Job ID = 1295000 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T02:21:47 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 44,627,620 reads read : 89,255,240 reads written : 89,255,240 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 01:18:38 44627620 reads; of these: 44627620 (100.00%) were paired; of these: 15987250 (35.82%) aligned concordantly 0 times 16163625 (36.22%) aligned concordantly exactly 1 time 12476745 (27.96%) aligned concordantly >1 times ---- 15987250 pairs aligned concordantly 0 times; of these: 444049 (2.78%) aligned discordantly 1 time ---- 15543201 pairs aligned 0 times concordantly or discordantly; of these: 31086402 mates make up the pairs; of these: 20380690 (65.56%) aligned 0 times 7256032 (23.34%) aligned exactly 1 time 3449680 (11.10%) aligned >1 times 77.17% overall alignment rate Time searching: 01:18:38 Overall time: 01:18:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 13751414 / 28647532 = 0.4800 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 @ Mon, 03 Jun 2019 13:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 13:03:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:03:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 13:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 13:03:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:03:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:03:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:03:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:03:06: 1000000 INFO @ Mon, 03 Jun 2019 13:03:07: 1000000 INFO @ Mon, 03 Jun 2019 13:03:07: 1000000 INFO @ Mon, 03 Jun 2019 13:03:11: 2000000 INFO @ Mon, 03 Jun 2019 13:03:14: 2000000 INFO @ Mon, 03 Jun 2019 13:03:14: 2000000 INFO @ Mon, 03 Jun 2019 13:03:17: 3000000 INFO @ Mon, 03 Jun 2019 13:03:20: 3000000 INFO @ Mon, 03 Jun 2019 13:03:20: 3000000 INFO @ Mon, 03 Jun 2019 13:03:23: 4000000 INFO @ Mon, 03 Jun 2019 13:03:27: 4000000 INFO @ Mon, 03 Jun 2019 13:03:27: 4000000 INFO @ Mon, 03 Jun 2019 13:03:29: 5000000 INFO @ Mon, 03 Jun 2019 13:03:34: 6000000 INFO @ Mon, 03 Jun 2019 13:03:34: 5000000 INFO @ Mon, 03 Jun 2019 13:03:34: 5000000 INFO @ Mon, 03 Jun 2019 13:03:40: 7000000 INFO @ Mon, 03 Jun 2019 13:03:41: 6000000 INFO @ Mon, 03 Jun 2019 13:03:41: 6000000 INFO @ Mon, 03 Jun 2019 13:03:46: 8000000 INFO @ Mon, 03 Jun 2019 13:03:48: 7000000 INFO @ Mon, 03 Jun 2019 13:03:48: 7000000 INFO @ Mon, 03 Jun 2019 13:03:51: 9000000 INFO @ Mon, 03 Jun 2019 13:03:55: 8000000 INFO @ Mon, 03 Jun 2019 13:03:55: 8000000 INFO @ Mon, 03 Jun 2019 13:03:57: 10000000 INFO @ Mon, 03 Jun 2019 13:04:01: 9000000 INFO @ Mon, 03 Jun 2019 13:04:02: 9000000 INFO @ Mon, 03 Jun 2019 13:04:03: 11000000 INFO @ Mon, 03 Jun 2019 13:04:08: 10000000 INFO @ Mon, 03 Jun 2019 13:04:08: 10000000 INFO @ Mon, 03 Jun 2019 13:04:09: 12000000 INFO @ Mon, 03 Jun 2019 13:04:14: 13000000 INFO @ Mon, 03 Jun 2019 13:04:15: 11000000 INFO @ Mon, 03 Jun 2019 13:04:15: 11000000 INFO @ Mon, 03 Jun 2019 13:04:20: 14000000 INFO @ Mon, 03 Jun 2019 13:04:21: 12000000 INFO @ Mon, 03 Jun 2019 13:04:22: 12000000 INFO @ Mon, 03 Jun 2019 13:04:26: 15000000 INFO @ Mon, 03 Jun 2019 13:04:28: 13000000 INFO @ Mon, 03 Jun 2019 13:04:28: 13000000 INFO @ Mon, 03 Jun 2019 13:04:31: 16000000 INFO @ Mon, 03 Jun 2019 13:04:34: 14000000 INFO @ Mon, 03 Jun 2019 13:04:34: 14000000 INFO @ Mon, 03 Jun 2019 13:04:37: 17000000 INFO @ Mon, 03 Jun 2019 13:04:41: 15000000 INFO @ Mon, 03 Jun 2019 13:04:41: 15000000 INFO @ Mon, 03 Jun 2019 13:04:43: 18000000 INFO @ Mon, 03 Jun 2019 13:04:47: 16000000 INFO @ Mon, 03 Jun 2019 13:04:47: 16000000 INFO @ Mon, 03 Jun 2019 13:04:48: 19000000 INFO @ Mon, 03 Jun 2019 13:04:53: 17000000 INFO @ Mon, 