Job ID = 2002158 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T01:37:19 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 ) 2019-07-05T01:49:20 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 : 27,670,187 reads read : 27,670,187 reads written : 27,670,187 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:59 27670187 reads; of these: 27670187 (100.00%) were unpaired; of these: 857248 (3.10%) aligned 0 times 21657478 (78.27%) aligned exactly 1 time 5155461 (18.63%) aligned >1 times 96.90% overall alignment rate Time searching: 00:24:02 Overall time: 00:24:02 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] 541179 / 26812939 = 0.0202 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 11:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.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 11:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.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 11:35:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:35:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:35:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:35:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.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 11:35:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:35:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:35:37: 1000000 INFO @ Fri, 05 Jul 2019 11:35:37: 1000000 INFO @ Fri, 05 Jul 2019 11:35:37: 1000000 INFO @ Fri, 05 Jul 2019 11:35:44: 2000000 INFO @ Fri, 05 Jul 2019 11:35:45: 2000000 INFO @ Fri, 05 Jul 2019 11:35:45: 2000000 INFO @ Fri, 05 Jul 2019 11:35:50: 3000000 INFO @ Fri, 05 Jul 2019 11:35:52: 3000000 INFO @ Fri, 05 Jul 2019 11:35:52: 3000000 INFO @ Fri, 05 Jul 2019 11:35:57: 4000000 INFO @ Fri, 05 Jul 2019 11:36:00: 4000000 INFO @ Fri, 05 Jul 2019 11:36:00: 4000000 INFO @ Fri, 05 Jul 2019 11:36:03: 5000000 INFO @ Fri, 05 Jul 2019 11:36:07: 5000000 INFO @ Fri, 05 Jul 2019 11:36:07: 5000000 INFO @ Fri, 05 Jul 2019 11:36:10: 6000000 INFO @ Fri, 05 Jul 2019 11:36:14: 6000000 INFO @ Fri, 05 Jul 2019 11:36:14: 6000000 INFO @ Fri, 05 Jul 2019 11:36:16: 7000000 INFO @ Fri, 05 Jul 2019 11:36:22: 7000000 INFO @ Fri, 05 Jul 2019 11:36:22: 7000000 INFO @ Fri, 05 Jul 2019 11:36:22: 8000000 INFO @ Fri, 05 Jul 2019 11:36:29: 9000000 INFO @ Fri, 05 Jul 2019 11:36:29: 8000000 INFO @ Fri, 05 Jul 2019 11:36:29: 8000000 INFO @ Fri, 05 Jul 2019 11:36:35: 10000000 INFO @ Fri, 05 Jul 2019 11:36:37: 9000000 INFO @ Fri, 05 Jul 2019 11:36:37: 9000000 INFO @ Fri, 05 Jul 2019 11:36:42: 11000000 INFO @ Fri, 05 Jul 2019 11:36:44: 10000000 INFO @ Fri, 05 Jul 2019 11:36:44: 10000000 INFO @ Fri, 05 Jul 2019 11:36:48: 12000000 INFO @ Fri, 05 Jul 2019 11:36:51: 11000000 INFO @ Fri, 05 Jul 2019 11:36:51: 11000000 INFO @ Fri, 05 Jul 2019 11:36:54: 13000000 INFO @ Fri, 05 Jul 2019 11:36:59: 12000000 INFO @ Fri, 05 Jul 2019 11:36:59: 12000000 INFO @ Fri, 05 Jul 2019 11:37:01: 14000000 INFO @ Fri, 05 Jul 2019 11:37:06: 13000000 INFO @ Fri, 05 Jul 2019 11:37:06: 13000000 INFO @ Fri, 05 Jul 2019 11:37:07: 15000000 INFO @ Fri, 05 Jul 2019 11:37:13: 14000000 INFO @ Fri, 05 Jul 2019 11:37:13: 14000000 INFO @ Fri, 05 Jul 2019 11:37:14: 16000000 INFO @ Fri, 05 Jul 2019 11:37:20: 17000000 INFO @ Fri, 05 Jul 2019 11:37:21: 15000000 INFO @ Fri, 05 Jul 2019 11:37:21: 15000000 INFO @ Fri, 05 Jul 2019 11:37:27: 18000000 INFO @ Fri, 05 Jul 2019 11:37:28: 16000000 INFO @ Fri, 05 Jul 2019 11:37:28: 16000000 INFO @ Fri, 05 Jul 2019 11:37:33: 19000000 INFO @ Fri, 05 Jul 2019 11:37:35: 17000000 INFO @ Fri, 05 Jul 2019 11:37:35: 17000000 INFO @ Fri, 05 Jul 2019 11:37:40: 20000000 INFO @ Fri, 05 Jul 2019 11:37:43: 18000000 INFO @ Fri, 05 Jul 2019 11:37:43: 18000000 INFO @ Fri, 05 Jul 2019 11:37:46: 21000000 INFO @ Fri, 05 Jul 2019 11:37:50: 19000000 INFO @ Fri, 05 Jul 2019 11:37:50: 19000000 INFO @ Fri, 05 Jul 2019 11:37:53: 22000000 INFO @ Fri, 05 Jul 2019 11:37:57: 20000000 INFO @ Fri, 05 Jul 2019 11:37:57: 20000000 INFO @ Fri, 05 Jul 2019 11:37:59: 23000000 INFO @ Fri, 05 Jul 2019 11:38:05: 21000000 INFO @ Fri, 05 Jul 2019 11:38:05: 21000000 INFO @ Fri, 05 Jul 2019 11:38:05: 24000000 INFO @ Fri, 05 Jul 2019 11:38:12: 25000000 INFO @ Fri, 05 Jul 2019 11:38:12: 22000000 INFO @ Fri, 05 Jul 2019 11:38:12: 22000000 INFO @ Fri, 05 Jul 2019 11:38:18: 26000000 INFO @ Fri, 05 Jul 2019 11:38:19: 23000000 INFO @ Fri, 05 Jul 2019 11:38:19: 23000000 INFO @ Fri, 05 Jul 2019 11:38:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:38:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:38:21: #1 total tags in treatment: 26271760 INFO @ Fri, 05 Jul 2019 11:38:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:38:21: #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 11:38:21: #1 tags after filtering in treatment: 26271584 INFO @ Fri, 05 Jul 2019 11:38:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:38:21: #1 finished! INFO @ Fri, 05 Jul 2019 11:38:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:38:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:38:27: 24000000 INFO @ Fri, 05 Jul 2019 11:38:27: 24000000 INFO @ Fri, 05 Jul 2019 11:38:29: #2 number of paired peaks: 126885 INFO @ Fri, 05 Jul 2019 11:38:29: start model_add_line... INFO @ Fri, 05 Jul 2019 11:38:29: start X-correlation... INFO @ Fri, 05 Jul 2019 11:38:29: end of X-cor INFO @ Fri, 05 Jul 2019 11:38:29: #2 finished! INFO @ Fri, 05 Jul 2019 11:38:29: #2 predicted fragment length is 252 bps INFO @ Fri, 05 Jul 2019 11:38:29: #2 alternative fragment length(s) may be 252 bps INFO @ Fri, 05 Jul 2019 11:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.20_model.r INFO @ Fri, 05 Jul 2019 11:38:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:38:34: 25000000 INFO @ Fri, 05 Jul 2019 11:38:34: 25000000 INFO @ Fri, 05 Jul 2019 11:38:42: 26000000 INFO @ Fri, 05 Jul 2019 11:38:42: 26000000 INFO @ Fri, 05 Jul 2019 11:38:44: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:38:44: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:38:44: #1 total tags in treatment: 26271760 INFO @ Fri, 05 Jul 2019 11:38:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:38:44: #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 11:38:44: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:38:44: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:38:44: #1 total tags in treatment: 26271760 INFO @ Fri, 05 Jul 2019 11:38:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:38:44: #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 11:38:45: #1 tags after filtering in treatment: 26271584 INFO @ Fri, 05 Jul 2019 11:38:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:38:45: #1 finished! INFO @ Fri, 05 Jul 2019 11:38:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:38:45: #1 tags after filtering in treatment: 26271584 INFO @ Fri, 05 Jul 2019 11:38:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:38:45: #1 finished! INFO @ Fri, 05 Jul 2019 11:38:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:38:52: #2 number of paired peaks: 126885 INFO @ Fri, 05 Jul 2019 11:38:52: start model_add_line... INFO @ Fri, 05 Jul 2019 11:38:52: #2 number of paired peaks: 126885 INFO @ Fri, 05 Jul 2019 11:38:52: start model_add_line... INFO @ Fri, 05 Jul 2019 11:38:52: start X-correlation... INFO @ Fri, 05 Jul 2019 11:38:52: end of X-cor INFO @ Fri, 05 Jul 2019 11:38:52: #2 finished! INFO @ Fri, 05 Jul 2019 11:38:52: #2 predicted fragment length is 252 bps INFO @ Fri, 05 Jul 2019 11:38:52: #2 alternative fragment length(s) may be 252 bps INFO @ Fri, 05 Jul 2019 11:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.05_model.r INFO @ Fri, 05 Jul 2019 11:38:52: start X-correlation... INFO @ Fri, 05 Jul 2019 11:38:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:38:52: end of X-cor INFO @ Fri, 05 Jul 2019 11:38:52: #2 finished! INFO @ Fri, 05 Jul 2019 11:38:52: #2 predicted fragment length is 252 bps INFO @ Fri, 05 Jul 2019 11:38:52: #2 alternative fragment length(s) may be 252 bps INFO @ Fri, 05 Jul 2019 11:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.10_model.r INFO @ Fri, 05 Jul 2019 11:38:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:39:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:40:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:40:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:40:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:40:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:40:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.20_summits.bed INFO @ Fri, 05 Jul 2019 11:40:37: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (594 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.10_summits.bed INFO @ Fri, 05 Jul 2019 11:41:06: Done! pass1 - making usageList (62 chroms): 3 millis pass2 - checking and writing primary data (6497 records, 4 fields): 14 millis INFO @ Fri, 05 Jul 2019 11:41:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:41:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:41:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120747/ERX1120747.05_summits.bed INFO @ Fri, 05 Jul 2019 11:41:08: Done! pass1 - making usageList (114 chroms): 7 millis pass2 - checking and writing primary data (31249 records, 4 fields): 70 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。