Job ID = 11597695 sra ファイルのダウンロード中... Completed: 2066670K bytes transferred in 21 seconds (792454K 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 18447129 spots for /home/okishinya/chipatlas/results/ce10/SRX5064643/SRR8246579.sra Written 18447129 spots for /home/okishinya/chipatlas/results/ce10/SRX5064643/SRR8246579.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: 00:49:11 18447129 reads; of these: 18447129 (100.00%) were paired; of these: 1009156 (5.47%) aligned concordantly 0 times 15284099 (82.85%) aligned concordantly exactly 1 time 2153874 (11.68%) aligned concordantly >1 times ---- 1009156 pairs aligned concordantly 0 times; of these: 358459 (35.52%) aligned discordantly 1 time ---- 650697 pairs aligned 0 times concordantly or discordantly; of these: 1301394 mates make up the pairs; of these: 979623 (75.27%) aligned 0 times 205292 (15.77%) aligned exactly 1 time 116479 (8.95%) aligned >1 times 97.34% overall alignment rate Time searching: 00:49:11 Overall time: 00:49:11 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] 4597139 / 17701063 = 0.2597 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 @ Wed, 30 Jan 2019 15:27:58: # Command line: callpeak -t SRX5064643.bam -f BAM -g ce -n SRX5064643.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5064643.20 # format = BAM # ChIP-seq file = ['SRX5064643.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 @ Wed, 30 Jan 2019 15:27:58: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:27:58: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:27:58: # Command line: callpeak -t SRX5064643.bam -f BAM -g ce -n SRX5064643.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5064643.10 # format = BAM # ChIP-seq file = ['SRX5064643.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 @ Wed, 30 Jan 2019 15:27:58: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:27:58: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:27:58: # Command line: callpeak -t SRX5064643.bam -f BAM -g ce -n SRX5064643.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5064643.05 # format = BAM # ChIP-seq file = ['SRX5064643.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 @ Wed, 30 Jan 2019 15:27:58: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:27:58: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:28:10: 1000000 INFO @ Wed, 30 Jan 2019 15:28:10: 1000000 INFO @ Wed, 30 Jan 2019 15:28:11: 1000000 INFO @ Wed, 30 Jan 2019 15:28:21: 2000000 INFO @ Wed, 30 Jan 2019 15:28:21: 2000000 INFO @ Wed, 30 Jan 2019 15:28:22: 2000000 INFO @ Wed, 30 Jan 2019 15:28:32: 3000000 INFO @ Wed, 30 Jan 2019 15:28:32: 3000000 INFO @ Wed, 30 Jan 2019 15:28:34: 3000000 INFO @ Wed, 30 Jan 2019 15:28:44: 4000000 INFO @ Wed, 30 Jan 2019 15:28:44: 4000000 INFO @ Wed, 30 Jan 2019 15:28:47: 4000000 INFO @ Wed, 30 Jan 2019 15:28:55: 5000000 INFO @ Wed, 30 Jan 2019 15:28:55: 5000000 INFO @ Wed, 30 Jan 2019 15:28:59: 5000000 INFO @ Wed, 30 Jan 2019 15:29:07: 6000000 INFO @ Wed, 30 Jan 2019 15:29:07: 6000000 INFO @ Wed, 30 Jan 2019 15:29:11: 6000000 INFO @ Wed, 30 Jan 2019 15:29:18: 7000000 INFO @ Wed, 30 Jan 2019 15:29:18: 7000000 INFO @ Wed, 30 Jan 2019 15:29:23: 7000000 INFO @ Wed, 30 Jan 2019 15:29:30: 8000000 INFO @ Wed, 30 Jan 2019 15:29:30: 8000000 INFO @ Wed, 30 Jan 2019 15:29:35: 8000000 INFO @ Wed, 30 Jan 2019 15:29:41: 9000000 INFO @ Wed, 30 Jan 2019 15:29:42: 9000000 INFO @ Wed, 30 Jan 2019 15:29:47: 9000000 INFO @ Wed, 30 Jan 2019 15:29:53: 10000000 INFO @ Wed, 30 Jan 2019 15:29:53: 10000000 INFO @ Wed, 30 Jan 2019 15:29:59: 10000000 INFO @ Wed, 30 Jan 2019 15:30:04: 11000000 INFO @ Wed, 30 Jan 2019 15:30:04: 11000000 INFO @ Wed, 30 Jan 2019 15:30:11: 11000000 INFO @ Wed, 30 Jan 2019 15:30:16: 12000000 INFO @ Wed, 30 Jan 2019 15:30:16: 12000000 INFO @ Wed, 30 Jan 2019 15:30:23: 12000000 INFO @ Wed, 30 Jan 2019 