Job ID = 2590345 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T11:53:18 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 ) 2019-08-12T11:53:18 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 ) 2019-08-12T11:53:51 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 ) 2019-08-12T11:53:51 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 : 11,910,876 reads read : 23,821,752 reads written : 11,910,876 reads 0-length : 11,910,876 spots read : 11,774,583 reads read : 23,549,166 reads written : 11,774,583 reads 0-length : 11,774,583 spots read : 11,908,647 reads read : 23,817,294 reads written : 11,908,647 reads 0-length : 11,908,647 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: 00:10:09 35594106 reads; of these: 35594106 (100.00%) were unpaired; of these: 1270677 (3.57%) aligned 0 times 27226342 (76.49%) aligned exactly 1 time 7097087 (19.94%) aligned >1 times 96.43% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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 16 files... [bam_rmdupse_core] 5712407 / 34323429 = 0.1664 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, 12 Aug 2019 21:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.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, 12 Aug 2019 21:24:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:24:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:24:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.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, 12 Aug 2019 21:24:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:24:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.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, 12 Aug 2019 21:24:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:24:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:24:55: 1000000 INFO @ Mon, 12 Aug 2019 21:24:56: 1000000 INFO @ Mon, 12 Aug 2019 21:24:58: 1000000 INFO @ Mon, 12 Aug 2019 21:25:03: 2000000 INFO @ Mon, 12 Aug 2019 21:25:05: 2000000 INFO @ Mon, 12 Aug 2019 21:25:07: 2000000 INFO @ Mon, 12 Aug 2019 21:25:11: 3000000 INFO @ Mon, 12 Aug 2019 21:25:14: 3000000 INFO @ Mon, 12 Aug 2019 21:25:17: 3000000 INFO @ Mon, 12 Aug 2019 21:25:20: 4000000 INFO @ Mon, 12 Aug 2019 21:25:22: 4000000 INFO @ Mon, 12 Aug 2019 21:25:27: 4000000 INFO @ Mon, 12 Aug 2019 21:25:28: 5000000 INFO @ Mon, 12 Aug 2019 21:25:31: 5000000 INFO @ Mon, 12 Aug 2019 21:25:36: 5000000 INFO @ Mon, 12 Aug 2019 21:25:36: 6000000 INFO @ Mon, 12 Aug 2019 21:25:40: 6000000 INFO @ Mon, 12 Aug 2019 21:25:45: 7000000 INFO @ Mon, 12 Aug 2019 21:25:46: 6000000 INFO @ Mon, 12 Aug 2019 21:25:49: 7000000 INFO @ Mon, 12 Aug 2019 21:25:53: 8000000 INFO @ Mon, 12 Aug 2019 21:25:55: 7000000 INFO @ Mon, 12 Aug 2019 21:25:58: 8000000 INFO @ Mon, 12 Aug 2019 21:26:01: 9000000 INFO @ Mon, 12 Aug 2019 21:26:05: 8000000 INFO @ Mon, 12 Aug 2019 21:26:06: 9000000 INFO @ Mon, 12 Aug 2019 21:26:10: 10000000 INFO @ Mon, 12 Aug 2019 21:26:15: 9000000 INFO @ Mon, 12 Aug 2019 21:26:15: 10000000 INFO @ Mon, 12 Aug 2019 21:26:18: 11000000 INFO @ Mon, 12 Aug 2019 21:26:24: 11000000 INFO @ Mon, 12 Aug 2019 21:26:24: 10000000 INFO @ Mon, 12 Aug 2019 21:26:26: 12000000 INFO @ Mon, 12 Aug 2019 21:26:33: 12000000 INFO @ Mon, 12 Aug 2019 21:26:34: 11000000 INFO @ Mon, 12 Aug 2019 21:26:35: 13000000 INFO @ Mon, 12 Aug 2019 21:26:42: 13000000 INFO @ Mon, 12 Aug 2019 21:26:43: 14000000 INFO @ Mon, 12 Aug 2019 21:26:44: 12000000 INFO @ Mon, 12 Aug 2019 21:26:50: 14000000 INFO @ Mon, 12 Aug 2019 21:26:52: 15000000 INFO @ Mon, 12 Aug 2019 21:26:53: 13000000 INFO @ Mon, 12 Aug 2019 21:26:58: 15000000 INFO @ Mon, 12 Aug 2019 21:27:00: 16000000 INFO @ Mon, 12 Aug 2019 21:27:03: 14000000 INFO @ Mon, 12 Aug 2019 21:27:07: 16000000 INFO @ Mon, 12 Aug 2019 21:27:09: 17000000 INFO @ Mon, 12 Aug 2019 21:27:12: 15000000 INFO @ Mon, 12 Aug 2019 21:27:15: 17000000 INFO @ Mon, 12 Aug 2019 21:27:18: 18000000 INFO @ Mon, 12 Aug 2019 21:27:22: 16000000 INFO @ Mon, 12 Aug 2019 21:27:23: 18000000 INFO @ Mon, 12 Aug 2019 21:27:26: 19000000 INFO @ Mon, 12 Aug 2019 21:27:32: 17000000 INFO @ Mon, 12 Aug 2019 21:27:32: 19000000 INFO @ Mon, 12 Aug 2019 21:27:34: 20000000 INFO @ Mon, 12 Aug 2019 21:27:41: 20000000 INFO @ Mon, 12 Aug 2019 21:27:41: 18000000 INFO @ Mon, 12 Aug 2019 21:27:43: 21000000 INFO @ Mon, 12 Aug 2019 21:27:50: 21000000 INFO @ Mon, 12 Aug 2019 21:27:50: 19000000 INFO @ Mon, 12 Aug 2019 21:27:51: 22000000 INFO @ Mon, 12 Aug 2019 21:27:58: 22000000 INFO @ Mon, 12 Aug 2019 21:27:59: 23000000 INFO @ Mon, 12 Aug 2019 21:28:00: 20000000 INFO @ Mon, 12 Aug 2019 21:28:07: 23000000 INFO @ Mon, 12 Aug 2019 21:28:07: 24000000 INFO @ Mon, 12 Aug 2019 21:28:10: 21000000 INFO @ Mon, 12 Aug 2019 21:28:16: 25000000 INFO @ Mon, 12 Aug 2019 21:28:16: 24000000 INFO @ Mon, 12 Aug 2019 21:28:19: 22000000 INFO @ Mon, 12 Aug 2019 21:28:24: 26000000 INFO @ Mon, 12 Aug 2019 21:28:25: 25000000 INFO @ Mon, 12 Aug 2019 