Job ID = 11158466 sra ファイルのダウンロード中... Completed: 3158407K bytes transferred in 31 seconds (824486K 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 37002202 spots for /home/okishinya/chipatlas/results/ce10/SRX4012480/SRR7082721.sra Written 37002202 spots for /home/okishinya/chipatlas/results/ce10/SRX4012480/SRR7082721.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: 01:35:56 37002202 reads; of these: 37002202 (100.00%) were paired; of these: 11021034 (29.78%) aligned concordantly 0 times 16648751 (44.99%) aligned concordantly exactly 1 time 9332417 (25.22%) aligned concordantly >1 times ---- 11021034 pairs aligned concordantly 0 times; of these: 699952 (6.35%) aligned discordantly 1 time ---- 10321082 pairs aligned 0 times concordantly or discordantly; of these: 20642164 mates make up the pairs; of these: 14071810 (68.17%) aligned 0 times 1724091 (8.35%) aligned exactly 1 time 4846263 (23.48%) aligned >1 times 80.99% overall alignment rate Time searching: 01:35:56 Overall time: 01:35:56 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] 9838433 / 26274500 = 0.3744 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 @ Tue, 04 Sep 2018 10:31:09: # Command line: callpeak -t SRX4012480.bam -f BAM -g ce -n SRX4012480.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4012480.10 # format = BAM # ChIP-seq file = ['SRX4012480.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 @ Tue, 04 Sep 2018 10:31:09: # Command line: callpeak -t SRX4012480.bam -f BAM -g ce -n SRX4012480.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4012480.20 # format = BAM # ChIP-seq file = ['SRX4012480.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 @ Tue, 04 Sep 2018 10:31:09: # Command line: callpeak -t SRX4012480.bam -f BAM -g ce -n SRX4012480.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4012480.05 # format = BAM # ChIP-seq file = ['SRX4012480.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 @ Tue, 04 Sep 2018 10:31:09: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:31:09: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:31:09: #1 read tag files... INFO @ Tue, 04 Sep 2018 10:31:09: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:31:09: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:31:09: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 10:31:17: 1000000 INFO @ Tue, 04 Sep 2018 10:31:17: 1000000 INFO @ Tue, 04 Sep 2018 10:31:17: 1000000 INFO @ Tue, 04 Sep 2018 10:31:26: 2000000 INFO @ Tue, 04 Sep 2018 10:31:26: 2000000 INFO @ Tue, 04 Sep 2018 10:31:26: 2000000 INFO @ Tue, 04 Sep 2018 10:31:35: 3000000 INFO @ Tue, 04 Sep 2018 10:31:35: 3000000 INFO @ Tue, 04 Sep 2018 10:31:35: 3000000 INFO @ Tue, 04 Sep 2018 10:31:44: 4000000 INFO @ Tue, 04 Sep 2018 10:31:44: 4000000 INFO @ Tue, 04 Sep 2018 10:31:44: 4000000 INFO @ Tue, 04 Sep 2018 10:31:53: 5000000 INFO @ Tue, 04 Sep 2018 10:31:53: 5000000 INFO @ Tue, 04 Sep 2018 10:31:53: 5000000 INFO @ Tue, 04 Sep 2018 10:32:02: 6000000 INFO @ Tue, 04 Sep 2018 10:32:02: 6000000 INFO @ Tue, 04 Sep 2018 10:32:02: 6000000 INFO @ Tue, 04 Sep 2018 10:32:11: 7000000 INFO @ Tue, 04 Sep 2018 10:32:11: 