Job ID = 2002157 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T01:36:48 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 ) 2019-07-05T01:36:53 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 ) 2019-07-05T01:40:47 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 : 26,293,761 reads read : 26,293,761 reads written : 26,293,761 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:22:46 26293761 reads; of these: 26293761 (100.00%) were unpaired; of these: 549534 (2.09%) aligned 0 times 20232694 (76.95%) aligned exactly 1 time 5511533 (20.96%) aligned >1 times 97.91% overall alignment rate Time searching: 00:22:47 Overall time: 00:22:47 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] 420290 / 25744227 = 0.0163 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 11:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.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 11:31:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:31:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.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 11:31:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:31:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.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 11:31:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:31:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:31:28: 1000000 INFO @ Fri, 05 Jul 2019 11:31:28: 1000000 INFO @ Fri, 05 Jul 2019 11:31:28: 1000000 INFO @ Fri, 05 Jul 2019 11:31:36: 2000000 INFO @ Fri, 05 Jul 2019 11:31:36: 2000000 INFO @ Fri, 05 Jul 2019 11:31:36: 2000000 INFO @ Fri, 05 Jul 2019 11:31:44: 3000000 INFO @ Fri, 05 Jul 2019 11:31:44: 3000000 INFO @ Fri, 05 Jul 2019 11:31:44: 3000000 INFO @ Fri, 05 Jul 2019 11:31:52: 4000000 INFO @ Fri, 05 Jul 2019 11:31:52: 4000000 INFO @ Fri, 05 Jul 2019 11:31:52: 4000000 INFO @ Fri, 05 Jul 2019 11:32:00: 5000000 INFO @ Fri, 05 Jul 2019 11:32:01: 5000000 INFO @ Fri, 05 Jul 2019 11:32:01: 5000000 INFO @ Fri, 05 Jul 2019 11:32:09: 6000000 INFO @ Fri, 05 Jul 2019 11:32:09: 6000000 INFO @ Fri, 05 Jul 2019 11:32:09: 6000000 INFO @ Fri, 05 Jul 2019 11:32:17: 7000000 INFO @ Fri, 05 Jul 2019 11:32:19: 7000000 INFO @ Fri, 05 Jul 2019 11:32:19: 7000000 INFO @ Fri, 05 Jul 2019 11:32:26: 8000000 INFO @ Fri, 05 Jul 2019 11:32:28: 8000000 INFO @ Fri, 05 Jul 2019 11:32:28: 8000000 INFO @ Fri, 05 Jul 2019 11:32:34: 9000000 INFO @ Fri, 05 Jul 2019 11:32:36: 9000000 INFO @ Fri, 05 Jul 2019 11:32:36: 9000000 INFO @ Fri, 05 Jul 2019 11:32:42: 10000000 INFO @ Fri, 05 Jul 2019 11:32:45: 10000000 INFO @ Fri, 05 Jul 2019 11:32:45: 10000000 INFO @ Fri, 05 Jul 2019 11:32:50: 11000000 INFO @ Fri, 05 Jul 2019 11:32:53: 11000000 INFO @ Fri, 05 Jul 2019 11:32:54: 11000000 INFO @ Fri, 05 Jul 2019 11:32:58: 12000000 INFO @ Fri, 05 Jul 2019 11:33:02: 12000000 INFO @ Fri, 05 Jul 2019 11:33:02: 12000000 INFO @ Fri, 05 Jul 2019 11:33:06: 13000000 INFO @ Fri, 05 Jul 2019 11:33:10: 13000000 INFO @ Fri, 05 Jul 2019 11:33:11: 13000000 INFO @ Fri, 05 Jul 2019 11:33:14: 14000000 INFO @ Fri, 05 Jul 2019 11:33:19: 14000000 INFO @ Fri, 05 Jul 2019 11:33:19: 14000000 INFO @ Fri, 05 Jul 2019 11:33:22: 15000000 INFO @ Fri, 05 Jul 2019 11:33:27: 15000000 INFO @ Fri, 05 Jul 2019 11:33:27: 15000000 INFO @ Fri, 05 Jul 2019 11:33:31: 16000000 INFO @ Fri, 05 Jul 2019 11:33:35: 16000000 INFO @ Fri, 05 Jul 2019 11:33:36: 16000000 INFO @ Fri, 05 Jul 