Job ID = 10714523 sra ファイルのダウンロード中... Completed: 1425692K bytes transferred in 20 seconds (575428K 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 21680904 spots for /home/okishinya/chipatlas/results/ce10/SRX4085438/SRR7167467.sra Written 21680904 spots for /home/okishinya/chipatlas/results/ce10/SRX4085438/SRR7167467.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: 00:00:01 Multiseed full-index search: 00:18:06 21680904 reads; of these: 21680904 (100.00%) were paired; of these: 9300014 (42.89%) aligned concordantly 0 times 9825906 (45.32%) aligned concordantly exactly 1 time 2554984 (11.78%) aligned concordantly >1 times ---- 9300014 pairs aligned concordantly 0 times; of these: 179352 (1.93%) aligned discordantly 1 time ---- 9120662 pairs aligned 0 times concordantly or discordantly; of these: 18241324 mates make up the pairs; of these: 15033369 (82.41%) aligned 0 times 2803039 (15.37%) aligned exactly 1 time 404916 (2.22%) aligned >1 times 65.33% overall alignment rate Time searching: 00:18:07 Overall time: 00:18:07 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 12 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] 1941118 / 12497626 = 0.1553 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 13:36:24: # Command line: callpeak -t SRX4085438.bam -f BAM -g ce -n SRX4085438.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085438.20 # format = BAM # ChIP-seq file = ['SRX4085438.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 13:36:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:24: # Command line: callpeak -t SRX4085438.bam -f BAM -g ce -n SRX4085438.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085438.05 # format = BAM # ChIP-seq file = ['SRX4085438.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 13:36:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:24: # Command line: callpeak -t SRX4085438.bam -f BAM -g ce -n SRX4085438.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085438.10 # format = BAM # ChIP-seq file = ['SRX4085438.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 13:36:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:36:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:36:31: 1000000 INFO @ Sun, 03 Jun 2018 13:36:31: 1000000 INFO @ Sun, 03 Jun 2018 13:36:31: 1000000 INFO @ Sun, 03 Jun 2018 13:36:37: 2000000 INFO @ Sun, 03 Jun 2018 13:36:39: 2000000 INFO @ Sun, 03 Jun 2018 13:36:39: 2000000 INFO @ Sun, 03 Jun 2018 13:36:44: 3000000 INFO @ Sun, 03 Jun 2018 13:36:46: 3000000 INFO @ Sun, 03 Jun 2018 13:36:46: 3000000 INFO @ Sun, 03 Jun 2018 13:36:50: 4000000 INFO @ Sun, 03 Jun 2018 13:36:54: 4000000 INFO @ Sun, 03 Jun 2018 13:36:54: 4000000 INFO @ Sun, 03 Jun 2018 13:36:57: 5000000 INFO @ Sun, 03 Jun 2018 13:37:01: 5000000 INFO @ Sun, 03 Jun 2018 13:37:01: 5000000 INFO @ Sun, 03 Jun 2018 13:37:04: 6000000 INFO @ Sun, 03 Jun 2018 13:37:08: 6000000 INFO @ Sun, 03 Jun 2018 13:37:08: 6000000 INFO @ Sun, 03 Jun 2018 13:37:10: 7000000 INFO @ Sun, 03 Jun 2018 13:37:16: 7000000 INFO @ Sun, 03 Jun 2018 13:37:16: 7000000 INFO @ Sun, 03 Jun 2018 13:37:17: 8000000 INFO @ Sun, 03 Jun 2018 13:37:23: 8000000 INFO @ Sun, 03 Jun 2018 13:37:23: 8000000 INFO @ Sun, 03 Jun 2018 13:37:23: 9000000 INFO @ Sun, 03 Jun 2018 13:37:30: 10000000 INFO @ Sun, 03 Jun 2018 13:37:30: 9000000 INFO @ Sun, 03 Jun 2018 13:37:30: 9000000 INFO @ Sun, 03 Jun 2018 13:37:37: 11000000 INFO @ Sun, 03 Jun 2018 13:37:37: 10000000 INFO @ Sun, 03 Jun 2018 13:37:37: 10000000 INFO @ Sun, 03 Jun 2018 13:37:43: 12000000 INFO @ Sun, 03 Jun 2018 13:37:45: 11000000 INFO @ Sun, 03 Jun 2018 13:37:45: 11000000 INFO @ Sun, 03 Jun 2018 13:37:50: 13000000 INFO @ Sun, 03 Jun 2018 13:37:52: 12000000 INFO @ Sun, 03 Jun 2018 13:37:52: 12000000 INFO @ Sun, 03 Jun 2018 13:37:57: 14000000 INFO @ Sun, 03 Jun 2018 13:37:59: 13000000 INFO @ Sun, 03 Jun 2018 13:37:59: 13000000 INFO @ Sun, 03 Jun 2018 13:38:03: 15000000 INFO @ Sun, 03 Jun 2018 13:38:07: 14000000 INFO @ Sun, 03 Jun 2018 13:38:07: 14000000 INFO @ Sun, 03 Jun 2018 13:38:11: 16000000 INFO @ Sun, 03 Jun 2018 13:38:16: 15000000 INFO @ Sun, 03 Jun 2018 13:38:16: 15000000 INFO @ Sun, 03 Jun 2018 13:38:18: 17000000 INFO @ Sun, 03 Jun 2018 13:38:25: 16000000 INFO @ Sun, 03 Jun 2018 13:38:25: 16000000 INFO @ Sun, 03 Jun 2018 13:38:26: 18000000 INFO @ Sun, 03 Jun 2018 13:38:33: 19000000 INFO @ Sun, 03 Jun 2018 13:38:34: 17000000 INFO @ Sun, 03 Jun 2018 13:38:34: 17000000 INFO @ Sun, 03 Jun 2018 13:38:41: 20000000 INFO @ Sun, 03 Jun 2018 13:38:43: 18000000 INFO @ Sun, 03 Jun 2018 13:38:43: 18000000 INFO @ Sun, 03 Jun 2018 13:38:48: 21000000 INFO @ Sun, 03 Jun 2018 13:38:52: 19000000 INFO @ Sun, 03 Jun 2018 13:38:52: 19000000 INFO @ Sun, 03 Jun 2018 13:38:56: 22000000 INFO @ Sun, 03 Jun 2018 13:39:01: 20000000 INFO @ Sun, 03 Jun 2018 13:39:01: 20000000 INFO @ Sun, 03 Jun 2018 13:39:03: 23000000 INFO @ Sun, 03 Jun 2018 13:39:10: 21000000 INFO @ Sun, 03 Jun 2018 13:39:10: 21000000 INFO @ Sun, 03 Jun 2018 13:39:10: 24000000 INFO @ Sun, 03 Jun 2018 13:39:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:13: #1 total