7000000 INFO @ Tue, 04 Sep 2018 10:32:11: 7000000 INFO @ Tue, 04 Sep 2018 10:32:20: 8000000 INFO @ Tue, 04 Sep 2018 10:32:20: 8000000 INFO @ Tue, 04 Sep 2018 10:32:20: 8000000 INFO @ Tue, 04 Sep 2018 10:32:29: 9000000 INFO @ Tue, 04 Sep 2018 10:32:29: 9000000 INFO @ Tue, 04 Sep 2018 10:32:29: 9000000 INFO @ Tue, 04 Sep 2018 10:32:38: 10000000 INFO @ Tue, 04 Sep 2018 10:32:38: 10000000 INFO @ Tue, 04 Sep 2018 10:32:38: 10000000 INFO @ Tue, 04 Sep 2018 10:32:47: 11000000 INFO @ Tue, 04 Sep 2018 10:32:47: 11000000 INFO @ Tue, 04 Sep 2018 10:32:47: 11000000 INFO @ Tue, 04 Sep 2018 10:32:56: 12000000 INFO @ Tue, 04 Sep 2018 10:32:56: 12000000 INFO @ Tue, 04 Sep 2018 10:32:56: 12000000 INFO @ Tue, 04 Sep 2018 10:33:05: 13000000 INFO @ Tue, 04 Sep 2018 10:33:05: 13000000 INFO @ Tue, 04 Sep 2018 10:33:05: 13000000 INFO @ Tue, 04 Sep 2018 10:33:13: 14000000 INFO @ Tue, 04 Sep 2018 10:33:13: 14000000 INFO @ Tue, 04 Sep 2018 10:33:13: 14000000 INFO @ Tue, 04 Sep 2018 10:33:22: 15000000 INFO @ Tue, 04 Sep 2018 10:33:22: 15000000 INFO @ Tue, 04 Sep 2018 10:33:22: 15000000 INFO @ Tue, 04 Sep 2018 10:33:31: 16000000 INFO @ Tue, 04 Sep 2018 10:33:31: 16000000 INFO @ Tue, 04 Sep 2018 10:33:31: 16000000 INFO @ Tue, 04 Sep 2018 10:33:40: 17000000 INFO @ Tue, 04 Sep 2018 10:33:40: 17000000 INFO @ Tue, 04 Sep 2018 10:33:40: 17000000 INFO @ Tue, 04 Sep 2018 10:33:49: 18000000 INFO @ Tue, 04 Sep 2018 10:33:49: 18000000 INFO @ Tue, 04 Sep 2018 10:33:49: 18000000 INFO @ Tue, 04 Sep 2018 10:33:58: 19000000 INFO @ Tue, 04 Sep 2018 10:33:58: 19000000 INFO @ Tue, 04 Sep 2018 10:33:58: 19000000 INFO @ Tue, 04 Sep 2018 10:34:07: 20000000 INFO @ Tue, 04 Sep 2018 10:34:07: 20000000 INFO @ Tue, 04 Sep 2018 10:34:07: 20000000 INFO @ Tue, 04 Sep 2018 10:34:16: 21000000 INFO @ Tue, 04 Sep 2018 10:34:16: 21000000 INFO @ Tue, 04 Sep 2018 10:34:16: 21000000 INFO @ Tue, 04 Sep 2018 10:34:25: 22000000 INFO @ Tue, 04 Sep 2018 10:34:25: 22000000 INFO @ Tue, 04 Sep 2018 10:34:25: 22000000 INFO @ Tue, 04 Sep 2018 10:34:34: 23000000 INFO @ Tue, 04 Sep 2018 10:34:34: 23000000 INFO @ Tue, 04 Sep 2018 10:34:34: 23000000 INFO @ Tue, 04 Sep 2018 10:34:43: 24000000 INFO @ Tue, 04 Sep 2018 10:34:43: 24000000 INFO @ Tue, 04 Sep 2018 10:34:43: 24000000 INFO @ Tue, 04 Sep 2018 10:34:51: 25000000 INFO @ Tue, 04 Sep 2018 10:34:51: 25000000 INFO @ Tue, 04 Sep 2018 10:34:51: 25000000 INFO @ Tue, 04 Sep 2018 10:35:00: 26000000 INFO @ Tue, 04 Sep 2018 10:35:00: 26000000 INFO @ Tue, 04 Sep 2018 10:35:00: 26000000 INFO @ Tue, 04 Sep 2018 10:35:09: 27000000 INFO @ Tue, 04 Sep 2018 10:35:09: 27000000 INFO @ Tue, 04 Sep 2018 10:35:09: 27000000 INFO @ Tue, 04 Sep 2018 10:35:18: 28000000 INFO @ Tue, 04 Sep 2018 10:35:18: 28000000 INFO @ Tue, 04 Sep 2018 10:35:18: 28000000 INFO @ Tue, 04 Sep 2018 10:35:27: 29000000 INFO @ Tue, 04 Sep 2018 10:35:27: 29000000 INFO @ Tue, 04 Sep 2018 10:35:27: 29000000 INFO @ Tue, 04 Sep 2018 10:35:36: 30000000 INFO @ Tue, 04 Sep 2018 10:35:36: 30000000 INFO @ Tue, 04 Sep 2018 10:35:36: 30000000 INFO @ Tue, 04 Sep 2018 10:35:45: 31000000 INFO @ Tue, 04 Sep 2018 10:35:45: 31000000 INFO @ Tue, 04 Sep 2018 10:35:45: 