03 Jun 2019 13:04:54: 17000000 INFO @ Mon, 03 Jun 2019 13:04:54: 20000000 INFO @ Mon, 03 Jun 2019 13:05:00: 21000000 INFO @ Mon, 03 Jun 2019 13:05:00: 18000000 INFO @ Mon, 03 Jun 2019 13:05:00: 18000000 INFO @ Mon, 03 Jun 2019 13:05:05: 22000000 INFO @ Mon, 03 Jun 2019 13:05:06: 19000000 INFO @ Mon, 03 Jun 2019 13:05:06: 19000000 INFO @ Mon, 03 Jun 2019 13:05:11: 23000000 INFO @ Mon, 03 Jun 2019 13:05:12: 20000000 INFO @ Mon, 03 Jun 2019 13:05:13: 20000000 INFO @ Mon, 03 Jun 2019 13:05:16: 24000000 INFO @ Mon, 03 Jun 2019 13:05:19: 21000000 INFO @ Mon, 03 Jun 2019 13:05:19: 21000000 INFO @ Mon, 03 Jun 2019 13:05:22: 25000000 INFO @ Mon, 03 Jun 2019 13:05:25: 22000000 INFO @ Mon, 03 Jun 2019 13:05:25: 22000000 INFO @ Mon, 03 Jun 2019 13:05:28: 26000000 INFO @ Mon, 03 Jun 2019 13:05:31: 23000000 INFO @ Mon, 03 Jun 2019 13:05:32: 23000000 INFO @ Mon, 03 Jun 2019 13:05:33: 27000000 INFO @ Mon, 03 Jun 2019 13:05:37: 24000000 INFO @ Mon, 03 Jun 2019 13:05:38: 24000000 INFO @ Mon, 03 Jun 2019 13:05:39: 28000000 INFO @ Mon, 03 Jun 2019 13:05:44: 25000000 INFO @ Mon, 03 Jun 2019 13:05:44: 25000000 INFO @ Mon, 03 Jun 2019 13:05:45: 29000000 INFO @ Mon, 03 Jun 2019 13:05:50: 26000000 INFO @ Mon, 03 Jun 2019 13:05:50: 26000000 INFO @ Mon, 03 Jun 2019 13:05:51: 30000000 INFO @ Mon, 03 Jun 2019 13:05:56: 27000000 INFO @ Mon, 03 Jun 2019 13:05:56: 31000000 INFO @ Mon, 03 Jun 2019 13:05:57: 27000000 INFO @ Mon, 03 Jun 2019 13:06:02: 32000000 INFO @ Mon, 03 Jun 2019 13:06:03: 28000000 INFO @ Mon, 03 Jun 2019 13:06:03: 28000000 INFO @ Mon, 03 Jun 2019 13:06:08: 33000000 INFO @ Mon, 03 Jun 2019 13:06:09: 29000000 INFO @ Mon, 03 Jun 2019 13:06:09: 29000000 INFO @ Mon, 03 Jun 2019 13:06:13: 34000000 INFO @ Mon, 03 Jun 2019 13:06:15: 30000000 INFO @ Mon, 03 Jun 2019 13:06:16: 30000000 INFO @ Mon, 03 Jun 2019 13:06:19: 35000000 INFO @ Mon, 03 Jun 2019 13:06:21: 31000000 INFO @ Mon, 03 Jun 2019 13:06:22: 31000000 INFO @ Mon, 03 Jun 2019 13:06:25: 36000000 INFO @ Mon, 03 Jun 2019 13:06:28: 32000000 INFO @ Mon, 03 Jun 2019 13:06:28: 32000000 INFO @ Mon, 03 Jun 2019 13:06:31: 37000000 INFO @ Mon, 03 Jun 2019 13:06:34: 33000000 INFO @ Mon, 03 Jun 2019 13:06:35: 33000000 INFO @ Mon, 03 Jun 2019 13:06:36: 38000000 INFO @ Mon, 03 Jun 2019 13:06:40: 34000000 INFO @ Mon, 03 Jun 2019 13:06:41: 34000000 INFO @ Mon, 03 Jun 2019 13:06:42: 39000000 INFO @ Mon, 03 Jun 2019 13:06:46: 35000000 INFO @ Mon, 03 Jun 2019 13:06:48: 35000000 INFO @ Mon, 03 Jun 2019 13:06:48: 40000000 INFO @ Mon, 03 Jun 2019 13:06:53: 36000000 INFO @ Mon, 03 Jun 2019 13:06:54: 41000000 INFO @ Mon, 03 Jun 2019 13:06:54: 36000000 INFO @ Mon, 03 Jun 2019 13:06:56: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 13:06:56: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 13:06:56: #1 total tags in treatment: 14926395 INFO @ Mon, 03 Jun 2019 13:06:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:06:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:06:57: #1 tags after filtering in treatment: 9024311 INFO @ Mon, 03 Jun 2019 13:06:57: #1 Redundant rate of treatment: 0.40 INFO @ Mon, 03 Jun 2019 13:06:57: #1 finished! INFO @ Mon, 03 Jun 2019 13:06:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:06:58: #2 number of paired peaks: 1848 INFO @ Mon, 03 Jun 2019 13:06:58: start model_add_line... INFO @ Mon, 03 Jun 2019 13:06:58: start X-correlation... INFO @ Mon, 03 Jun 2019 13:06:58: end of X-cor INFO @ Mon, 03 Jun 2019 13:06:58: #2 finished! INFO @ Mon, 03 Jun 2019 13:06:58: #2 predicted fragment length is 88 bps INFO @ Mon, 03 Jun 2019 13:06:58: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 03 Jun 2019 13:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.10_model.r