Job ID = 4288906 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:33:04 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:34:33 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 ) 2019-12-10T03:35:20 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 : 33,280,368 reads read : 66,560,736 reads written : 33,280,368 reads 0-length : 33,280,368 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: 00:25:11 33280368 reads; of these: 33280368 (100.00%) were unpaired; of these: 2570604 (7.72%) aligned 0 times 22561382 (67.79%) aligned exactly 1 time 8148382 (24.48%) aligned >1 times 92.28% overall alignment rate Time searching: 00:25:13 Overall time: 00:25:13 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 16 files... [bam_rmdupse_core] 9405761 / 30709764 = 0.3063 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.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 @ Tue, 10 Dec 2019 13:14:56: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:14:56: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:15:03: 1000000 INFO @ Tue, 10 Dec 2019 13:15:10: 2000000 INFO @ Tue, 10 Dec 2019 13:15:18: 3000000 INFO @ Tue, 10 Dec 2019 13:15:25: 4000000 INFO @ Tue, 10 Dec 2019 13:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.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 @ Tue, 10 Dec 2019 13:15:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:15:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:15:32: 5000000 INFO @ Tue, 10 Dec 2019 13:15:34: 1000000 INFO @ Tue, 10 Dec 2019 13:15:40: 6000000 INFO @ Tue, 10 Dec 2019 13:15:43: 2000000 INFO @ Tue, 10 Dec 2019 13:15:48: 7000000 INFO @ Tue, 10 Dec 2019 13:15:52: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:15:55: 8000000 INFO @ Tue, 10 Dec 2019 13:15:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.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 @ Tue, 10 Dec 2019 13:15:55: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:15:55: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:16:01: 4000000 INFO @ Tue, 10 Dec 2019 13:16:03: 9000000 INFO @ Tue, 10 Dec 2019 13:16:04: 1000000 INFO @ Tue, 10 Dec 2019 13:16:09: 5000000 INFO @ Tue, 10 Dec 2019 13:16:10: 10000000 INFO @ Tue, 10 Dec 2019 13:16:12: 2000000 INFO @ Tue, 10 Dec 2019 13:16:18: 11000000 INFO @ Tue, 10 Dec 2019 13:16:18: 6000000 INFO @ Tue, 10 Dec 2019 13:16:21: 3000000 INFO @ Tue, 10 Dec 2019 13:16:25: 12000000 INFO @ Tue, 10 Dec 2019 13:16:28: 7000000 INFO @ Tue, 10 Dec 2019 13:16:29: 4000000 INFO @ Tue, 10 Dec 2019 13:16:33: 13000000 INFO @ Tue, 10 Dec 2019 13:16:36: 8000000 INFO @ Tue, 10 Dec 2019 13:16:38: 5000000 INFO @ Tue, 10 Dec 2019 13:16:41: 14000000 INFO @ Tue, 10 Dec 2019 13:16:45: 9000000 INFO @ Tue, 10 Dec 2019 13:16:46: 6000000 INFO @ Tue, 10 Dec 2019 13:16:48: 15000000 INFO @ Tue, 10 Dec 2019 13:16:54: 10000000 INFO @ Tue, 10 Dec 2019 13:16:55: 7000000 INFO @ Tue, 10 Dec 2019 13:16:56: 16000000 INFO @ Tue, 10 Dec 2019 13:17:03: 11000000 INFO @ Tue, 10 Dec 2019 13:17:03: 8000000 INFO @ Tue, 10 Dec 2019 13:17:03: 17000000 INFO @ Tue, 10 Dec 2019 13:17:11: 18000000 INFO @ Tue, 10 Dec 2019 13:17:12: 9000000 INFO @ Tue, 10 Dec 2019 13:17:12: 12000000 INFO @ Tue, 10 Dec 2019 13:17:19: 19000000 INFO @ Tue, 10 Dec 2019 13:17:20: 10000000 INFO @ Tue, 10 Dec 2019 13:17:21: 13000000 INFO @ Tue, 10 Dec 2019 13:17:27: 20000000 INFO @ Tue, 10 Dec 2019 13:17:29: 11000000 INFO @ Tue, 10 Dec 2019 13:17:29: 14000000 INFO @ Tue, 10 Dec 2019 13:17:34: 21000000 INFO @ Tue, 10 Dec 2019 13:17:37: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:17:37: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:17:37: #1 total tags in treatment: 21304003 INFO @ Tue, 10 Dec 2019 13:17:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:17:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:17:37: 12000000 INFO @ Tue, 10 Dec 2019 13:17:37: #1 tags after filtering in treatment: 21303865 INFO @ Tue, 10 Dec 2019 13:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:17:37: #1 finished! INFO @ Tue, 10 Dec 2019 13:17:37: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:17:38: 15000000 INFO @ Tue, 10 Dec 2019 13:17:42: #2 number of paired