31000000 INFO @ Tue, 04 Sep 2018 10:35:53: 32000000 INFO @ Tue, 04 Sep 2018 10:35:53: 32000000 INFO @ Tue, 04 Sep 2018 10:35:53: 32000000 INFO @ Tue, 04 Sep 2018 10:36:02: 33000000 INFO @ Tue, 04 Sep 2018 10:36:02: 33000000 INFO @ Tue, 04 Sep 2018 10:36:02: 33000000 INFO @ Tue, 04 Sep 2018 10:36:11: 34000000 INFO @ Tue, 04 Sep 2018 10:36:11: 34000000 INFO @ Tue, 04 Sep 2018 10:36:11: 34000000 INFO @ Tue, 04 Sep 2018 10:36:20: 35000000 INFO @ Tue, 04 Sep 2018 10:36:20: 35000000 INFO @ Tue, 04 Sep 2018 10:36:20: 35000000 INFO @ Tue, 04 Sep 2018 10:36:29: 36000000 INFO @ Tue, 04 Sep 2018 10:36:29: 36000000 INFO @ Tue, 04 Sep 2018 10:36:29: 36000000 INFO @ Tue, 04 Sep 2018 10:36:37: 37000000 INFO @ Tue, 04 Sep 2018 10:36:37: 37000000 INFO @ Tue, 04 Sep 2018 10:36:37: 37000000 INFO @ Tue, 04 Sep 2018 10:36:46: 38000000 INFO @ Tue, 04 Sep 2018 10:36:46: 38000000 INFO @ Tue, 04 Sep 2018 10:36:46: 38000000 INFO @ Tue, 04 Sep 2018 10:36:55: 39000000 INFO @ Tue, 04 Sep 2018 10:36:55: 39000000 INFO @ Tue, 04 Sep 2018 10:36:55: 39000000 INFO @ Tue, 04 Sep 2018 10:37:04: 40000000 INFO @ Tue, 04 Sep 2018 10:37:04: 40000000 INFO @ Tue, 04 Sep 2018 10:37:04: 40000000 INFO @ Tue, 04 Sep 2018 10:37:06: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:37:06: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:37:06: #1 tag size is determined as 75 bps INFO @ Tue, 04 Sep 2018 10:37:06: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:37:06: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:37:06: #1 tag size = 75 INFO @ Tue, 04 Sep 2018 10:37:06: #1 total tags in treatment: 16224744 INFO @ Tue, 04 Sep 2018 10:37:06: #1 total tags in treatment: 16224744 INFO @ Tue, 04 Sep 2018 10:37:06: #1 total tags in treatment: 16224744 INFO @ Tue, 04 Sep 2018 10:37:06: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:37:06: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:37:06: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 10:37:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:37:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:37:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 10:37:06: #1 tags after filtering in treatment: 7078210 INFO @ Tue, 04 Sep 2018 10:37:06: #1 tags after filtering in treatment: 7078210 INFO @ Tue, 04 Sep 2018 10:37:06: #1 tags after filtering in treatment: 7078210 INFO @ Tue, 04 Sep 2018 10:37:06: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 04 Sep 2018 10:37:06: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 04 Sep 2018 10:37:06: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 04 Sep 2018 10:37:06: #1 finished! INFO @ Tue, 04 Sep 2018 10:37:06: #1 finished! INFO @ Tue, 04 Sep 2018 10:37:06: #1 finished! INFO @ Tue, 04 Sep 2018 10:37:06: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:37:06: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:37:06: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 10:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 10:37:08: #2 number of paired peaks: 6766 INFO @ Tue, 04 Sep 2018 10:37:08: start model_add_line... INFO @ Tue, 04 Sep 2018 10:37:08: #2 number of paired