Job ID = 10714521 sra ファイルのダウンロード中... Completed: 1564184K bytes transferred in 20 seconds (640077K 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 24333421 spots for /home/okishinya/chipatlas/results/ce10/SRX4085436/SRR7167465.sra Written 24333421 spots for /home/okishinya/chipatlas/results/ce10/SRX4085436/SRR7167465.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: 00:12:39 24333421 reads; of these: 24333421 (100.00%) were paired; of these: 16443540 (67.58%) aligned concordantly 0 times 6714181 (27.59%) aligned concordantly exactly 1 time 1175700 (4.83%) aligned concordantly >1 times ---- 16443540 pairs aligned concordantly 0 times; of these: 102618 (0.62%) aligned discordantly 1 time ---- 16340922 pairs aligned 0 times concordantly or discordantly; of these: 32681844 mates make up the pairs; of these: 29132745 (89.14%) aligned 0 times 3095141 (9.47%) aligned exactly 1 time 453958 (1.39%) aligned >1 times 40.14% overall alignment rate Time searching: 00:12:39 Overall time: 00:12:39 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 8 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] 3290826 / 7957974 = 0.4135 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 13:25:17: # Command line: callpeak -t SRX4085436.bam -f BAM -g ce -n SRX4085436.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085436.05 # format = BAM # ChIP-seq file = ['SRX4085436.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 13:25:17: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:25:17: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:25:17: # Command line: callpeak -t SRX4085436.bam -f BAM -g ce -n SRX4085436.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085436.10 # format = BAM # ChIP-seq file = ['SRX4085436.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 13:25:17: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:25:17: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:25:17: # Command line: callpeak -t SRX4085436.bam -f BAM -g ce -n SRX4085436.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085436.20 # format = BAM # ChIP-seq file = ['SRX4085436.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 13:25:17: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:25:17: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:25:24: 1000000 INFO @ Sun, 03 Jun 2018 13:25:24: 1000000 INFO @ Sun, 03 Jun 2018 13:25:24: 1000000 INFO @ Sun, 03 Jun 2018 13:25:30: 2000000 INFO @ Sun, 03 Jun 2018 13:25:31: 2000000 INFO @ Sun, 03 Jun 2018 13:25:31: 2000000 INFO @ Sun, 03 Jun 2018 13:25:37: 3000000 INFO @ Sun, 03 Jun 2018 13:25:37: 3000000 INFO @ Sun, 03 Jun 2018 13:25:37: 3000000 INFO @ Sun, 03 Jun 2018 13:25:44: 4000000 INFO @ Sun, 03 Jun 2018 13:25:44: 4000000 INFO @ Sun, 03 Jun 2018 13:25:44: 4000000 INFO @ Sun, 03 Jun 2018 13:25:51: 5000000 INFO @ Sun, 03 Jun 2018 13:25:51: 5000000 INFO @ Sun, 03 Jun 2018 13:25:51: 5000000 INFO @ Sun, 03 Jun 2018 13:25:57: 6000000 INFO @ Sun, 03 Jun 2018 13:25:57: 6000000 INFO @ Sun, 03 Jun 2018 13:25:57: 6000000 INFO @ Sun, 03 Jun 2018 13:26:04: 7000000 INFO @ Sun, 03 Jun 2018 13:26:04: 7000000 INFO @ Sun, 03 Jun 2018 13:26:04: 7000000 INFO @ Sun, 03 Jun 2018 13:26:10: 8000000 INFO @ Sun, 03 Jun 2018 13:26:11: 8000000 INFO @ Sun, 03 Jun 2018 13:26:11: 8000000 INFO @ Sun, 03 Jun 2018 13:26:17: 9000000 INFO @ Sun, 03 Jun 2018 13:26:18: 9000000 INFO @ Sun, 03 Jun 2018 13:26:18: 9000000 INFO @ Sun, 03 Jun 2018 13:26:23: 10000000 INFO @ Sun, 03 Jun 2018 13:26:24: 10000000 INFO @ Sun, 03 Jun 2018 13:26:25: 10000000 INFO @ Sun, 03 Jun 2018 13:26:30: 11000000 INFO @ Sun, 03 Jun 2018 13:26:31: 11000000 INFO @ Sun, 03 Jun 2018 13:26:31: 11000000 INFO @ Sun, 03 Jun 2018 13:26:37: 12000000 INFO @ Sun, 03 Jun 2018 13:26:38: 12000000 INFO @ Sun, 03 Jun 2018 13:26:38: 12000000 INFO @ Sun, 03 Jun 2018 13:26:43: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:26:43: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:26:43: #1 total tags in treatment: 4621699 INFO @ Sun, 03 Jun 2018 13:26:43: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:26:43: #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 13:26:43: #1 tags after filtering in treatment: 4238505 INFO @ Sun, 03 Jun 2018 13:26:43: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 13:26:43: #1 finished! INFO @ Sun, 03 Jun 2018 13:26:43: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:26:43: #2 number