Job ID = 11170832 sra ファイルのダウンロード中... Completed: 2931496K bytes transferred in 158 seconds (151795K 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 23526471 spots for /home/okishinya/chipatlas/results/ce10/SRX3058059/SRR5892350.sra Written 23526471 spots for /home/okishinya/chipatlas/results/ce10/SRX3058059/SRR5892350.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: 01:00:39 23526471 reads; of these: 23526471 (100.00%) were paired; of these: 1381647 (5.87%) aligned concordantly 0 times 19510125 (82.93%) aligned concordantly exactly 1 time 2634699 (11.20%) aligned concordantly >1 times ---- 1381647 pairs aligned concordantly 0 times; of these: 209926 (15.19%) aligned discordantly 1 time ---- 1171721 pairs aligned 0 times concordantly or discordantly; of these: 2343442 mates make up the pairs; of these: 2027241 (86.51%) aligned 0 times 213125 (9.09%) aligned exactly 1 time 103076 (4.40%) aligned >1 times 95.69% overall alignment rate Time searching: 01:00:39 Overall time: 01:00:39 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 36 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] 2954355 / 22337313 = 0.1323 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 @ Sat, 08 Sep 2018 12:53:48: # Command line: callpeak -t SRX3058059.bam -f BAM -g ce -n SRX3058059.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3058059.05 # format = BAM # ChIP-seq file = ['SRX3058059.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 @ Sat, 08 Sep 2018 12:53:48: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:53:48: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:53:48: # Command line: callpeak -t SRX3058059.bam -f BAM -g ce -n SRX3058059.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3058059.10 # format = BAM # ChIP-seq file = ['SRX3058059.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 @ Sat, 08 Sep 2018 12:53:48: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:53:48: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:53:48: # Command line: callpeak -t SRX3058059.bam -f BAM -g ce -n SRX3058059.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3058059.20 # format = BAM # ChIP-seq file = ['SRX3058059.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 @ Sat, 08 Sep 2018 12:53:48: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:53:48: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:53:58: 1000000 INFO @ Sat, 08 Sep 2018 12:53:59: 1000000 INFO @ Sat, 08 Sep 2018 12:53:59: 1000000 INFO @ Sat, 08 Sep 2018 12:54:07: 2000000 INFO @ Sat, 08 Sep 2018 12:54:09: 2000000 INFO @ Sat, 08 Sep 2018 12:54:09: 2000000 INFO @ Sat, 08 Sep 2018 12:54:17: 3000000 INFO @ Sat, 08 Sep 2018 12:54:20: 3000000 INFO @ Sat, 08 Sep 2018 12:54:20: 3000000 INFO @ Sat, 08 Sep 2018 12:54:26: 4000000 INFO @ Sat, 08 Sep 2018 12:54:30: 4000000 INFO @ Sat, 08 Sep 2018 12:54:30: 4000000 INFO @ Sat, 08 Sep 2018 12:54:35: 5000000 INFO @ Sat, 08 Sep 2018 12:54:40: 5000000 INFO @ Sat, 08 Sep 2018 12:54:40: 5000000 INFO @ Sat, 08 Sep 2018 12:54:44: 6000000 INFO @ Sat, 08 Sep 2018 12:54:51: 6000000 INFO @ Sat, 08 Sep 2018 12:54:51: 6000000 INFO @ Sat, 08 Sep 2018 12:54:53: 7000000 INFO @ Sat, 08 Sep 2018 12:55:01: 7000000 INFO @ Sat, 08 Sep 2018 12:55:01: 7000000 INFO @ Sat, 08 Sep 2018 12:55:03: 8000000 INFO @ Sat, 08 Sep 2018 12:55:13: 8000000 INFO @ Sat, 08 Sep 2018 12:55:13: 8000000 INFO @ Sat, 08 Sep 2018 12:55:15: 9000000 INFO @ Sat, 08 Sep 2018 12:55:25: 9000000 INFO @ Sat, 08 Sep 2018 12:55:25: 9000000 INFO @ Sat, 08 Sep 2018 12:55:27: 10000000 INFO @ Sat, 08 Sep 2018 12:55:37: 10000000 INFO @ Sat, 08 Sep 2018 12:55:37: 10000000 INFO @ Sat, 08 Sep 2018 12:55:39: 11000000 INFO @ Sat, 08 Sep 2018 12:55:49: 11000000 INFO @ Sat, 08 Sep 2018 12:55:49: 11000000 INFO @ Sat, 08 Sep 2018 12:55:51: 12000000 INFO @ Sat, 08 Sep 2018 12:56:01: 12000000 INFO @ Sat, 08 Sep 2018 12:56:01: 12000000 INFO @ Sat, 08 Sep 2018 12:56:03: 13000000 INFO @ Sat, 08 Sep 2018 12:56:14: 13000000 INFO @ Sat, 08 Sep 2018 12:56:14: 13000000 INFO @ Sat, 08 Sep 2018 12:56:15: 14000000 INFO @ Sat, 08 Sep 2018 12:56:26: 14000000 INFO @ Sat, 08 Sep 2018 12:56:26: 14000000 INFO @ Sat, 08 Sep 2018 12:56:27: 15000000 INFO @ Sat, 08 Sep 2018 12:56:37: 15000000 INFO @ Sat, 08 Sep 2018 12:56:37: 15000000 INFO @ Sat, 08 Sep 2018 12:56:39: 16000000 INFO @ Sat, 08 Sep 2018 12:56:49: 16000000 INFO @ Sat, 08 Sep 2018 12:56:49: 16000000 INFO @ Sat, 08 Sep 2018 12:56:51: 17000000 INFO @ Sat, 08 Sep 2018 12:57:01: 17000000 INFO @ Sat, 08 Sep 2018 12:57:01: 17000000 INFO @ Sat, 08 Sep 2018 12:57:03: 18000000 INFO @ Sat, 08 Sep 2018 12:57:14: 18000000 INFO @ Sat, 08 Sep 2018 12:57:14: 18000000 INFO @ Sat, 08 Sep 2018 12:57:16: 19000000 INFO @ Sat, 08 Sep 2018 12:57:26: 19000000 INFO @ Sat, 08 Sep 2018 12:57:26: 19000000 INFO @ Sat, 08 Sep 2018 12:57:27: 20000000 INFO @ Sat, 08 Sep 2018 12:57:37: 20000000 INFO @ Sat, 08 Sep 2018 12:57:37: 20000000 INFO @ Sat, 08 Sep 2018 12:57:39: 21000000 INFO @ Sat, 08 Sep 2018 12:57:49: 21000000 INFO @ Sat, 08 Sep 2018 12:57:49: 21000000 INFO @ Sat, 08 Sep 2018 12:57:51: 22000000 INFO @ Sat, 08 Sep 2018 12:58:01: 22000000 INFO @ Sat, 08 Sep 2018 12:58:01: 22000000 INFO @ Sat, 08 Sep 2018 12:58:03: 23000000 INFO @ Sat, 08 Sep 2018 12:58:13: 23000000 INFO @ Sat, 08 Sep 2018 12:58:13: 23000000 INFO @ Sat, 08 Sep 2018 12:58:15: 24000000 INFO @ Sat, 08 Sep 2018 12:58:25: 24000000 INFO @ Sat, 08 Sep 2018 12:58:25: 24000000 INFO @ Sat, 08 Sep 2018 12:58:27: 25000000 INFO @ Sat, 08 Sep 2018 12:58:37: 25000000 INFO @ Sat, 08 Sep 2018 12:58:37: 25000000 INFO @ Sat, 08 Sep 2018 12:58:39: 26000000 INFO @ Sat, 08 Sep 2018 12:58:49: 26000000 INFO @ Sat, 08 Sep 2018 12:58:49: 26000000 INFO @ Sat, 08 Sep 2018 12:58:51: 27000000 INFO @ Sat, 08 Sep 2018 12:59:01: 27000000 INFO @ Sat, 08 Sep 2018 12:59:01: 27000000 INFO @ Sat, 08 Sep 2018 12:59:03: 28000000 INFO @ Sat, 08 Sep 2018 12:59:13: 28000000 INFO @ Sat, 08 Sep 2018 12:59:14: 28000000 INFO @ Sat, 08 Sep 2018 12:59:15: 29000000 INFO @ Sat, 08 Sep 2018 12:59:25: 29000000 INFO @ Sat, 08 Sep 2018 12:59:27: 29000000 INFO @ Sat, 08 Sep 2018 12:59:27: 30000000 INFO @ Sat, 08 Sep 2018 12:59:38: 30000000 INFO @ Sat, 08 Sep 2018 12:59:39: 30000000 INFO @ Sat, 08 Sep 2018 12:59:40: 31000000 INFO @ Sat, 08 Sep 2018 12:59:50: 31000000 INFO @ Sat, 08 Sep 2018 12:59:52: 32000000 INFO @ Sat, 08 Sep 2018 12:59:53: 31000000 INFO @ Sat, 08 Sep 2018 13:00:02: 32000000 INFO @ Sat, 08 Sep 2018 13:00:04: 33000000 INFO @ Sat, 08 Sep 2018 13:00:05: 32000000 INFO @ Sat, 08 Sep 2018 13:00:14: 33000000 INFO @ Sat, 08 Sep 2018 13:00:17: 34000000 INFO @ Sat, 08 Sep 2018 13:00:18: 33000000 INFO @ Sat, 08 Sep 