peaks: 6766 INFO @ Tue, 04 Sep 2018 10:37:08: start model_add_line... INFO @ Tue, 04 Sep 2018 10:37:08: #2 number of paired peaks: 6766 INFO @ Tue, 04 Sep 2018 10:37:08: start model_add_line... INFO @ Tue, 04 Sep 2018 10:37:08: start X-correlation... INFO @ Tue, 04 Sep 2018 10:37:08: start X-correlation... INFO @ Tue, 04 Sep 2018 10:37:08: start X-correlation... INFO @ Tue, 04 Sep 2018 10:37:08: end of X-cor INFO @ Tue, 04 Sep 2018 10:37:08: end of X-cor INFO @ Tue, 04 Sep 2018 10:37:08: #2 finished! INFO @ Tue, 04 Sep 2018 10:37:08: #2 finished! INFO @ Tue, 04 Sep 2018 10:37:08: end of X-cor INFO @ Tue, 04 Sep 2018 10:37:08: #2 finished! INFO @ Tue, 04 Sep 2018 10:37:08: #2 predicted fragment length is 342 bps INFO @ Tue, 04 Sep 2018 10:37:08: #2 predicted fragment length is 342 bps INFO @ Tue, 04 Sep 2018 10:37:08: #2 predicted fragment length is 342 bps INFO @ Tue, 04 Sep 2018 10:37:08: #2 alternative fragment length(s) may be 342 bps INFO @ Tue, 04 Sep 2018 10:37:08: #2 alternative fragment length(s) may be 342 bps INFO @ Tue, 04 Sep 2018 10:37:08: #2 alternative fragment length(s) may be 342 bps INFO @ Tue, 04 Sep 2018 10:37:08: #2.2 Generate R script for model : SRX4012480.20_model.r INFO @ Tue, 04 Sep 2018 10:37:08: #2.2 Generate R script for model : SRX4012480.05_model.r INFO @ Tue, 04 Sep 2018 10:37:08: #2.2 Generate R script for model : SRX4012480.10_model.r INFO @ Tue, 04 Sep 2018 10:37:08: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:37:08: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:37:08: #3 Call peaks... INFO @ Tue, 04 Sep 2018 10:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 10:37:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 04 Sep 2018 10:37:54: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:37:54: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:37:55: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 10:38:06: #4 Write output xls file... SRX4012480.20_peaks.xls INFO @ Tue, 04 Sep 2018 10:38:06: #4 Write peak in narrowPeak format file... SRX4012480.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:38:06: #4 Write summits bed file... SRX4012480.20_summits.bed INFO @ Tue, 04 Sep 2018 10:38:06: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5293 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:38:06: #4 Write output xls file... SRX4012480.10_peaks.xls INFO @ Tue, 04 Sep 2018 10:38:06: #4 Write peak in narrowPeak format file... SRX4012480.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:38:06: #4 Write summits bed file... SRX4012480.10_summits.bed INFO @ Tue, 04 Sep 2018 10:38:06: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6274 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 10:38:06: #4 Write output xls file... SRX4012480.05_peaks.xls INFO @ Tue, 04 Sep 2018 10:38:07: #4 Write peak in narrowPeak format file... SRX4012480.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 10:38:07: #4 Write summits bed file... SRX4012480.05_summits.bed INFO @ Tue, 04 Sep 2018 10:38:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7375 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。