of paired peaks: 428 WARNING @ Sun, 03 Jun 2018 13:26:43: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sun, 03 Jun 2018 13:26:43: start model_add_line... INFO @ Sun, 03 Jun 2018 13:26:43: start X-correlation... INFO @ Sun, 03 Jun 2018 13:26:43: end of X-cor INFO @ Sun, 03 Jun 2018 13:26:43: #2 finished! INFO @ Sun, 03 Jun 2018 13:26:43: #2 predicted fragment length is 135 bps INFO @ Sun, 03 Jun 2018 13:26:43: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 03 Jun 2018 13:26:43: #2.2 Generate R script for model : SRX4085436.20_model.r INFO @ Sun, 03 Jun 2018 13:26:43: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:26:44: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:26:44: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:26:44: #1 total tags in treatment: 4621699 INFO @ Sun, 03 Jun 2018 13:26:44: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:26:44: #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 13:26:44: #1 tags after filtering in treatment: 4238505 INFO @ Sun, 03 Jun 2018 13:26:44: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 13:26:44: #1 finished! INFO @ Sun, 03 Jun 2018 13:26:44: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:26:45: #2 number of paired peaks: 428 WARNING @ Sun, 03 Jun 2018 13:26:45: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sun, 03 Jun 2018 13:26:45: start model_add_line... INFO @ Sun, 03 Jun 2018 13:26:45: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:26:45: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:26:45: #1 total tags in treatment: 4621699 INFO @ Sun, 03 Jun 2018 13:26:45: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:26:45: #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 13:26:45: start X-correlation... INFO @ Sun, 03 Jun 2018 13:26:45: end of X-cor INFO @ Sun, 03 Jun 2018 13:26:45: #2 finished! INFO @ Sun, 03 Jun 2018 13:26:45: #2 predicted fragment length is 135 bps INFO @ Sun, 03 Jun 2018 13:26:45: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 03 Jun 2018 13:26:45: #2.2 Generate R script for model : SRX4085436.05_model.r INFO @ Sun, 03 Jun 2018 13:26:45: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:26:45: #1 tags after filtering in treatment: 4238505 INFO @ Sun, 03 Jun 2018 13:26:45: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 13:26:45: #1 finished! INFO @ Sun, 03 Jun 2018 13:26:45: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:26:45: #2 number of paired peaks: 428 WARNING @ Sun, 03 Jun 2018 13:26:45: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sun, 03 Jun 2018 13:26:45: start model_add_line... INFO @ Sun, 03 Jun 2018 13:26:45: start X-correlation... INFO @ Sun, 03 Jun 2018 13:26:45: end of X-cor INFO @ Sun, 03 Jun 2018 13:26:45: #2 finished! INFO @ Sun, 03 Jun 2018 13:26:45: #2 predicted fragment length is 135 bps INFO @ Sun, 03 Jun 2018 13:26:45: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 03 Jun 2018 13:26:45: #2.2 Generate R script for model : SRX4085436.10_model.r INFO @ Sun, 03 Jun 2018 13:26:45: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:26:54: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:26:55: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:26:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:27:00: #4 Write output xls file... SRX4085436.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:27:00: #4 Write peak in narrowPeak format file... SRX4085436.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:27:00: #4 Write summits bed file... SRX4085436.20_summits.bed INFO @ Sun, 03 Jun 2018 13:27:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:27:01: #4 Write output xls file... SRX4085436.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:27:01: #4 Write peak in narrowPeak format file... SRX4085436.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:27:01: #4 Write summits bed file... SRX4085436.05_summits.bed INFO @ Sun, 03 Jun 2018 13:27:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:27:01: #4 Write output xls file... SRX4085436.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:27:01: #4 Write peak in narrowPeak format file... SRX4085436.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:27:01: #4 Write summits bed file... SRX4085436.10_summits.bed INFO @ Sun, 03 Jun 2018 13:27:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (313 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。