Job ID = 2640610 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:06:11 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 : 26,575,578 reads read : 53,151,156 reads written : 26,575,578 reads 0-length : 26,575,578 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:17:52 26575578 reads; of these: 26575578 (100.00%) were unpaired; of these: 648594 (2.44%) aligned 0 times 20593741 (77.49%) aligned exactly 1 time 5333243 (20.07%) aligned >1 times 97.56% overall alignment rate Time searching: 00:17:54 Overall time: 00:17:54 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] 3210736 / 25926984 = 0.1238 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.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 @ Sat, 24 Aug 2019 18:35:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:35:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:35:53: 1000000 INFO @ Sat, 24 Aug 2019 18:36:00: 2000000 INFO @ Sat, 24 Aug 2019 18:36:06: 3000000 INFO @ Sat, 24 Aug 2019 18:36:13: 4000000 INFO @ Sat, 24 Aug 2019 18:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.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 @ Sat, 24 Aug 2019 18:36:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:36:20: 5000000 INFO @ Sat, 24 Aug 2019 18:36:22: 1000000 INFO @ Sat, 24 Aug 2019 18:36:27: 6000000 INFO @ Sat, 24 Aug 2019 18:36:28: 2000000 INFO @ Sat, 24 Aug 2019 18:36:34: 7000000 INFO @ Sat, 24 Aug 2019 18:36:35: 3000000 INFO @ Sat, 24 Aug 2019 18:36:41: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:36:42: 4000000 INFO @ Sat, 24 Aug 2019 18:36:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.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 @ Sat, 24 Aug 2019 18:36:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:36:48: 9000000 INFO @ Sat, 24 Aug 2019 18:36:49: 5000000 INFO @ Sat, 24 Aug 2019 18:36:51: 1000000 INFO @ Sat, 24 Aug 2019 18:36:55: 10000000 INFO @ Sat, 24 Aug 2019 18:36:56: 6000000 INFO @ Sat, 24 Aug 2019 18:36:59: 2000000 INFO @ Sat, 24 Aug 2019 18:37:02: 7000000 INFO @ Sat, 24 Aug 2019 18:37:02: 11000000 INFO @ Sat, 24 Aug 2019 18:37:08: 3000000 INFO @ Sat, 24 Aug 2019 18:37:09: 8000000 INFO @ Sat, 24 Aug 2019 18:37:10: 12000000 INFO @ Sat, 24 Aug 2019 18:37:16: 9000000 INFO @ Sat, 24 Aug 2019 18:37:17: 4000000 INFO @ Sat, 24 Aug 2019 18:37:17: 13000000 INFO @ Sat, 24 Aug 2019 18:37:23: 10000000 INFO @ Sat, 24 Aug 2019 18:37:24: 5000000 INFO @ Sat, 24 Aug 2019 18:37:25: 14000000 INFO @ Sat, 24 Aug 2019 18:37:30: 11000000 INFO @ Sat, 24 Aug 2019 18:37:32: 6000000 INFO @ Sat, 24 Aug 2019 18:37:32: 15000000 INFO @ Sat, 24 Aug 2019 18:37:36: 12000000 INFO @ Sat, 24 Aug 2019 18:37:39: 7000000 INFO @ Sat, 24 Aug 2019 18:37:39: 16000000 INFO @ Sat, 24 Aug 2019 18:37:43: 13000000 INFO @ Sat, 24 Aug 2019 18:37:46: 8000000 INFO @ Sat, 24 Aug 2019 18:37:46: 17000000 INFO @ Sat, 24 Aug 2019 18:37:49: 14000000 INFO @ Sat, 24 Aug 2019 18:37:53: 18000000 INFO @ Sat, 24 Aug 2019 18:37:55: 9000000 INFO @ Sat, 24 Aug 2019 18:37:56: 15000000 INFO @ Sat, 24 Aug 2019 18:38:00: 19000000 INFO @ Sat, 24 Aug 2019 18:38:04: 10000000 INFO @ Sat, 24 Aug 2019 18:38:04: 16000000 INFO @ Sat, 24 Aug 2019 18:38:07: 20000000 INFO @ Sat, 24 Aug 2019 18:38:13: 11000000 INFO @ Sat, 24 Aug 2019 18:38:14: 17000000 INFO @ Sat, 24 Aug 2019 18:38:14: 21000000 INFO @ Sat, 24 Aug 2019 18:38:20: 18000000 INFO @ Sat, 24 Aug 2019 18:38:22: 12000000 INFO @ Sat, 24 Aug 2019 18:38:22: 22000000 INFO @ Sat, 24 Aug 2019 18:38:27: 19000000 INFO @ Sat, 24 Aug 2019 18:38:27: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:38:27: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:38:27: #1 total tags in treatment: 22716248 INFO @ Sat, 24 Aug 2019 18:38:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:38:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:38:28: #1 tags after filtering in treatment: 22716083 INFO @ Sat, 24 Aug 2019 18:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:38:28: #1 finished! INFO @ Sat, 24 Aug 2019 18:38:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:38:30: 13000000 INFO @ Sat, 