Job ID = 10714482 sra ファイルのダウンロード中... Completed: 2606399K bytes transferred in 44 seconds (484966K 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 38357635 spots for /home/okishinya/chipatlas/results/ce10/SRX4085398/SRR7167427.sra Written 38357635 spots for /home/okishinya/chipatlas/results/ce10/SRX4085398/SRR7167427.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: 00:37:06 38357635 reads; of these: 38357635 (100.00%) were paired; of these: 3589466 (9.36%) aligned concordantly 0 times 30832213 (80.38%) aligned concordantly exactly 1 time 3935956 (10.26%) aligned concordantly >1 times ---- 3589466 pairs aligned concordantly 0 times; of these: 1399324 (38.98%) aligned discordantly 1 time ---- 2190142 pairs aligned 0 times concordantly or discordantly; of these: 4380284 mates make up the pairs; of these: 2668165 (60.91%) aligned 0 times 1098750 (25.08%) aligned exactly 1 time 613369 (14.00%) aligned >1 times 96.52% overall alignment rate Time searching: 00:37:06 Overall time: 00:37:06 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 32 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] 21618010 / 35054694 = 0.6167 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 13:42:34: # Command line: callpeak -t SRX4085398.bam -f BAM -g ce -n SRX4085398.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085398.05 # format = BAM # ChIP-seq file = ['SRX4085398.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 13:42:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:34: # Command line: callpeak -t SRX4085398.bam -f BAM -g ce -n SRX4085398.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085398.10 # format = BAM # ChIP-seq file = ['SRX4085398.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 13:42:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:34: # Command line: callpeak -t SRX4085398.bam -f BAM -g ce -n SRX4085398.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085398.20 # format = BAM # ChIP-seq file = ['SRX4085398.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 13:42:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:42:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:42:40: 1000000 INFO @ Sun, 03 Jun 2018 13:42:40: 1000000 INFO @ Sun, 03 Jun 2018 13:42:40: 1000000 INFO @ Sun, 03 Jun 2018 13:42:47: 2000000 INFO @ Sun, 03 Jun 2018 13:42:47: 2000000 INFO @ Sun, 03 Jun 2018 13:42:47: 2000000 INFO @ Sun, 03 Jun 2018 13:42:53: 3000000 INFO @ Sun, 03 Jun 2018 13:42:54: 3000000 INFO @ Sun, 03 Jun 2018 13:42:54: 3000000 INFO @ Sun, 03 Jun 2018 13:43:00: 4000000 INFO @ Sun, 03 Jun 2018 13:43:00: 4000000 INFO @ Sun, 03 Jun 2018 13:43:00: 4000000 INFO @ Sun, 03 Jun 2018 13:43:06: 5000000 INFO @ Sun, 03 Jun 2018 13:43:07: 5000000 INFO @ Sun, 03 Jun 2018 13:43:07: 5000000 INFO @ Sun, 03 Jun 2018 13:43:12: 6000000 INFO @ Sun, 03 Jun 2018 13:43:13: 6000000 INFO @ Sun, 03 Jun 2018 13:43:14: 6000000 INFO @ Sun, 03 Jun 2018 13:43:19: 7000000 INFO @ Sun, 03 Jun 2018 13:43:20: 7000000 INFO @ Sun, 03 Jun 2018 13:43:21: 7000000 INFO @ Sun, 03 Jun 2018 13:43:25: 8000000 INFO @ Sun, 03 Jun 2018 13:43:27: 8000000 INFO @ Sun, 03 Jun 2018 13:43:27: 8000000 INFO @ Sun, 03 Jun 2018 13:43:32: 9000000 INFO @ Sun, 03 Jun 2018 13:43:34: 9000000 INFO @ Sun, 03 Jun 2018 13:43:34: 9000000 INFO @ Sun, 03 Jun 2018 13:43:39: 10000000 INFO @ Sun, 03 Jun 2018 13:43:40: 10000000 INFO @ Sun, 03 Jun 2018 13:43:41: 10000000 INFO @ Sun, 03 Jun 2018 13:43:46: 11000000 INFO @ Sun, 03 Jun 2018 13:43:46: 11000000 INFO @ Sun, 03 Jun 2018 13:43:48: 11000000 INFO @ Sun, 03 Jun 2018 13:43:52: 12000000 INFO @ Sun, 03 Jun 2018 13:43:52: 12000000 INFO @ Sun, 03 Jun 2018 13:43:54: 12000000 INFO @ Sun, 03 Jun 2018 13:43:59: 13000000 