INFO @ Mon, 03 Jun 2019 13:06:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:06:59: 37000000 INFO @ Mon, 03 Jun 2019 13:07:00: 37000000 INFO @ Mon, 03 Jun 2019 13:07:05: 38000000 INFO @ Mon, 03 Jun 2019 13:07:06: 38000000 INFO @ Mon, 03 Jun 2019 13:07:11: 39000000 INFO @ Mon, 03 Jun 2019 13:07:13: 39000000 INFO @ Mon, 03 Jun 2019 13:07:17: 40000000 INFO @ Mon, 03 Jun 2019 13:07:19: 40000000 INFO @ Mon, 03 Jun 2019 13:07:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:07:23: 41000000 INFO @ Mon, 03 Jun 2019 13:07:25: 41000000 INFO @ Mon, 03 Jun 2019 13:07:26: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 13:07:26: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 13:07:26: #1 total tags in treatment: 14926395 INFO @ Mon, 03 Jun 2019 13:07:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:07:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:07:26: #1 tags after filtering in treatment: 9024311 INFO @ Mon, 03 Jun 2019 13:07:26: #1 Redundant rate of treatment: 0.40 INFO @ Mon, 03 Jun 2019 13:07:26: #1 finished! INFO @ Mon, 03 Jun 2019 13:07:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:07:27: #2 number of paired peaks: 1848 INFO @ Mon, 03 Jun 2019 13:07:27: start model_add_line... INFO @ Mon, 03 Jun 2019 13:07:27: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 13:07:27: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 13:07:27: #1 total tags in treatment: 14926395 INFO @ Mon, 03 Jun 2019 13:07:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:07:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:07:27: start X-correlation... INFO @ Mon, 03 Jun 2019 13:07:27: end of X-cor INFO @ Mon, 03 Jun 2019 13:07:27: #2 finished! INFO @ Mon, 03 Jun 2019 13:07:27: #2 predicted fragment length is 88 bps INFO @ Mon, 03 Jun 2019 13:07:27: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 03 Jun 2019 13:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.05_model.r INFO @ Mon, 03 Jun 2019 13:07:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:07:28: #1 tags after filtering in treatment: 9024311 INFO @ Mon, 03 Jun 2019 13:07:28: #1 Redundant rate of treatment: 0.40 INFO @ Mon, 03 Jun 2019 13:07:28: #1 finished! INFO @ Mon, 03 Jun 2019 13:07:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:07:29: #2 number of paired peaks: 1848 INFO @ Mon, 03 Jun 2019 13:07:29: start model_add_line... INFO @ Mon, 03 Jun 2019 13:07:29: start X-correlation... INFO @ Mon, 03 Jun 2019 13:07:29: end of X-cor INFO @ Mon, 03 Jun 2019 13:07:29: #2 finished! INFO @ Mon, 03 Jun 2019 13:07:29: #2 predicted fragment length is 88 bps INFO @ Mon, 03 Jun 2019 13:07:29: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 03 Jun 2019 13:07:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.20_model.r INFO @ Mon, 03 Jun 2019 13:07:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:07:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:07:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.10_summits.bed INFO @ Mon, 03 Jun 2019 13:07:37: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (15475 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:07:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:07:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:08:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.05_summits.bed INFO @ Mon, 03 Jun 2019 13:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300934/SRX300934.20_summits.bed INFO @ Mon, 03 Jun 2019 13:08:08: Done! INFO @ Mon, 03 Jun 2019 13:08:08: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3230 records, 4 fields): 11 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (28626 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。