tags in treatment: 10451747 INFO @ Sun, 03 Jun 2018 13:39:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:13: #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 13:39:14: #1 tags after filtering in treatment: 8625575 INFO @ Sun, 03 Jun 2018 13:39:14: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:39:14: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:14: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:14: #2 number of paired peaks: 534 WARNING @ Sun, 03 Jun 2018 13:39:14: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:14: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:14: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:14: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:14: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:14: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 13:39:14: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 03 Jun 2018 13:39:14: #2.2 Generate R script for model : SRX4085438.10_model.r INFO @ Sun, 03 Jun 2018 13:39:14: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:19: 22000000 INFO @ Sun, 03 Jun 2018 13:39:19: 22000000 INFO @ Sun, 03 Jun 2018 13:39:28: 23000000 INFO @ Sun, 03 Jun 2018 13:39:28: 23000000 INFO @ Sun, 03 Jun 2018 13:39:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:35: 24000000 INFO @ Sun, 03 Jun 2018 13:39:35: 24000000 INFO @ Sun, 03 Jun 2018 13:39:38: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:38: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:38: #1 total tags in treatment: 10451747 INFO @ Sun, 03 Jun 2018 13:39:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:38: #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 13:39:38: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:39:38: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:39:38: #1 total tags in treatment: 10451747 INFO @ Sun, 03 Jun 2018 13:39:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:38: #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 13:39:38: #1 tags after filtering in treatment: 8625575 INFO @ Sun, 03 Jun 2018 13:39:38: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:39:38: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:38: #1 tags after filtering in treatment: 8625575 INFO @ Sun, 03 Jun 2018 13:39:38: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 03 Jun 2018 13:39:38: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:38: #2 number of paired peaks: 534 WARNING @ Sun, 03 Jun 2018 13:39:38: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:38: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:39: #2 number of paired peaks: 534 WARNING @ Sun, 03 Jun 2018 13:39:39: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Sun, 03 Jun 2018 13:39:39: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:39: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:39: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:39: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:39: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 13:39:39: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 03 Jun 2018 13:39:39: #2.2 Generate R script for model : SRX4085438.05_model.r INFO @ Sun, 03 Jun 2018 13:39:39: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:39: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:39: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:39: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:39: #2 predicted fragment length is 107 bps INFO @ Sun, 03 Jun 2018 13:39:39: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 03 Jun 2018 13:39:39: #2.2 Generate R script for model : SRX4085438.20_model.r INFO @ Sun, 03 Jun 2018 13:39:39: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:45: #4 Write output xls file... SRX4085438.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:39:45: #4 Write peak in narrowPeak format file... SRX4085438.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:39:45: #4 Write summits bed file... SRX4085438.10_summits.bed INFO @ Sun, 03 Jun 2018 13:39:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2855 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:39:58: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:39:59: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:08: #4 Write output xls file... SRX4085438.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:08: #4 Write peak in narrowPeak format file... SRX4085438.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:08: #4 Write summits bed file... SRX4085438.20_summits.bed INFO @ Sun, 03 Jun 2018 13:40:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1490 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:10: #4 Write output xls file... SRX4085438.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:10: #4 Write peak in narrowPeak format file... SRX4085438.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:10: #4 Write summits bed file... SRX4085438.05_summits.bed INFO @ Sun, 03 Jun 2018 13:40:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4494 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。