INFO @ Sun, 03 Jun 2018 13:43:59: 13000000 INFO @ Sun, 03 Jun 2018 13:44:01: 13000000 INFO @ Sun, 03 Jun 2018 13:44:05: 14000000 INFO @ Sun, 03 Jun 2018 13:44:06: 14000000 INFO @ Sun, 03 Jun 2018 13:44:08: 14000000 INFO @ Sun, 03 Jun 2018 13:44:11: 15000000 INFO @ Sun, 03 Jun 2018 13:44:12: 15000000 INFO @ Sun, 03 Jun 2018 13:44:14: 15000000 INFO @ Sun, 03 Jun 2018 13:44:18: 16000000 INFO @ Sun, 03 Jun 2018 13:44:19: 16000000 INFO @ Sun, 03 Jun 2018 13:44:21: 16000000 INFO @ Sun, 03 Jun 2018 13:44:24: 17000000 INFO @ Sun, 03 Jun 2018 13:44:26: 17000000 INFO @ Sun, 03 Jun 2018 13:44:28: 17000000 INFO @ Sun, 03 Jun 2018 13:44:30: 18000000 INFO @ Sun, 03 Jun 2018 13:44:32: 18000000 INFO @ Sun, 03 Jun 2018 13:44:34: 18000000 INFO @ Sun, 03 Jun 2018 13:44:36: 19000000 INFO @ Sun, 03 Jun 2018 13:44:39: 19000000 INFO @ Sun, 03 Jun 2018 13:44:41: 19000000 INFO @ Sun, 03 Jun 2018 13:44:43: 20000000 INFO @ Sun, 03 Jun 2018 13:44:46: 20000000 INFO @ Sun, 03 Jun 2018 13:44:48: 20000000 INFO @ Sun, 03 Jun 2018 13:44:49: 21000000 INFO @ Sun, 03 Jun 2018 13:44:52: 21000000 INFO @ Sun, 03 Jun 2018 13:44:54: 21000000 INFO @ Sun, 03 Jun 2018 13:44:55: 22000000 INFO @ Sun, 03 Jun 2018 13:44:59: 22000000 INFO @ Sun, 03 Jun 2018 13:45:01: 22000000 INFO @ Sun, 03 Jun 2018 13:45:01: 23000000 INFO @ Sun, 03 Jun 2018 13:45:06: 23000000 INFO @ Sun, 03 Jun 2018 13:45:08: 23000000 INFO @ Sun, 03 Jun 2018 13:45:08: 24000000 INFO @ Sun, 03 Jun 2018 13:45:12: 24000000 INFO @ Sun, 03 Jun 2018 13:45:14: 24000000 INFO @ Sun, 03 Jun 2018 13:45:14: 25000000 INFO @ Sun, 03 Jun 2018 13:45:19: 25000000 INFO @ Sun, 03 Jun 2018 13:45:21: 26000000 INFO @ Sun, 03 Jun 2018 13:45:21: 25000000 INFO @ Sun, 03 Jun 2018 13:45:26: 26000000 INFO @ Sun, 03 Jun 2018 13:45:27: 27000000 INFO @ Sun, 03 Jun 2018 13:45:27: 26000000 INFO @ Sun, 03 Jun 2018 13:45:32: 27000000 INFO @ Sun, 03 Jun 2018 13:45:33: 28000000 INFO @ Sun, 03 Jun 2018 13:45:34: 27000000 INFO @ Sun, 03 Jun 2018 13:45:39: 28000000 INFO @ Sun, 03 Jun 2018 13:45:39: 29000000 INFO @ Sun, 03 Jun 2018 13:45:41: 28000000 INFO @ Sun, 03 Jun 2018 13:45:46: 29000000 INFO @ Sun, 03 Jun 2018 13:45:46: 30000000 INFO @ Sun, 03 Jun 2018 13:45:47: 29000000 INFO @ Sun, 03 Jun 2018 13:45:51: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:45:51: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:45:51: #1 total tags in treatment: 13325548 INFO @ Sun, 03 Jun 2018 13:45:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:45:51: #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 13:45:51: #1 tags after filtering in treatment: 11187461 INFO @ Sun, 03 Jun 2018 13:45:51: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:45:51: #1 finished! INFO @ Sun, 03 Jun 2018 13:45:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:45:52: 30000000 INFO @ Sun, 03 Jun 2018 13:45:52: #2 number of paired peaks: 410 WARNING @ Sun, 03 Jun 2018 13:45:52: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Sun, 03 Jun 2018 13:45:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:45:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:45:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:45:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:45:52: #2 predicted fragment length is 109 bps INFO @ Sun, 03 Jun 2018 13:45:52: #2 alternative fragment length(s) may be 4,109 bps INFO @ Sun, 03 Jun 2018 13:45:52: #2.2 Generate R script for model : SRX4085398.10_model.r INFO @ Sun, 03 Jun 2018 13:45:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:45:53: 30000000 INFO @ Sun, 03 Jun 2018 13:45:57: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:45:57: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:45:57: #1 total tags in