24 Aug 2019 18:38:33: #2 number of paired peaks: 56424 INFO @ Sat, 24 Aug 2019 18:38:33: start model_add_line... INFO @ Sat, 24 Aug 2019 18:38:33: start X-correlation... INFO @ Sat, 24 Aug 2019 18:38:33: end of X-cor INFO @ Sat, 24 Aug 2019 18:38:33: #2 finished! INFO @ Sat, 24 Aug 2019 18:38:33: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:38:33: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.05_model.r INFO @ Sat, 24 Aug 2019 18:38:33: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:38:33: 20000000 INFO @ Sat, 24 Aug 2019 18:38:38: 14000000 INFO @ Sat, 24 Aug 2019 18:38:40: 21000000 INFO @ Sat, 24 Aug 2019 18:38:46: 15000000 INFO @ Sat, 24 Aug 2019 18:38:47: 22000000 INFO @ Sat, 24 Aug 2019 18:38:52: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:38:52: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:38:52: #1 total tags in treatment: 22716248 INFO @ Sat, 24 Aug 2019 18:38:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:38:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:38:52: #1 tags after filtering in treatment: 22716083 INFO @ Sat, 24 Aug 2019 18:38:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:38:52: #1 finished! INFO @ Sat, 24 Aug 2019 18:38:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:38:55: 16000000 INFO @ Sat, 24 Aug 2019 18:38:57: #2 number of paired peaks: 56424 INFO @ Sat, 24 Aug 2019 18:38:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:38:58: start X-correlation... INFO @ Sat, 24 Aug 2019 18:38:58: end of X-cor INFO @ Sat, 24 Aug 2019 18:38:58: #2 finished! INFO @ Sat, 24 Aug 2019 18:38:58: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:38:58: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.10_model.r INFO @ Sat, 24 Aug 2019 18:38:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:39:03: 17000000 INFO @ Sat, 24 Aug 2019 18:39:12: 18000000 INFO @ Sat, 24 Aug 2019 18:39:21: 19000000 INFO @ Sat, 24 Aug 2019 18:39:29: 20000000 INFO @ Sat, 24 Aug 2019 18:39:38: 21000000 INFO @ Sat, 24 Aug 2019 18:39:47: 22000000 INFO @ Sat, 24 Aug 2019 18:39:54: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:39:54: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:39:54: #1 total tags in treatment: 22716248 INFO @ Sat, 24 Aug 2019 18:39:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:39:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:39:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:39:55: #1 tags after filtering in treatment: 22716083 INFO @ Sat, 24 Aug 2019 18:39:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:39:55: #1 finished! INFO @ Sat, 24 Aug 2019 18:39:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:40:00: #2 number of paired peaks: 56424 INFO @ Sat, 24 Aug 2019 18:40:00: start model_add_line... INFO @ Sat, 24 Aug 2019 18:40:00: start X-correlation... INFO @ Sat, 24 Aug 2019 18:40:00: end of X-cor INFO @ Sat, 24 Aug 2019 18:40:00: #2 finished! INFO @ Sat, 24 Aug 2019 18:40:00: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:40:00: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.20_model.r INFO @ Sat, 24 Aug 2019 18:40:00: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:40:13: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:40:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:40:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.05_summits.bed INFO @ Sat, 24 Aug 2019 18:40:36: Done! pass1 - making usageList (97 chroms): 6 millis pass2 - checking and writing primary data (15555 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:40:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.10_summits.bed INFO @ Sat, 24 Aug 2019 18:40:51: Done! pass1 - making usageList (85 chroms): 5 millis pass2 - checking and writing primary data (12416 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:41:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375037/SRX5375037.20_summits.bed INFO @ Sat, 24 Aug 2019 18:41:56: Done! pass1 - making usageList (60 chroms): 4 millis pass2 - checking and writing primary data (8769 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。