.bam -f BAM -g ce -n SRX4029334.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4029334.05 # format = BAM # ChIP-seq file = ['SRX4029334.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 @ Tue, 04 Sep 2018 10:39:09: # Command line: callpeak -t SRX4029334.bam -f BAM -g ce -n SRX4029334.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4029334.10 # format = BAM # ChIP-seq file = ['SRX4029334.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 @ Tue, 04 Sep 2018 10:39:09: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:39:09: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:39:09: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:39:09: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:39:09: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:39:09: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:39:17: 1000000 INFO @ Tue, 04 Sep 2018 10:39:17: 1000000 INFO @ Tue, 04 Sep 2018 10:39:18: 1000000 INFO @ Tue, 04 Sep 2018 10:39:25: 2000000 INFO @ Tue, 04 Sep 2018 10:39:25: 2000000 INFO @ Tue, 04 Sep 2018 10:39:28: 2000000 INFO @ Tue, 04 Sep 2018 10:39:33: 3000000 INFO @ Tue, 04 Sep 2018 10:39:33: 3000000 INFO @ Tue, 04 Sep 2018 10:39:37: 3000000 INFO @ Tue, 04 Sep 2018 10:39:41: 4000000 INFO @ Tue, 04 Sep 2018 10:39:41: 4000000 INFO @ Tue, 04 Sep 2018 10:39:46: 4000000 INFO @ Tue, 04 Sep 2018 10:39:49: 5000000 INFO @ Tue, 04 Sep 2018 10:39:49: 5000000 INFO @ Tue, 04 Sep 2018 10:39:55: 5000000 INFO @ Tue, 04 Sep 2018 10:39:57: 6000000 INFO @ Tue, 04 Sep 2018 10:39:57: 6000000 INFO @ Tue, 04 Sep 2018 10:40:04: 6000000 INFO @ Tue, 04 Sep 2018 10:40:05: 7000000 INFO @ Tue, 04 Sep 2018 10:40:05: 7000000 INFO @ Tue, 04 Sep 2018 10:40:13: 8000000 INFO @ Tue, 04 Sep 2018 10:40:13: 8000000 INFO @ Tue, 04 Sep 2018 10:40:14: 7000000 INFO @ Tue, 04 Sep 2018 10:40:21: 9000000 INFO @ Tue, 04 Sep 2018 10:40:21: 9000000 INFO @ Tue, 04 Sep 2018 10:40:22: 8000000 INFO @ Tue, 04 Sep 2018 10:40:28: 10000000 INFO @ Tue, 04 Sep 2018 10:40:28: 10000000 INFO @ Tue, 04 Sep 2018 10:40:31: 9000000 INFO @ Tue, 04 Sep 2018 10:40:36: 11000000 INFO @ Tue, 04 Sep 2018 10:40:36: 11000000 INFO @ Tue, 04 Sep 2018 10:40:38: 10000000 INFO @ Tue, 04 Sep 2018 10:40:42: 12000000 INFO @ Tue, 04 Sep 2018 10:40:43: 12000000 INFO @ Tue, 04 Sep 2018 10:40:45: 11000000 INFO @ Tue, 04 Sep 2018 10:40:49: 13000000 INFO @ Tue, 04 Sep 2018 10:40:50: 13000000 INFO @ Tue, 04 Sep 2018 10:40:52: 12000000 INFO @ Tue, 04 Sep 2018 10:40:56: 14000000 INFO @ Tue, 04 Sep 2018 10:40:58: 14000000 INFO @ Tue, 04 Sep 2018 10:40:59: 13000000 INFO @ Tue, 04 Sep 2018 10:41:03: 15000000 INFO @ Tue, 04 Sep 2018 10:41:05: 15000000 INFO @ Tue, 04 Sep 2018 10:41:06: 14000000 INFO @ Tue, 04 Sep 2018 10:41:11: 16000000 INFO @ Tue, 04 Sep 2018 10:41:13: 16000000 INFO @ Tue, 04 Sep 2018 10:41:13: 15000000 INFO @ Tue, 04 Sep 2018 10:41:18: 17000000 INFO @ Tue, 04 Sep 2018 10:41:20: 16000000 INFO @ Tue, 04 Sep 2018 10:41:20: 17000000 INFO @ Tue, 04 Sep 2018 10:41:25: 18000000 INFO @ Tue, 04 Sep 2018 10:41:27: 17000000 INFO @ Tue, 04 Sep 2018 10:41:28: 18000000 INFO @ Tue, 04 Sep 2018 10:41:32: 19000000 INFO @ Tue, 04 Sep 2018 10:41:34: 18000000 INFO @ Tue, 04 Sep 2018 10:41:35: 19000000 INFO @ Tue, 04 Sep 2018 10:41:39: 20000000 INFO @ Tue, 04 Sep 2018 10:41:41: 19000000 INFO @ Tue, 04 Sep 2018 10:41:43: 20000000 INFO @ Tue, 04 Sep 2018 10:41:46: 21000000 INFO @ Tue, 04 Sep 2018 10:41:48: 20000000 