treatment: 13325548 INFO @ Sun, 03 Jun 2018 13:45:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:45:57: #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 13:45:57: #1 tags after filtering in treatment: 11187461 INFO @ Sun, 03 Jun 2018 13:45:57: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:45:57: #1 finished! INFO @ Sun, 03 Jun 2018 13:45:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:45:58: #2 number of paired peaks: 410 WARNING @ Sun, 03 Jun 2018 13:45:58: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Sun, 03 Jun 2018 13:45:58: start model_add_line... INFO @ Sun, 03 Jun 2018 13:45:58: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:45:58: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:45:58: #1 total tags in treatment: 13325548 INFO @ Sun, 03 Jun 2018 13:45:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:45:58: #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 13:45:58: start X-correlation... INFO @ Sun, 03 Jun 2018 13:45:58: end of X-cor INFO @ Sun, 03 Jun 2018 13:45:58: #2 finished! INFO @ Sun, 03 Jun 2018 13:45:58: #2 predicted fragment length is 109 bps INFO @ Sun, 03 Jun 2018 13:45:58: #2 alternative fragment length(s) may be 4,109 bps INFO @ Sun, 03 Jun 2018 13:45:58: #2.2 Generate R script for model : SRX4085398.20_model.r INFO @ Sun, 03 Jun 2018 13:45:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:45:58: #1 tags after filtering in treatment: 11187461 INFO @ Sun, 03 Jun 2018 13:45:58: #1 Redundant rate of treatment: 0.16 INFO @ Sun, 03 Jun 2018 13:45:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:45:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:45:59: #2 number of paired peaks: 410 WARNING @ Sun, 03 Jun 2018 13:45:59: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Sun, 03 Jun 2018 13:45:59: start model_add_line... INFO @ Sun, 03 Jun 2018 13:45:59: start X-correlation... INFO @ Sun, 03 Jun 2018 13:45:59: end of X-cor INFO @ Sun, 03 Jun 2018 13:45:59: #2 finished! INFO @ Sun, 03 Jun 2018 13:45:59: #2 predicted fragment length is 109 bps INFO @ Sun, 03 Jun 2018 13:45:59: #2 alternative fragment length(s) may be 4,109 bps INFO @ Sun, 03 Jun 2018 13:45:59: #2.2 Generate R script for model : SRX4085398.05_model.r INFO @ Sun, 03 Jun 2018 13:45:59: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:46:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:46:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:46:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:46:30: #4 Write output xls file... SRX4085398.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:46:30: #4 Write peak in narrowPeak format file... SRX4085398.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:46:30: #4 Write summits bed file... SRX4085398.10_summits.bed INFO @ Sun, 03 Jun 2018 13:46:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2042 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:46:35: #4 Write output xls file... SRX4085398.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:46:36: #4 Write peak in narrowPeak format file... SRX4085398.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:46:36: #4 Write summits bed file... SRX4085398.20_summits.bed INFO @ Sun, 03 Jun 2018 13:46:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:46:36: #4 Write output xls file... SRX4085398.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:46:36: #4 Write peak in narrowPeak format file... SRX4085398.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:46:36: #4 Write summits bed file... SRX4085398.05_summits.bed INFO @ Sun, 03 Jun 2018 13:46:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3996 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。