Job ID = 2001530 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T19:21:08 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 ) 2019-07-04T19:23:25 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 ) 2019-07-04T19:23:25 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 : 26,192,097 reads read : 26,192,097 reads written : 26,192,097 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: 00:00:00 Multiseed full-index search: 00:10:27 26192097 reads; of these: 26192097 (100.00%) were unpaired; of these: 772486 (2.95%) aligned 0 times 19205503 (73.33%) aligned exactly 1 time 6214108 (23.73%) aligned >1 times 97.05% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 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 8 files... [bam_rmdupse_core] 1324317 / 25419611 = 0.0521 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 04:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.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 04:43:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:43:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.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 04:43:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:43:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.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 04:43:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:43:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:43:50: 1000000 INFO @ Fri, 05 Jul 2019 04:43:50: 1000000 INFO @ Fri, 05 Jul 2019 04:43:51: 1000000 INFO @ Fri, 05 Jul 2019 04:43:57: 2000000 INFO @ Fri, 05 Jul 2019 04:43:58: 2000000 INFO @ Fri, 05 Jul 2019 04:43:58: 2000000 INFO @ Fri, 05 Jul 2019 04:44:04: 3000000 INFO @ Fri, 05 Jul 2019 04:44:05: 3000000 INFO @ Fri, 05 Jul 2019 04:44:06: 3000000 INFO @ Fri, 05 Jul 2019 04:44:11: 4000000 INFO @ Fri, 05 Jul 2019 04:44:12: 4000000 INFO @ Fri, 05 Jul 2019 04:44:14: 4000000 INFO @ Fri, 05 Jul 2019 04:44:18: 5000000 INFO @ Fri, 05 Jul 2019 04:44:19: 5000000 INFO @ Fri, 05 Jul 2019 04:44:21: 5000000 INFO @ Fri, 05 Jul 2019 04:44:25: 6000000 INFO @ Fri, 05 Jul 2019 04:44:25: 6000000 INFO @ Fri, 05 Jul 2019 04:44:29: 6000000 INFO @ Fri, 05 Jul 2019 04:44:32: 7000000 INFO @ Fri, 05 Jul 2019 04:44:32: 7000000 INFO @ Fri, 05 Jul 2019 04:44:36: 7000000 INFO @ Fri, 05 Jul 2019 04:44:38: 8000000 INFO @ Fri, 05 Jul 2019 04:44:39: 8000000 INFO @ Fri, 05 Jul 2019 04:44:44: 8000000 INFO @ Fri, 05 Jul 2019 04:44:45: 9000000 INFO @ Fri, 05 Jul 2019 04:44:46: 9000000 INFO @ Fri, 05 Jul 2019 04:44:51: 9000000 INFO @ Fri, 05 Jul 2019 04:44:52: 10000000 INFO @ Fri, 05 Jul 2019 04:44:53: 10000000 INFO @ Fri, 05 Jul 2019 04:44:59: 11000000 INFO @ Fri, 05 Jul 2019 04:44:59: 10000000 INFO @ Fri, 05 Jul 2019 04:44:59: 11000000 INFO @ Fri, 05 Jul 2019 04:45:06: 12000000 INFO @ Fri, 05 Jul 2019 04:45:06: 12000000 INFO @ Fri, 05 Jul 2019 04:45:07: 11000000 INFO @ Fri, 05 Jul 2019 04:45:13: 13000000 INFO @ Fri, 05 Jul 2019 04:45:14: 13000000 INFO @ Fri, 05 Jul 2019 04:45:14: 12000000 INFO @ Fri, 05 Jul 2019 04:45:20: 14000000 INFO @ Fri, 05 Jul 2019 04:45:20: 14000000 INFO @ Fri, 05 Jul 2019 04:45:22: 13000000 INFO @ Fri, 05 Jul 2019 04:45:26: 15000000 INFO @ Fri, 05 Jul 2019 04:45:27: 15000000 INFO @ Fri, 05 Jul 2019 04:45:29: 14000000 INFO @ Fri, 05 Jul 2019 04:45:33: 16000000 INFO @ Fri, 05 Jul 2019 04:45:34: 16000000 INFO @ Fri, 05 Jul 2019 04:45:37: 15000000 INFO @ Fri, 05 Jul 2019 04:45:40: 17000000 INFO @ Fri, 05 Jul 2019 04:45:41: 17000000 INFO @ Fri, 05 Jul 2019 04:45:45: 16000000 INFO @ Fri, 05 Jul 2019 04:45:47: 18000000 INFO @ Fri, 05 Jul 2019 04:45:48: 18000000 INFO @ Fri, 05 Jul 2019 04:45:52: 17000000 INFO @ Fri, 05 Jul 2019 04:45:54: 19000000 INFO @ Fri, 05 Jul 2019 04:45:55: 19000000 INFO @ Fri, 05 Jul 2019 04:46:00: 18000000 INFO @ Fri, 05 Jul 2019 04:46:01: 20000000 INFO @ Fri, 05 Jul 2019 04:46:02: 20000000 INFO @ Fri, 05 Jul 2019 04:46:07: 19000000 INFO @ Fri, 05 Jul 2019 04:46:07: 21000000 INFO @ Fri, 05 Jul 2019 04:46:08: 21000000 INFO @ Fri, 05 Jul 2019 04:46:14: 22000000 INFO @ Fri, 05 Jul 2019 04:46:15: 20000000 INFO @ Fri, 05 Jul 2019 04:46:15: 22000000 INFO @ Fri, 05 Jul 2019 04:46:21: 23000000 INFO @ Fri, 05 Jul 2019 04:46:22: 23000000 