INFO @ Tue, 04 Sep 2018 10:41:50: 21000000 INFO @ Tue, 04 Sep 2018 10:41:53: 22000000 INFO @ Tue, 04 Sep 2018 10:41:55: 21000000 INFO @ Tue, 04 Sep 2018 10:41:58: 22000000 INFO @ Tue, 04 Sep 2018 10:42:00: 23000000 INFO @ Tue, 04 Sep 2018 10:42:02: 22000000 INFO @ Tue, 04 Sep 2018 10:42:05: 23000000 INFO @ Tue, 04 Sep 2018 10:42:07: 24000000 INFO @ Tue, 04 Sep 2018 10:42:09: 23000000 INFO @ Tue, 04 Sep 2018 10:42:13: 24000000 INFO @ Tue, 04 Sep 2018 10:42:14: 25000000 INFO @ Tue, 04 Sep 2018 10:42:16: 24000000 INFO @ Tue, 04 Sep 2018 10:42:20: 25000000 INFO @ Tue, 04 Sep 2018 10:42:21: 26000000 INFO @ Tue, 04 Sep 2018 10:42:23: 25000000 INFO @ Tue, 04 Sep 2018 10:42:27: 26000000 INFO @ Tue, 04 Sep 2018 10:42:28: 27000000 INFO @ Tue, 04 Sep 2018 10:42:30: 26000000 INFO @ Tue, 04 Sep 2018 10:42:35: 27000000 INFO @ Tue, 04 Sep 2018 10:42:35: 28000000 INFO @ Tue, 04 Sep 2018 10:42:37: 27000000 INFO @ Tue, 04 Sep 2018 10:42:42: 28000000 INFO @ Tue, 04 Sep 2018 10:42:43: 29000000 INFO @ Tue, 04 Sep 2018 10:42:44: 28000000 INFO @ Tue, 04 Sep 2018 10:42:49: 29000000 INFO @ Tue, 04 Sep 2018 10:42:50: 30000000 INFO @ Tue, 04 Sep 2018 10:42:51: 29000000 INFO @ Tue, 04 Sep 2018 10:42:56: 30000000 INFO @ Tue, 04 Sep 2018 10:42:57: 31000000 INFO @ Tue, 04 Sep 2018 10:42:58: 30000000 INFO @ Tue, 04 Sep 2018 10:43:03: 31000000 INFO @ Tue, 04 Sep 2018 10:43:04: 32000000 INFO @ Tue, 04 Sep 2018 10:43:05: 31000000 INFO @ Tue, 04 Sep 2018 10:43:11: 32000000 INFO @ Tue, 04 Sep 2018 10:43:11: 33000000 INFO @ Tue, 04 Sep 2018 10:43:12: 32000000 INFO @ Tue, 04 Sep 2018 10:43:18: 33000000 INFO @ Tue, 04 Sep 2018 10:43:18: 34000000 INFO @ Tue, 04 Sep 2018 10:43:19: 33000000 INFO @ Tue, 04 Sep 2018 10:43:24: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 10:43:24: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 10:43:24: #1 total tags in treatment: 14126962 INFO @ Tue, 04 Sep 2018 10:43:24: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:43:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:43:25: #1 tags after filtering in treatment: 12103311 INFO @ Tue, 04 Sep 2018 10:43:25: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 04 Sep 2018 10:43:25: #1 finished! INFO @ Tue, 04 Sep 2018 10:43:25: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:43:25: 34000000 INFO @ Tue, 04 Sep 2018 10:43:26: 34000000 INFO @ Tue, 04 Sep 2018 10:43:26: #2 number of paired peaks: 522 WARNING @ Tue, 04 Sep 2018 10:43:26: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 04 Sep 2018 10:43:26: start model_add_line... INFO @ Tue, 04 Sep 2018 10:43:26: start X-correlation... INFO @ Tue, 04 Sep 2018 10:43:26: end of X-cor INFO @ Tue, 04 Sep 2018 10:43:26: #2 finished! INFO @ Tue, 04 Sep 2018 10:43:26: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 10:43:26: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 10:43:26: #2.2 Generate R script for model : SRX4029334.05_model.r INFO @ Tue, 04 Sep 2018 10:43:26: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:43:30: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 10:43:30: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 10:43:30: #1 total tags in treatment: 14126962 INFO @ Tue, 04 Sep 2018 10:43:30: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:43:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:43:31: #1 tags after filtering in treatment: 12103311 INFO @ Tue, 04 Sep 2018 