15:30:28: 13000000 INFO @ Wed, 30 Jan 2019 15:30:28: 13000000 INFO @ Wed, 30 Jan 2019 15:30:35: 13000000 INFO @ Wed, 30 Jan 2019 15:30:39: 14000000 INFO @ Wed, 30 Jan 2019 15:30:39: 14000000 INFO @ Wed, 30 Jan 2019 15:30:47: 14000000 INFO @ Wed, 30 Jan 2019 15:30:51: 15000000 INFO @ Wed, 30 Jan 2019 15:30:51: 15000000 INFO @ Wed, 30 Jan 2019 15:30:59: 15000000 INFO @ Wed, 30 Jan 2019 15:31:03: 16000000 INFO @ Wed, 30 Jan 2019 15:31:03: 16000000 INFO @ Wed, 30 Jan 2019 15:31:10: 16000000 INFO @ Wed, 30 Jan 2019 15:31:15: 17000000 INFO @ Wed, 30 Jan 2019 15:31:15: 17000000 INFO @ Wed, 30 Jan 2019 15:31:22: 17000000 INFO @ Wed, 30 Jan 2019 15:31:26: 18000000 INFO @ Wed, 30 Jan 2019 15:31:27: 18000000 INFO @ Wed, 30 Jan 2019 15:31:34: 18000000 INFO @ Wed, 30 Jan 2019 15:31:38: 19000000 INFO @ Wed, 30 Jan 2019 15:31:38: 19000000 INFO @ Wed, 30 Jan 2019 15:31:46: 19000000 INFO @ Wed, 30 Jan 2019 15:31:50: 20000000 INFO @ Wed, 30 Jan 2019 15:31:50: 20000000 INFO @ Wed, 30 Jan 2019 15:31:57: 20000000 INFO @ Wed, 30 Jan 2019 15:32:02: 21000000 INFO @ Wed, 30 Jan 2019 15:32:02: 21000000 INFO @ Wed, 30 Jan 2019 15:32:09: 21000000 INFO @ Wed, 30 Jan 2019 15:32:13: 22000000 INFO @ Wed, 30 Jan 2019 15:32:14: 22000000 INFO @ Wed, 30 Jan 2019 15:32:20: 22000000 INFO @ Wed, 30 Jan 2019 15:32:25: 23000000 INFO @ Wed, 30 Jan 2019 15:32:25: 23000000 INFO @ Wed, 30 Jan 2019 15:32:32: 23000000 INFO @ Wed, 30 Jan 2019 15:32:37: 24000000 INFO @ Wed, 30 Jan 2019 15:32:37: 24000000 INFO @ Wed, 30 Jan 2019 15:32:44: 24000000 INFO @ Wed, 30 Jan 2019 15:32:48: 25000000 INFO @ Wed, 30 Jan 2019 15:32:48: 25000000 INFO @ Wed, 30 Jan 2019 15:32:56: 25000000 INFO @ Wed, 30 Jan 2019 15:33:00: 26000000 INFO @ Wed, 30 Jan 2019 15:33:00: 26000000 INFO @ Wed, 30 Jan 2019 15:33:08: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 15:33:08: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 15:33:08: #1 total tags in treatment: 12895152 INFO @ Wed, 30 Jan 2019 15:33:08: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:33:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:33:08: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 15:33:08: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 15:33:08: #1 total tags in treatment: 12895152 INFO @ Wed, 30 Jan 2019 15:33:08: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:33:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:33:08: #1 tags after filtering in treatment: 11901884 INFO @ Wed, 30 Jan 2019 15:33:08: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 30 Jan 2019 15:33:08: #1 finished! INFO @ Wed, 30 Jan 2019 15:33:08: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:33:08: #1 tags after filtering in treatment: 11901884 INFO @ Wed, 30 Jan 2019 15:33:08: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 30 Jan 2019 15:33:08: #1 finished! INFO @ Wed, 30 Jan 2019 15:33:08: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:33:08: 26000000 INFO @ Wed, 30 Jan 2019 15:33:09: #2 number of paired peaks: 336 WARNING @ Wed, 30 Jan 2019 15:33:09: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Wed, 30 Jan 2019 15:33:09: start model_add_line... INFO @ Wed, 30 Jan 2019 15:33:09: #2 number of paired peaks: 336 WARNING @ Wed, 30 Jan 2019 15:33:09: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Wed, 30 Jan 2019 15:33:09: start model_add_line... INFO @ Wed, 30 Jan 2019 15:33:09: start X-correlation... INFO @ Wed, 30 Jan 2019 15:33:09: end of X-cor INFO @ Wed, 30 Jan 2019 15:33:09: #2 finished! INFO @ Wed, 30 Jan 2019 15:33:09: #2 predicted fragment length is 217 bps INFO @ Wed, 30 Jan 2019 15:33:09: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 30 Jan 2019 15:33:09: #2.2 Generate R script for model : SRX5064643.20_model.r WARNING @ Wed, 30 Jan 2019 15:33:09: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:33:09: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 