Job ID = 1294997 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T02:08:20 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 ) 2019-06-03T02:08:20 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 ) 2019-06-03T02:08:20 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 : 29,453,482 reads read : 58,906,964 reads written : 58,906,964 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:44:28 29453482 reads; of these: 29453482 (100.00%) were paired; of these: 9889001 (33.57%) aligned concordantly 0 times 13568923 (46.07%) aligned concordantly exactly 1 time 5995558 (20.36%) aligned concordantly >1 times ---- 9889001 pairs aligned concordantly 0 times; of these: 239999 (2.43%) aligned discordantly 1 time ---- 9649002 pairs aligned 0 times concordantly or discordantly; of these: 19298004 mates make up the pairs; of these: 11865963 (61.49%) aligned 0 times 5097836 (26.42%) aligned exactly 1 time 2334205 (12.10%) aligned >1 times 79.86% overall alignment rate Time searching: 00:44:29 Overall time: 00:44:29 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 12 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] 3665035 / 19591369 = 0.1871 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 12:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.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 12:17:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.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 12:17:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.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 12:17:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:07: 1000000 INFO @ Mon, 03 Jun 2019 12:17:08: 1000000 INFO @ Mon, 03 Jun 2019 12:17:08: 1000000 INFO @ Mon, 03 Jun 2019 12:17:13: 2000000 INFO @ Mon, 03 Jun 2019 12:17:14: 2000000 INFO @ Mon, 03 Jun 2019 12:17:14: 2000000 INFO @ Mon, 03 Jun 2019 12:17:19: 3000000 INFO @ Mon, 03 Jun 2019 12:17:20: 3000000 INFO @ Mon, 03 Jun 2019 12:17:20: 3000000 INFO @ Mon, 03 Jun 2019 12:17:25: 4000000 INFO @ Mon, 03 Jun 2019 12:17:25: 4000000 INFO @ Mon, 03 Jun 2019 12:17:27: 4000000 INFO @ Mon, 03 Jun 2019 12:17:31: 5000000 INFO @ Mon, 03 Jun 2019 12:17:31: 5000000 INFO @ Mon, 03 Jun 2019 12:17:33: 5000000 INFO @ Mon, 03 Jun 2019 12:17:37: 6000000 INFO @ Mon, 03 Jun 2019 12:17:37: 6000000 INFO @ Mon, 03 Jun 2019 12:17:39: 6000000 INFO @ Mon, 03 Jun 2019 12:17:43: 7000000 INFO @ Mon, 03 Jun 2019 12:17:44: 7000000 INFO @ Mon, 03 Jun 2019 12:17:45: 7000000 INFO @ Mon, 03 Jun 2019 12:17:49: 8000000 INFO @ Mon, 03 Jun 2019 12:17:49: 8000000 INFO @ Mon, 03 Jun 2019 12:17:51: 8000000 INFO @ Mon, 03 Jun 2019 12:17:54: 9000000 INFO @ Mon, 03 Jun 2019 12:17:55: 9000000 INFO @ Mon, 03 Jun 2019 12:17:58: 9000000 INFO @ Mon, 03 Jun 2019 12:18:00: 10000000 INFO @ Mon, 03 Jun 2019 12:18:01: 10000000 INFO @ Mon, 03 Jun 2019 12:18:04: 10000000 INFO @ Mon, 03 Jun 2019 12:18:06: 11000000 INFO @ Mon, 03 Jun 2019 12:18:07: 11000000 INFO @ Mon, 03 Jun 2019 12:18:10: 11000000 INFO @ Mon, 03 Jun 2019 12:18:12: 12000000 INFO @ Mon, 03 Jun 2019 12:18:14: 12000000 INFO @ Mon, 03 Jun 2019 12:18:17: 12000000 INFO @ Mon, 03 Jun 2019 12:18:18: 13000000 INFO @ Mon, 03 Jun 2019 12:18:20: 13000000 INFO @ Mon, 03 Jun 2019 12:18:23: 13000000 INFO @ Mon, 03 Jun 2019 12:18:24: 14000000 INFO @ Mon, 03 Jun 2019 12:18:26: 14000000 INFO @ Mon, 03 Jun 2019 12:18:29: 14000000 INFO @ Mon, 03 Jun 2019 12:18:29: 15000000 INFO @ Mon, 03 Jun 2019 12:18:32: 15000000 INFO @ Mon, 03 Jun 2019 12:18:35: 16000000 INFO @ Mon, 03 Jun 2019 12:18:35: 15000000 INFO @ Mon, 03 Jun 2019 12:18:38: 16000000 INFO @ Mon, 03 Jun 2019 12:18:41: 17000000 INFO @ Mon, 03 Jun 2019 12:18:41: 16000000 INFO @ Mon, 03 Jun 2019 12:18:44: 17000000 INFO @ Mon, 03 Jun 2019 12:18:46: 18000000 INFO @ Mon, 03 Jun 2019 12:18:48: 17000000 INFO @ Mon, 03 Jun 2019 12:18:49: 18000000 INFO @ Mon, 03 Jun 2019 12:18:52: 19000000 INFO @ Mon, 03 Jun 2019 12:18:54: 18000000 INFO @ Mon, 03 Jun 2019 12:18:55: 19000000 INFO @ Mon, 03 Jun 2019 12:18:58: 20000000 INFO @ Mon, 03 Jun 2019 12:19:00: 19000000 INFO @ Mon, 03 Jun 2019 12:19:01: 20000000 INFO @ Mon, 03 Jun 2019 12:19:04: 21000000 INFO @ Mon, 03 Jun 2019 12:19:06: 20000000 INFO @ Mon, 03 Jun 2019 12:19:07: 21000000 INFO @ Mon, 03 Jun 2019 12:19:09: 22000000 INFO @ Mon, 03 Jun 2019 12:19:12: 21000000 INFO @ Mon, 03 Jun 2019 12:19:13: 22000000 INFO @ Mon, 03 Jun 2019 12:19:15: 23000000 INFO @ Mon, 03 Jun 2019 12:19:18: 22000000 INFO @ Mon, 03 Jun 2019 12:19:19: 23000000 INFO @ Mon, 03 Jun 2019 12:19:21: 24000000 INFO @ Mon, 03 Jun 2019 12:19:24: 24000000 INFO @ Mon, 03 Jun 2019 12:19:25: 23000000 INFO @ Mon, 03 Jun 2019 12:19:26: 25000000 INFO @ Mon, 03 Jun 2019 12:19:31: 25000000 INFO @ Mon, 03 Jun 2019 12:19:31: 24000000 INFO @ Mon, 03 Jun 2019 12:19:32: 26000000 INFO @ Mon, 03 Jun 2019 12:19:37: 25000000 INFO @ Mon, 03 Jun 2019 12:19:38: 26000000 INFO @ Mon, 03 Jun 2019 12:19:38: 27000000 INFO @ Mon, 03 Jun 2019 12:19:44: 26000000 INFO @ Mon, 03 Jun 2019 12:19:44: 27000000 INFO @ Mon, 03 Jun 2019 12:19:44: 28000000 INFO @ Mon, 03 Jun 2019 12:19:49: 28000000 INFO @ Mon, 03 Jun 2019 12:19:50: 27000000 INFO @ Mon, 03 Jun 2019 12:19:50: 29000000 INFO @ Mon, 03 Jun 2019 12:19:55: 29000000 INFO @ Mon, 03 Jun 2019 12:19:55: 30000000 INFO @ Mon, 03 Jun 2019 12:19:56: 28000000 INFO @ Mon, 03 Jun 2019 12:20:01: 31000000 INFO @ Mon, 03 Jun 2019 12:20:01: 30000000 INFO @ Mon, 03 Jun 2019 12:20:02: 29000000 INFO @ Mon, 03 Jun 2019 12:20:07: 32000000 INFO @ Mon, 03 Jun 2019 12:20:07: 31000000 INFO @ Mon, 03 Jun 2019 12:20:08: 30000000 INFO @ Mon, 03 Jun 2019 12:20:12: 33000000 INFO @ Mon, 03 Jun 2019 12:20:13: 32000000 INFO @ Mon, 03 Jun 2019 12:20:14: 31000000 INFO @ Mon, 03 Jun 2019 12:20:18: 34000000 INFO @ Mon, 03 Jun 2019 12:20:18: 33000000 INFO @ Mon, 03 Jun 2019 12:20:20: 32000000 INFO @ Mon, 03 Jun 2019 12:20:23: 35000000 INFO @ Mon, 03 Jun 2019 12:20:24: 34000000 INFO @ Mon, 03 Jun 2019 12:20:26: 33000000 INFO @ Mon, 03 Jun 2019 12:20:29: 36000000 INFO @ Mon, 03 Jun 2019 12:20:30: 35000000 INFO @ Mon, 03 Jun 2019 12:20:32: 34000000 INFO @ Mon, 03 Jun 2019 12:20:34: 37000000 INFO @ Mon, 03 Jun 2019 12:20:35: 36000000 INFO @ Mon, 03 Jun 2019 12:20:38: 35000000 INFO @ Mon, 03 Jun 2019 12:20:40: 38000000 INFO @ Mon, 03 Jun 2019 12:20:41: 37000000 INFO @ Mon, 03 Jun 2019 12:20:44: 36000000 INFO @ Mon, 03 Jun 2019 12:20:45: 39000000 INFO @ Mon, 03 Jun 2019 12:20:47: 38000000 INFO @ Mon, 03 Jun 2019 12:20:49: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:20:49: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:20:49: #1 total tags in treatment: 15902123 INFO @ Mon, 03 Jun 2019 12:20:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:20:49: #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 12:20:50: 37000000 INFO @ Mon, 03 Jun 2019 12:20:50: #1 tags after filtering in treatment: 11531451 INFO @ Mon, 03 Jun 2019 12:20:50: #1 Redundant rate of treatment: 0.27 INFO @ Mon, 03 Jun 2019 12:20:50: #1 finished! INFO @ Mon, 03 Jun 2019 12:20:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:20:51: #2 number of paired peaks: 380 WARNING @ Mon, 03 Jun 2019 12:20:51: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Mon, 03 Jun 2019 12:20:51: start model_add_line... INFO @ Mon, 03 Jun 2019 12:20:51: start X-correlation... INFO @ Mon, 03 Jun 2019 12:20:51: end of X-cor INFO @ Mon, 03 Jun 2019 12:20:51: #2 finished! INFO @ Mon, 03 Jun 2019 12:20:51: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 12:20:51: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 03 Jun 2019 12:20:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.10_model.r