10:43:31: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 04 Sep 2018 10:43:31: #1 finished! INFO @ Tue, 04 Sep 2018 10:43:31: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:43:31: #1 tag size is determined as 76 bps INFO @ Tue, 04 Sep 2018 10:43:31: #1 tag size = 76 INFO @ Tue, 04 Sep 2018 10:43:31: #1 total tags in treatment: 14126962 INFO @ Tue, 04 Sep 2018 10:43:31: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:43:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:43:32: #2 number of paired peaks: 522 WARNING @ Tue, 04 Sep 2018 10:43:32: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 04 Sep 2018 10:43:32: start model_add_line... INFO @ Tue, 04 Sep 2018 10:43:32: #1 tags after filtering in treatment: 12103311 INFO @ Tue, 04 Sep 2018 10:43:32: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 04 Sep 2018 10:43:32: #1 finished! INFO @ Tue, 04 Sep 2018 10:43:32: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:43:32: start X-correlation... INFO @ Tue, 04 Sep 2018 10:43:32: end of X-cor INFO @ Tue, 04 Sep 2018 10:43:32: #2 finished! INFO @ Tue, 04 Sep 2018 10:43:32: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 10:43:32: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 10:43:32: #2.2 Generate R script for model : SRX4029334.20_model.r INFO @ Tue, 04 Sep 2018 10:43:32: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:43:33: #2 number of paired peaks: 522 WARNING @ Tue, 04 Sep 2018 10:43:33: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 04 Sep 2018 10:43:33: start model_add_line... INFO @ Tue, 04 Sep 2018 10:43:33: start X-correlation... INFO @ Tue, 04 Sep 2018 10:43:33: end of X-cor INFO @ Tue, 04 Sep 2018 10:43:33: #2 finished! INFO @ Tue, 04 Sep 2018 10:43:33: #2 predicted fragment length is 181 bps INFO @ Tue, 04 Sep 2018 10:43:33: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 04 Sep 2018 10:43:33: #2.2 Generate R script for model : SRX4029334.10_model.r INFO @ Tue, 04 Sep 2018 10:43:33: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:43:57: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:44:01: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:44:02: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:44:12: #4 Write output xls file... SRX4029334.05_peaks.xls INFO @ Tue, 04 Sep 2018 10:44:12: #4 Write peak in narrowPeak format file... SRX4029334.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:44:12: #4 Write summits bed file... SRX4029334.05_summits.bed INFO @ Tue, 04 Sep 2018 10:44:12: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3357 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:44:16: #4 Write output xls file... SRX4029334.10_peaks.xls INFO @ Tue, 04 Sep 2018 10:44:16: #4 Write peak in narrowPeak format file... SRX4029334.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:44:16: #4 Write summits bed file... SRX4029334.10_summits.bed INFO @ Tue, 04 Sep 2018 10:44:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1940 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:44:17: #4 Write output xls file... SRX4029334.20_peaks.xls INFO @ Tue, 04 Sep 2018 10:44:17: #4 Write peak in narrowPeak format file... SRX4029334.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:44:17: #4 Write summits bed file... SRX4029334.20_summits.bed INFO @ Tue, 04 Sep 2018 10:44:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (862 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。