2018 13:00:27: 34000000 INFO @ Sat, 08 Sep 2018 13:00:29: 35000000 INFO @ Sat, 08 Sep 2018 13:00:31: 34000000 INFO @ Sat, 08 Sep 2018 13:00:39: 35000000 INFO @ Sat, 08 Sep 2018 13:00:41: 36000000 INFO @ Sat, 08 Sep 2018 13:00:43: 35000000 INFO @ Sat, 08 Sep 2018 13:00:51: 36000000 INFO @ Sat, 08 Sep 2018 13:00:53: 37000000 INFO @ Sat, 08 Sep 2018 13:00:56: 36000000 INFO @ Sat, 08 Sep 2018 13:01:03: 37000000 INFO @ Sat, 08 Sep 2018 13:01:04: 38000000 INFO @ Sat, 08 Sep 2018 13:01:07: 37000000 INFO @ Sat, 08 Sep 2018 13:01:13: 38000000 INFO @ Sat, 08 Sep 2018 13:01:15: 39000000 INFO @ Sat, 08 Sep 2018 13:01:16: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 13:01:16: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 13:01:16: #1 total tags in treatment: 19207767 INFO @ Sat, 08 Sep 2018 13:01:16: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:01:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:01:16: #1 tags after filtering in treatment: 17365778 INFO @ Sat, 08 Sep 2018 13:01:16: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Sep 2018 13:01:16: #1 finished! INFO @ Sat, 08 Sep 2018 13:01:16: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:01:16: 38000000 INFO @ Sat, 08 Sep 2018 13:01:17: #2 number of paired peaks: 237 WARNING @ Sat, 08 Sep 2018 13:01:17: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Sat, 08 Sep 2018 13:01:17: start model_add_line... INFO @ Sat, 08 Sep 2018 13:01:17: start X-correlation... INFO @ Sat, 08 Sep 2018 13:01:17: end of X-cor INFO @ Sat, 08 Sep 2018 13:01:17: #2 finished! INFO @ Sat, 08 Sep 2018 13:01:17: #2 predicted fragment length is 216 bps INFO @ Sat, 08 Sep 2018 13:01:17: #2 alternative fragment length(s) may be 4,216,228 bps INFO @ Sat, 08 Sep 2018 13:01:17: #2.2 Generate R script for model : SRX3058059.10_model.r WARNING @ Sat, 08 Sep 2018 13:01:17: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:01:17: #2 You may need to consider one of the other alternative d(s): 4,216,228 WARNING @ Sat, 08 Sep 2018 13:01:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:01:17: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:01:22: 39000000 INFO @ Sat, 08 Sep 2018 13:01:23: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 13:01:23: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 13:01:23: #1 total tags in treatment: 19207767 INFO @ Sat, 08 Sep 2018 13:01:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:01:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:01:24: #1 tags after filtering in treatment: 17365778 INFO @ Sat, 08 Sep 2018 13:01:24: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Sep 2018 13:01:24: #1 finished! INFO @ Sat, 08 Sep 2018 13:01:24: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:01:25: #2 number of paired peaks: 237 WARNING @ Sat, 08 Sep 2018 13:01:25: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Sat, 08 Sep 2018 13:01:25: start model_add_line... INFO @ Sat, 08 Sep 2018 13:01:25: start X-correlation... INFO @ Sat, 08 Sep 2018 13:01:25: end of X-cor INFO @ Sat, 08 Sep 2018 13:01:25: #2 finished! INFO @ Sat, 08 Sep 2018 13:01:25: #2 predicted fragment length is 216 bps INFO @ Sat, 08 Sep 2018 13:01:25: #2 alternative fragment length(s) may be 4,216,228 bps INFO @ Sat, 08 Sep 2018 13:01:25: #2.2 Generate R script for model : SRX3058059.05_model.r