INFO @ Fri, 05 Jul 2019 04:46:22: 21000000 INFO @ Fri, 05 Jul 2019 04:46:28: 24000000 INFO @ Fri, 05 Jul 2019 04:46:29: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:46:29: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:46:29: #1 total tags in treatment: 24095294 INFO @ Fri, 05 Jul 2019 04:46:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:46:29: #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 04:46:29: 24000000 INFO @ Fri, 05 Jul 2019 04:46:29: #1 tags after filtering in treatment: 24095143 INFO @ Fri, 05 Jul 2019 04:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:46:29: #1 finished! INFO @ Fri, 05 Jul 2019 04:46:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:46:30: 22000000 INFO @ Fri, 05 Jul 2019 04:46:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:46:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:46:30: #1 total tags in treatment: 24095294 INFO @ Fri, 05 Jul 2019 04:46:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:46:30: #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 04:46:30: #1 tags after filtering in treatment: 24095143 INFO @ Fri, 05 Jul 2019 04:46:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:46:30: #1 finished! INFO @ Fri, 05 Jul 2019 04:46:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:46:34: #2 number of paired peaks: 44348 INFO @ Fri, 05 Jul 2019 04:46:34: start model_add_line... INFO @ Fri, 05 Jul 2019 04:46:34: start X-correlation... INFO @ Fri, 05 Jul 2019 04:46:34: end of X-cor INFO @ Fri, 05 Jul 2019 04:46:34: #2 finished! INFO @ Fri, 05 Jul 2019 04:46:34: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 04:46:34: #2 alternative fragment length(s) may be 2,136 bps INFO @ Fri, 05 Jul 2019 04:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.05_model.r INFO @ Fri, 05 Jul 2019 04:46:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:46:35: #2 number of paired peaks: 44348 INFO @ Fri, 05 Jul 2019 04:46:35: start model_add_line... INFO @ Fri, 05 Jul 2019 04:46:35: start X-correlation... INFO @ Fri, 05 Jul 2019 04:46:35: end of X-cor INFO @ Fri, 05 Jul 2019 04:46:35: #2 finished! INFO @ Fri, 05 Jul 2019 04:46:35: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 04:46:35: #2 alternative fragment length(s) may be 2,136 bps INFO @ Fri, 05 Jul 2019 04:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.20_model.r INFO @ Fri, 05 Jul 2019 04:46:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:46:37: 23000000 INFO @ Fri, 05 Jul 2019 04:46:45: 24000000 INFO @ Fri, 05 Jul 2019 04:46:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:46:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:46:46: #1 total tags in treatment: 24095294 INFO @ Fri, 05 Jul 2019 04:46:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:46:46: #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 04:46:46: #1 tags after filtering in treatment: 24095143 INFO @ Fri, 05 Jul 2019 04:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:46:46: #1 finished! INFO @ Fri, 05 Jul 2019 04:46:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:46:51: #2 number of paired peaks: 44348 INFO @ Fri, 05 Jul 2019 04:46:51: start model_add_line... INFO @ Fri, 05 Jul 2019 04:46:51: start X-correlation... INFO @ Fri, 05 Jul 2019 04:46:51: end of X-cor INFO @ Fri, 05 Jul 2019 04:46:51: #2 finished! INFO @ Fri, 05 Jul 2019 04:46:51: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 04:46:51: #2 alternative fragment length(s) may be 2,136 bps INFO @ Fri, 05 Jul 2019 04:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.10_model.r INFO @ Fri, 05 Jul 2019 04:46:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:47:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:47:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:48:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.20_summits.bed INFO @ Fri, 05 Jul 2019 04:48:32: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.05_summits.bed INFO @ Fri, 05 Jul 2019 04:48:33: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (2583 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101874/ERX101874.10_summits.bed INFO @ Fri, 05 Jul 2019 04:48:49: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。