INFO @ Mon, 03 Jun 2019 12:20:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:20:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:20:53: 39000000 INFO @ Mon, 03 Jun 2019 12:20:56: 38000000 INFO @ Mon, 03 Jun 2019 12:20:58: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:20:58: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:20:58: #1 total tags in treatment: 15902123 INFO @ Mon, 03 Jun 2019 12:20:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:20:58: #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 12:20:58: #1 tags after filtering in treatment: 11531451 INFO @ Mon, 03 Jun 2019 12:20:58: #1 Redundant rate of treatment: 0.27 INFO @ Mon, 03 Jun 2019 12:20:58: #1 finished! INFO @ Mon, 03 Jun 2019 12:20:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:20:59: #2 number of paired peaks: 380 WARNING @ Mon, 03 Jun 2019 12:20:59: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Mon, 03 Jun 2019 12:20:59: start model_add_line... INFO @ Mon, 03 Jun 2019 12:20:59: start X-correlation... INFO @ Mon, 03 Jun 2019 12:20:59: end of X-cor INFO @ Mon, 03 Jun 2019 12:20:59: #2 finished! INFO @ Mon, 03 Jun 2019 12:20:59: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 12:20:59: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 03 Jun 2019 12:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.20_model.r INFO @ Mon, 03 Jun 2019 12:20:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:20:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:21:02: 39000000 INFO @ Mon, 03 Jun 2019 12:21:06: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:21:06: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:21:06: #1 total tags in treatment: 15902123 INFO @ Mon, 03 Jun 2019 12:21:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:21:06: #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 12:21:06: #1 tags after filtering in treatment: 11531451 INFO @ Mon, 03 Jun 2019 12:21:06: #1 Redundant rate of treatment: 0.27 INFO @ Mon, 03 Jun 2019 12:21:06: #1 finished! INFO @ Mon, 03 Jun 2019 12:21:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:21:08: #2 number of paired peaks: 380 WARNING @ Mon, 03 Jun 2019 12:21:08: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Mon, 03 Jun 2019 12:21:08: start model_add_line... INFO @ Mon, 03 Jun 2019 12:21:08: start X-correlation... INFO @ Mon, 03 Jun 2019 12:21:08: end of X-cor INFO @ Mon, 03 Jun 2019 12:21:08: #2 finished! INFO @ Mon, 03 Jun 2019 12:21:08: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 12:21:08: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 03 Jun 2019 12:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.05_model.r INFO @ Mon, 03 Jun 2019 12:21:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:21:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:21:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:21:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:21:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:21:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:21:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:21:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.10_summits.bed INFO @ Mon, 03 Jun 2019 12:21:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1493 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:21:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:21:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:21:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.20_summits.bed INFO @ Mon, 03 Jun 2019 12:21:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (890 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300931/SRX300931.05_summits.bed INFO @ Mon, 03 Jun 2019 12:21:55: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5085 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。