Job ID = 2003181 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T03:01:39 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 : 41,690,339 reads read : 41,690,339 reads written : 41,690,339 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR498448.sra.cache’: 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: 00:00:01 Multiseed full-index search: 00:17:15 41690339 reads; of these: 41690339 (100.00%) were unpaired; of these: 6192465 (14.85%) aligned 0 times 31633157 (75.88%) aligned exactly 1 time 3864717 (9.27%) aligned >1 times 85.15% overall alignment rate Time searching: 00:17:16 Overall time: 00:17:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14650813 / 35497874 = 0.4127 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 @ Fri, 05 Jul 2019 12:33:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:33:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:33:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:33:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:33:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:33:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:33:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:33:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:34:02: 1000000 INFO @ Fri, 05 Jul 2019 12:34:02: 1000000 INFO @ Fri, 05 Jul 2019 12:34:03: 1000000 INFO @ Fri, 05 Jul 2019 12:34:10: 2000000 INFO @ Fri, 05 Jul 2019 12:34:10: 2000000 INFO @ Fri, 05 Jul 2019 12:34:11: 2000000 INFO @ Fri, 05 Jul 2019 12:34:18: 3000000 INFO @ Fri, 05 Jul 2019 12:34:19: 3000000 INFO @ Fri, 05 Jul 2019 12:34:19: 3000000 INFO @ Fri, 05 Jul 2019 12:34:26: 4000000 INFO @ Fri, 05 Jul 2019 12:34:27: 4000000 INFO @ Fri, 05 Jul 2019 12:34:27: 4000000 INFO @ Fri, 05 Jul 2019 12:34:35: 5000000 INFO @ Fri, 05 Jul 2019 12:34:35: 5000000 INFO @ Fri, 05 Jul 2019 12:34:36: 5000000 INFO @ Fri, 05 Jul 2019 12:34:43: 6000000 INFO @ Fri, 05 Jul 2019 12:34:43: 6000000 INFO @ Fri, 05 Jul 2019 12:34:44: 6000000 INFO @ Fri, 05 Jul 2019 12:34:51: 7000000 INFO @ Fri, 05 Jul 2019 12:34:52: 7000000 INFO @ Fri, 05 Jul 2019 12:34:52: 7000000 INFO @ Fri, 05 Jul 2019 12:34:59: 8000000 INFO @ Fri, 05 Jul 2019 12:35:00: 8000000 INFO @ Fri, 05 Jul 2019 12:35:00: 8000000 INFO @ Fri, 05 Jul 2019 12:35:07: 9000000 INFO @ Fri, 05 Jul 2019 12:35:08: 9000000 INFO @ Fri, 05 Jul 2019 12:35:08: 9000000 INFO @ Fri, 05 Jul 2019 12:35:16: 10000000 INFO @ Fri, 05 Jul 2019 12:35:16: 10000000 INFO @ Fri, 05 Jul 2019 12:35:17: 10000000 INFO @ Fri, 05 Jul 2019 12:35:24: 11000000 INFO @ Fri, 05 Jul 2019 12:35:25: 11000000 INFO @ Fri, 05 Jul 2019 12:35:25: 11000000 INFO @ Fri, 05 Jul 2019 12:35:32: 12000000 INFO @ Fri, 05 Jul 2019 12:35:33: 12000000 INFO @ Fri, 05 Jul 2019 12:35:33: 12000000 INFO @ Fri, 05 Jul 2019 12:35:41: 13000000 INFO @ Fri, 05 Jul 2019 12:35:42: 13000000 INFO @ Fri, 05 Jul 2019 12:35:42: 13000000 INFO @ Fri, 05 Jul 2019 12:35:49: 14000000 INFO @ Fri, 05 Jul 2019 12:35:51: 14000000 INFO @ Fri, 05 Jul 2019 12:35:51: 14000000 INFO @ Fri, 05 Jul 2019 12:35:57: 15000000 INFO @ Fri, 05 Jul 2019 12:35:59: 15000000 INFO @ Fri, 05 Jul 2019 12:35:59: 15000000 INFO @ Fri, 05 Jul 2019 12:36:06: 16000000 INFO @ Fri, 05 Jul 2019 12:36:07: 16000000 INFO @ Fri, 05 Jul 2019 12:36:08: 16000000 INFO @ Fri, 05 Jul 2019 12:36:14: 17000000 INFO @ Fri, 05 Jul 2019 12:36:16: 17000000 INFO @ Fri, 05 Jul 2019 12:36:16: 17000000 INFO @ Fri, 05 Jul 2019 12:36:22: 18000000 INFO @ Fri, 05 Jul 2019 12:36:24: 18000000 INFO @ Fri, 05 Jul 2019 12:36:24: 18000000 INFO @ Fri, 05 Jul 2019 12:36:31: 19000000 INFO @ Fri, 05 Jul 2019 12:36:32: 19000000 INFO @ Fri, 05 Jul 2019 12:36:33: 19000000 INFO @ Fri, 05 Jul 2019 12:36:39: 20000000 INFO @ Fri, 05 Jul 2019 12:36:41: 20000000 INFO @ Fri, 05 Jul 2019 12:36:41: 20000000 INFO @ Fri, 05 Jul 2019 12:36:47: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:36:47: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:36:47: #1 total tags in treatment: 20847061 INFO @ Fri, 05 Jul 2019 12:36:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:36:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:36:48: #1 tags after filtering in treatment: 20846818 INFO @ Fri, 05 Jul 2019 12:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:36:48: #1 finished! INFO @ Fri, 05 Jul 2019 12:36:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:36:49: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:36:49: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:36:49: #1 total tags in treatment: 20847061 INFO @ Fri, 05 Jul 2019 12:36:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:36:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:36:49: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:36:49: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:36:49: #1 total tags in treatment: 20847061 INFO @ Fri, 05 Jul 2019 12:36:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:36:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:36:49: #1 tags after filtering in treatment: 20846818 INFO @ Fri, 05 Jul 2019 12:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:36:49: #1 finished! INFO @ Fri, 05 Jul 2019 12:36:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:36:49: #1 tags after filtering in treatment: 20846818 INFO @ Fri, 05 Jul 2019 12:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:36:49: #1 finished! INFO @ Fri, 05 Jul 2019 12:36:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:36:51: #2 number of paired peaks: 29773 INFO @ Fri, 05 Jul 2019 12:36:51: start model_add_line... INFO @ Fri, 05 Jul 2019 12:36:52: start X-correlation... INFO @ Fri, 05 Jul 2019 12:36:52: end of X-cor INFO @ Fri, 05 Jul 2019 12:36:52: #2 finished! INFO @ Fri, 05 Jul 2019 12:36:52: #2 predicted fragment length is 222 bps INFO @ Fri, 05 Jul 2019 12:36:52: #2 alternative fragment length(s) may be 222 bps INFO @ Fri, 05 Jul 2019 12:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.10_model.r INFO @ Fri, 05 Jul 2019 12:36:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:36:53: #2 number of paired peaks: 29773 INFO @ Fri, 05 Jul 2019 12:36:53: start model_add_line... INFO @ Fri, 05 Jul 2019 12:36:53: #2 number of paired peaks: 29773 INFO @ Fri, 05 Jul 2019 12:36:53: start model_add_line... INFO @ Fri, 05 Jul 2019 12:36:53: start X-correlation... INFO @ Fri, 05 Jul 2019 12:36:53: end of X-cor INFO @ Fri, 05 Jul 2019 12:36:53: #2 finished! INFO @ Fri, 05 Jul 2019 12:36:53: #2 predicted fragment length is 222 bps INFO @ Fri, 05 Jul 2019 12:36:53: #2 alternative fragment length(s) may be 222 bps INFO @ Fri, 05 Jul 2019 12:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.20_model.r INFO @ Fri, 05 Jul 2019 12:36:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:36:53: start X-correlation... INFO @ Fri, 05 Jul 2019 12:36:53: end of X-cor INFO @ Fri, 05 Jul 2019 12:36:53: #2 finished! INFO @ Fri, 05 Jul 2019 12:36:53: #2 predicted fragment length is 222 bps INFO @ Fri, 05 Jul 2019 12:36:53: #2 alternative fragment length(s) may be 222 bps INFO @ Fri, 05 Jul 2019 12:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.05_model.r INFO @ Fri, 05 Jul 2019 12:36:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:36:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:38:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:38:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:38:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:38:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.10_summits.bed INFO @ Fri, 05 Jul 2019 12:38:35: Done! pass1 - making usageList (116 chroms): 8 millis pass2 - checking and writing primary data (22463 records, 4 fields): 36 millis INFO @ Fri, 05 Jul 2019 12:38:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:38:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.20_summits.bed INFO @ Fri, 05 Jul 2019 12:38:37: Done! INFO @ Fri, 05 Jul 2019 12:38:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:38:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.05_peaks.narrowPeak pass1 - making usageList (105 chroms): 5 millis pass2 - checking and writing primary data (19527 records, 4 fields): 30 millis INFO @ Fri, 05 Jul 2019 12:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148694/SRX148694.05_summits.bed INFO @ Fri, 05 Jul 2019 12:38:37: Done! pass1 - making usageList (124 chroms): 5 millis pass2 - checking and writing primary data (25519 records, 4 fields): 39 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。