Job ID = 4178510 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:42:10 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 : 27,047,648 reads read : 27,047,648 reads written : 27,047,648 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:16 27047648 reads; of these: 27047648 (100.00%) were unpaired; of these: 2767109 (10.23%) aligned 0 times 19689991 (72.80%) aligned exactly 1 time 4590548 (16.97%) aligned >1 times 89.77% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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_rmdupse_core] 10437758 / 24280539 = 0.4299 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:55:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.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 @ Thu, 05 Dec 2019 12:55:41: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:55:41: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:55:46: 1000000 INFO @ Thu, 05 Dec 2019 12:55:51: 2000000 INFO @ Thu, 05 Dec 2019 12:55:56: 3000000 INFO @ Thu, 05 Dec 2019 12:56:01: 4000000 INFO @ Thu, 05 Dec 2019 12:56:06: 5000000 INFO @ Thu, 05 Dec 2019 12:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.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 @ Thu, 05 Dec 2019 12:56:11: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:11: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:11: 6000000 INFO @ Thu, 05 Dec 2019 12:56:16: 7000000 INFO @ Thu, 05 Dec 2019 12:56:17: 1000000 INFO @ Thu, 05 Dec 2019 12:56:21: 8000000 INFO @ Thu, 05 Dec 2019 12:56:23: 2000000 INFO @ Thu, 05 Dec 2019 12:56:26: 9000000 INFO @ Thu, 05 Dec 2019 12:56:29: 3000000 INFO @ Thu, 05 Dec 2019 12:56:31: 10000000 INFO @ Thu, 05 Dec 2019 12:56:35: 4000000 INFO @ Thu, 05 Dec 2019 12:56:36: 11000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:56:41: 5000000 INFO @ Thu, 05 Dec 2019 12:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.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 @ Thu, 05 Dec 2019 12:56:41: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:56:41: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:56:41: 12000000 INFO @ Thu, 05 Dec 2019 12:56:46: 13000000 INFO @ Thu, 05 Dec 2019 12:56:46: 1000000 INFO @ Thu, 05 Dec 2019 12:56:47: 6000000 INFO @ Thu, 05 Dec 2019 12:56:50: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:56:50: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:56:50: #1 total tags in treatment: 13842781 INFO @ Thu, 05 Dec 2019 12:56:50: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:56:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:56:50: #1 tags after filtering in treatment: 13842781 INFO @ Thu, 05 Dec 2019 12:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:56:50: #1 finished! INFO @ Thu, 05 Dec 2019 12:56:50: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:56:50: 2000000 INFO @ Thu, 05 Dec 2019 12:56:51: #2 number of paired peaks: 3299 INFO @ Thu, 05 Dec 2019 12:56:51: start model_add_line... INFO @ Thu, 05 Dec 2019 12:56:51: start X-correlation... INFO @ Thu, 05 Dec 2019 12:56:51: end of X-cor INFO @ Thu, 05 Dec 2019 12:56:51: #2 finished! INFO @ Thu, 05 Dec 2019 12:56:51: #2 predicted fragment length is 272 bps INFO @ Thu, 05 Dec 2019 12:56:51: #2 alternative fragment length(s) may be 0,17,62,124,212,242,272 bps INFO @ Thu, 05 Dec 2019 12:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.05_model.r INFO @ Thu, 05 Dec 2019 12:56:51: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:56:53: 7000000 INFO @ Thu, 05 Dec 2019 12:56:55: 3000000 INFO @ Thu, 05 Dec 2019 12:56:58: 8000000 INFO @ Thu, 05 Dec 2019 12:56:59: 4000000 INFO @ Thu, 05 Dec 2019 12:57:04: 5000000 INFO @ Thu, 05 Dec 2019 12:57:04: 9000000 INFO @ Thu, 05 Dec 2019 12:57:09: 6000000 INFO @ Thu, 05 Dec 2019 12:57:10: 10000000 INFO @ Thu, 05 Dec 2019 12:57:13: 7000000 INFO @ Thu, 05 Dec 2019 12:57:16: 11000000 INFO @ Thu, 05 Dec 2019 12:57:18: 8000000 INFO @ Thu, 05 Dec 2019 12:57:22: 12000000 INFO @ Thu, 05 Dec 2019 12:57:22: 9000000 INFO @ Thu, 05 Dec 2019 12:57:27: 10000000 INFO @ Thu, 05 Dec 2019 12:57:28: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:57:28: 13000000 INFO @ Thu, 05 Dec 2019 12:57:31: 11000000 INFO @ Thu, 05 Dec 2019 12:57:33: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:57:33: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:57:33: #1 total tags in treatment: 13842781 INFO @ Thu, 05 Dec 2019 12:57:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:57:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:57:34: #1 tags after filtering in treatment: 13842781 INFO @ Thu, 05 Dec 2019 12:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:57:34: #1 finished! INFO @ Thu, 05 Dec 2019 12:57:34: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:57:35: #2 number of paired peaks: 3299 INFO @ Thu, 05 Dec 2019 12:57:35: start model_add_line... INFO @ Thu, 05 Dec 2019 12:57:35: start X-correlation... INFO @ Thu, 05 Dec 2019 12:57:35: end of X-cor INFO @ Thu, 05 Dec 2019 12:57:35: #2 finished! INFO @ Thu, 05 Dec 2019 12:57:35: #2 predicted fragment length is 272 bps INFO @ Thu, 05 Dec 2019 12:57:35: #2 alternative fragment length(s) may be 0,17,62,124,212,242,272 bps INFO @ Thu, 05 Dec 2019 12:57:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.10_model.r INFO @ Thu, 05 Dec 2019 12:57:35: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:57:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:57:37: 12000000 INFO @ Thu, 05 Dec 2019 12:57:42: 13000000 INFO @ Thu, 05 Dec 2019 12:57:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:57:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:57:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.05_summits.bed INFO @ Thu, 05 Dec 2019 12:57:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3856 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:57:46: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:57:46: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:57:46: #1 total tags in treatment: 13842781 INFO @ Thu, 05 Dec 2019 12:57:46: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:57:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:57:46: #1 tags after filtering in treatment: 13842781 INFO @ Thu, 05 Dec 2019 12:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:57:46: #1 finished! INFO @ Thu, 05 Dec 2019 12:57:46: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:57:48: #2 number of paired peaks: 3299 INFO @ Thu, 05 Dec 2019 12:57:48: start model_add_line... INFO @ Thu, 05 Dec 2019 12:57:48: start X-correlation... INFO @ Thu, 05 Dec 2019 12:57:48: end of X-cor INFO @ Thu, 05 Dec 2019 12:57:48: #2 finished! INFO @ Thu, 05 Dec 2019 12:57:48: #2 predicted fragment length is 272 bps INFO @ Thu, 05 Dec 2019 12:57:48: #2 alternative fragment length(s) may be 0,17,62,124,212,242,272 bps INFO @ Thu, 05 Dec 2019 12:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.20_model.r INFO @ Thu, 05 Dec 2019 12:57:48: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:58:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:58:25: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.10_summits.bed INFO @ Thu, 05 Dec 2019 12:58:27: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1771 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717032/SRX5717032.20_summits.bed INFO @ Thu, 05 Dec 2019 12:58:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (564 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。