30 Jan 2019 15:33:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:33:09: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:33:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:33:09: start X-correlation... INFO @ Wed, 30 Jan 2019 15:33:09: end of X-cor INFO @ Wed, 30 Jan 2019 15:33:09: #2 finished! INFO @ Wed, 30 Jan 2019 15:33:09: #2 predicted fragment length is 217 bps INFO @ Wed, 30 Jan 2019 15:33:09: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 30 Jan 2019 15:33:09: #2.2 Generate R script for model : SRX5064643.05_model.r WARNING @ Wed, 30 Jan 2019 15:33:09: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:33:09: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 30 Jan 2019 15:33:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:33:09: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:33:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:33:16: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 15:33:16: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 15:33:16: #1 total tags in treatment: 12895152 INFO @ Wed, 30 Jan 2019 15:33:16: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:33:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:33:17: #1 tags after filtering in treatment: 11901884 INFO @ Wed, 30 Jan 2019 15:33:17: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 30 Jan 2019 15:33:17: #1 finished! INFO @ Wed, 30 Jan 2019 15:33:17: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:33:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:33:18: #2 number of paired peaks: 336 WARNING @ Wed, 30 Jan 2019 15:33:18: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Wed, 30 Jan 2019 15:33:18: start model_add_line... INFO @ Wed, 30 Jan 2019 15:33:18: start X-correlation... INFO @ Wed, 30 Jan 2019 15:33:18: end of X-cor INFO @ Wed, 30 Jan 2019 15:33:18: #2 finished! INFO @ Wed, 30 Jan 2019 15:33:18: #2 predicted fragment length is 217 bps INFO @ Wed, 30 Jan 2019 15:33:18: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 30 Jan 2019 15:33:18: #2.2 Generate R script for model : SRX5064643.10_model.r WARNING @ Wed, 30 Jan 2019 15:33:18: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:33:18: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 30 Jan 2019 15:33:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:33:18: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:33:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:33:38: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:33:39: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:33:45: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:33:52: #4 Write output xls file... SRX5064643.20_peaks.xls INFO @ Wed, 30 Jan 2019 15:33:52: #4 Write peak in narrowPeak format file... SRX5064643.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:33:52: #4 Write summits bed file... SRX5064643.20_summits.bed INFO @ Wed, 30 Jan 2019 15:33:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 15:33:53: #4 Write output xls file... SRX5064643.05_peaks.xls INFO @ Wed, 30 Jan 2019 15:33:53: #4 Write peak in narrowPeak format file... SRX5064643.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:33:53: #4 Write summits bed file... SRX5064643.05_summits.bed INFO @ Wed, 30 Jan 2019 15:33:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (438 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 15:33:58: #4 Write output xls file... SRX5064643.10_peaks.xls INFO @ Wed, 30 Jan 2019 15:33:58: #4 Write peak in narrowPeak format file... SRX5064643.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:33:58: #4 Write summits bed file... SRX5064643.10_summits.bed INFO @ Wed, 30 Jan 2019 15:33:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (351 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。