21:28:29: 23000000 INFO @ Mon, 12 Aug 2019 21:28:33: 27000000 INFO @ Mon, 12 Aug 2019 21:28:34: 26000000 INFO @ Mon, 12 Aug 2019 21:28:39: 24000000 INFO @ Mon, 12 Aug 2019 21:28:41: 28000000 INFO @ Mon, 12 Aug 2019 21:28:42: 27000000 INFO @ Mon, 12 Aug 2019 21:28:46: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:28:46: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:28:46: #1 total tags in treatment: 28611022 INFO @ Mon, 12 Aug 2019 21:28:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:28:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:28:47: #1 tags after filtering in treatment: 28611022 INFO @ Mon, 12 Aug 2019 21:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:28:47: #1 finished! INFO @ Mon, 12 Aug 2019 21:28:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:28:48: 25000000 INFO @ Mon, 12 Aug 2019 21:28:49: #2 number of paired peaks: 652 WARNING @ Mon, 12 Aug 2019 21:28:49: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Mon, 12 Aug 2019 21:28:49: start model_add_line... INFO @ Mon, 12 Aug 2019 21:28:49: start X-correlation... INFO @ Mon, 12 Aug 2019 21:28:49: end of X-cor INFO @ Mon, 12 Aug 2019 21:28:49: #2 finished! INFO @ Mon, 12 Aug 2019 21:28:49: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 21:28:49: #2 alternative fragment length(s) may be 4,130,144 bps INFO @ Mon, 12 Aug 2019 21:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.05_model.r INFO @ Mon, 12 Aug 2019 21:28:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:28:51: 28000000 INFO @ Mon, 12 Aug 2019 21:28:56: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:28:56: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:28:56: #1 total tags in treatment: 28611022 INFO @ Mon, 12 Aug 2019 21:28:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:28:57: #1 tags after filtering in treatment: 28611022 INFO @ Mon, 12 Aug 2019 21:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:28:57: #1 finished! INFO @ Mon, 12 Aug 2019 21:28:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:28:58: 26000000 INFO @ Mon, 12 Aug 2019 21:28:59: #2 number of paired peaks: 652 WARNING @ Mon, 12 Aug 2019 21:28:59: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Mon, 12 Aug 2019 21:28:59: start model_add_line... INFO @ Mon, 12 Aug 2019 21:29:00: start X-correlation... INFO @ Mon, 12 Aug 2019 21:29:00: end of X-cor INFO @ Mon, 12 Aug 2019 21:29:00: #2 finished! INFO @ Mon, 12 Aug 2019 21:29:00: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 21:29:00: #2 alternative fragment length(s) may be 4,130,144 bps INFO @ Mon, 12 Aug 2019 21:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.10_model.r INFO @ Mon, 12 Aug 2019 21:29:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:29:07: 27000000 INFO @ Mon, 12 Aug 2019 21:29:16: 28000000 INFO @ Mon, 12 Aug 2019 21:29:21: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:29:21: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:29:21: #1 total tags in treatment: 28611022 INFO @ Mon, 12 Aug 2019 21:29:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:29:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:29:22: #1 tags after filtering in treatment: 28611022 INFO @ Mon, 12 Aug 2019 21:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:29:22: #1 finished! INFO @ Mon, 12 Aug 2019 21:29:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:29:24: #2 number of paired peaks: 652 WARNING @ Mon, 12 Aug 2019 21:29:24: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Mon, 12 Aug 2019 21:29:24: start model_add_line... INFO @ Mon, 12 Aug 2019 21:29:25: start X-correlation... INFO @ Mon, 12 Aug 2019 21:29:25: end of X-cor INFO @ Mon, 12 Aug 2019 21:29:25: #2 finished! INFO @ Mon, 12 Aug 2019 21:29:25: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 21:29:25: #2 alternative fragment length(s) may be 4,130,144 bps INFO @ Mon, 12 Aug 2019 21:29:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.20_model.r INFO @ Mon, 12 Aug 2019 21:29:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:29:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:30:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:30:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:30:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:30:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:30:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.05_summits.bed INFO @ Mon, 12 Aug 2019 21:30:36: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (10303 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:30:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.10_summits.bed INFO @ Mon, 12 Aug 2019 21:30:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6266 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981620/SRX3981620.20_summits.bed INFO @ Mon, 12 Aug 2019 21:31:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2389 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。