peaks: 57512 INFO @ Tue, 10 Dec 2019 13:17:42: start model_add_line... INFO @ Tue, 10 Dec 2019 13:17:42: start X-correlation... INFO @ Tue, 10 Dec 2019 13:17:42: end of X-cor INFO @ Tue, 10 Dec 2019 13:17:42: #2 finished! INFO @ Tue, 10 Dec 2019 13:17:42: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:17:42: #2 alternative fragment length(s) may be 3,154 bps INFO @ Tue, 10 Dec 2019 13:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.05_model.r INFO @ Tue, 10 Dec 2019 13:17:42: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:17:46: 13000000 INFO @ Tue, 10 Dec 2019 13:17:47: 16000000 INFO @ Tue, 10 Dec 2019 13:17:54: 14000000 INFO @ Tue, 10 Dec 2019 13:17:56: 17000000 INFO @ Tue, 10 Dec 2019 13:18:02: 15000000 INFO @ Tue, 10 Dec 2019 13:18:05: 18000000 INFO @ Tue, 10 Dec 2019 13:18:11: 16000000 INFO @ Tue, 10 Dec 2019 13:18:13: 19000000 INFO @ Tue, 10 Dec 2019 13:18:19: 17000000 INFO @ Tue, 10 Dec 2019 13:18:22: 20000000 INFO @ Tue, 10 Dec 2019 13:18:28: 18000000 INFO @ Tue, 10 Dec 2019 13:18:31: 21000000 INFO @ Tue, 10 Dec 2019 13:18:34: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:18:34: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:18:34: #1 total tags in treatment: 21304003 INFO @ Tue, 10 Dec 2019 13:18:34: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:18:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:18:34: #1 tags after filtering in treatment: 21303865 INFO @ Tue, 10 Dec 2019 13:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:18:34: #1 finished! INFO @ Tue, 10 Dec 2019 13:18:34: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:18:36: 19000000 INFO @ Tue, 10 Dec 2019 13:18:39: #2 number of paired peaks: 57512 INFO @ Tue, 10 Dec 2019 13:18:39: start model_add_line... INFO @ Tue, 10 Dec 2019 13:18:39: start X-correlation... INFO @ Tue, 10 Dec 2019 13:18:39: end of X-cor INFO @ Tue, 10 Dec 2019 13:18:39: #2 finished! INFO @ Tue, 10 Dec 2019 13:18:39: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:18:39: #2 alternative fragment length(s) may be 3,154 bps INFO @ Tue, 10 Dec 2019 13:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.10_model.r INFO @ Tue, 10 Dec 2019 13:18:39: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:18:45: 20000000 INFO @ Tue, 10 Dec 2019 13:18:50: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:18:53: 21000000 INFO @ Tue, 10 Dec 2019 13:18:56: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:18:56: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:18:56: #1 total tags in treatment: 21304003 INFO @ Tue, 10 Dec 2019 13:18:56: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:18:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:18:56: #1 tags after filtering in treatment: 21303865 INFO @ Tue, 10 Dec 2019 13:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:18:56: #1 finished! INFO @ Tue, 10 Dec 2019 13:18:56: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:19:01: #2 number of paired peaks: 57512 INFO @ Tue, 10 Dec 2019 13:19:01: start model_add_line... INFO @ Tue, 10 Dec 2019 13:19:01: start X-correlation... INFO @ Tue, 10 Dec 2019 13:19:01: end of X-cor INFO @ Tue, 10 Dec 2019 13:19:01: #2 finished! INFO @ Tue, 10 Dec 2019 13:19:01: #2 predicted fragment length is 154 bps INFO @ Tue, 10 Dec 2019 13:19:01: #2 alternative fragment length(s) may be 3,154 bps INFO @ Tue, 10 Dec 2019 13:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.20_model.r INFO @ Tue, 10 Dec 2019 13:19:01: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.05_summits.bed INFO @ Tue, 10 Dec 2019 13:19:25: Done! pass1 - making usageList (87 chroms): 3 millis pass2 - checking and writing primary data (4973 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:19:48: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:20:09: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.10_summits.bed INFO @ Tue, 10 Dec 2019 13:20:23: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (778 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779826/SRX4779826.20_summits.bed INFO @ Tue, 10 Dec 2019 13:20:44: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (230 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。