WARNING @ Sat, 08 Sep 2018 13:01:25: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:01:25: #2 You may need to consider one of the other alternative d(s): 4,216,228 WARNING @ Sat, 08 Sep 2018 13:01:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:01:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:01:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:01:25: 39000000 INFO @ Sat, 08 Sep 2018 13:01:26: #1 tag size is determined as 150 bps INFO @ Sat, 08 Sep 2018 13:01:26: #1 tag size = 150 INFO @ Sat, 08 Sep 2018 13:01:26: #1 total tags in treatment: 19207767 INFO @ Sat, 08 Sep 2018 13:01:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:01:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:01:27: #1 tags after filtering in treatment: 17365778 INFO @ Sat, 08 Sep 2018 13:01:27: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Sep 2018 13:01:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:01:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:01:28: #2 number of paired peaks: 237 WARNING @ Sat, 08 Sep 2018 13:01:28: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Sat, 08 Sep 2018 13:01:28: start model_add_line... INFO @ Sat, 08 Sep 2018 13:01:28: start X-correlation... INFO @ Sat, 08 Sep 2018 13:01:28: end of X-cor INFO @ Sat, 08 Sep 2018 13:01:28: #2 finished! INFO @ Sat, 08 Sep 2018 13:01:28: #2 predicted fragment length is 216 bps INFO @ Sat, 08 Sep 2018 13:01:28: #2 alternative fragment length(s) may be 4,216,228 bps INFO @ Sat, 08 Sep 2018 13:01:28: #2.2 Generate R script for model : SRX3058059.20_model.r WARNING @ Sat, 08 Sep 2018 13:01:28: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:01:28: #2 You may need to consider one of the other alternative d(s): 4,216,228 WARNING @ Sat, 08 Sep 2018 13:01:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:01:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:01:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:02:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:02:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:02:11: #4 Write output xls file... SRX3058059.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:02:11: #4 Write peak in narrowPeak format file... SRX3058059.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:02:11: #4 Write summits bed file... SRX3058059.10_summits.bed INFO @ Sat, 08 Sep 2018 13:02:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (365 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:02:19: #4 Write output xls file... SRX3058059.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:02:19: #4 Write peak in narrowPeak format file... SRX3058059.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:02:19: #4 Write summits bed file... SRX3058059.05_summits.bed INFO @ Sat, 08 Sep 2018 13:02:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (439 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:02:27: #4 Write output xls file... SRX3058059.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:02:27: #4 Write peak in narrowPeak format file... SRX3058059.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:02:27: #4 Write summits bed file... SRX3058059.20_summits.bed INFO @ Sat, 08 Sep 2018 13:02:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (252 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。