2019 11:33:38: 17000000 INFO @ Fri, 05 Jul 2019 11:33:44: 17000000 INFO @ Fri, 05 Jul 2019 11:33:44: 17000000 INFO @ Fri, 05 Jul 2019 11:33:46: 18000000 INFO @ Fri, 05 Jul 2019 11:33:52: 18000000 INFO @ Fri, 05 Jul 2019 11:33:52: 18000000 INFO @ Fri, 05 Jul 2019 11:33:54: 19000000 INFO @ Fri, 05 Jul 2019 11:34:00: 19000000 INFO @ Fri, 05 Jul 2019 11:34:00: 19000000 INFO @ Fri, 05 Jul 2019 11:34:03: 20000000 INFO @ Fri, 05 Jul 2019 11:34:08: 20000000 INFO @ Fri, 05 Jul 2019 11:34:09: 20000000 INFO @ Fri, 05 Jul 2019 11:34:11: 21000000 INFO @ Fri, 05 Jul 2019 11:34:17: 21000000 INFO @ Fri, 05 Jul 2019 11:34:17: 21000000 INFO @ Fri, 05 Jul 2019 11:34:19: 22000000 INFO @ Fri, 05 Jul 2019 11:34:25: 22000000 INFO @ Fri, 05 Jul 2019 11:34:26: 22000000 INFO @ Fri, 05 Jul 2019 11:34:27: 23000000 INFO @ Fri, 05 Jul 2019 11:34:33: 23000000 INFO @ Fri, 05 Jul 2019 11:34:34: 23000000 INFO @ Fri, 05 Jul 2019 11:34:35: 24000000 INFO @ Fri, 05 Jul 2019 11:34:41: 24000000 INFO @ Fri, 05 Jul 2019 11:34:42: 24000000 INFO @ Fri, 05 Jul 2019 11:34:43: 25000000 INFO @ Fri, 05 Jul 2019 11:34:46: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:34:48: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:34:48: #1 total tags in treatment: 25323937 INFO @ Fri, 05 Jul 2019 11:34:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:34:48: #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 11:34:48: #1 tags after filtering in treatment: 25323795 INFO @ Fri, 05 Jul 2019 11:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:34:48: #1 finished! INFO @ Fri, 05 Jul 2019 11:34:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:34:50: 25000000 INFO @ Fri, 05 Jul 2019 11:34:50: 25000000 INFO @ Fri, 05 Jul 2019 11:34:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:34:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:34:53: #1 total tags in treatment: 25323937 INFO @ Fri, 05 Jul 2019 11:34:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:34:53: #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 11:34:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:34:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:34:53: #1 total tags in treatment: 25323937 INFO @ Fri, 05 Jul 2019 11:34:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:34:53: #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 11:34:53: #1 tags after filtering in treatment: 25323795 INFO @ Fri, 05 Jul 2019 11:34:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:34:53: #1 finished! INFO @ Fri, 05 Jul 2019 11:34:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:34:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:34:54: #1 tags after filtering in treatment: 25323795 INFO @ Fri, 05 Jul 2019 11:34:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:34:54: #1 finished! INFO @ Fri, 05 Jul 2019 11:34:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:34:54: #2 number of paired peaks: 83082 INFO @ Fri, 05 Jul 2019 11:34:54: start model_add_line... INFO @ Fri, 05 Jul 2019 11:34:55: start X-correlation... INFO @ Fri, 05 Jul 2019 11:34:55: end of X-cor INFO @ Fri, 05 Jul 2019 11:34:55: #2 finished! INFO @ Fri, 05 Jul 2019 11:34:55: #2 predicted fragment length is 264 bps INFO @ Fri, 05 Jul 2019 11:34:55: #2 alternative fragment length(s) may be 264 bps INFO @ Fri, 05 Jul 2019 11:34:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.05_model.r INFO @ Fri, 05 Jul 2019 11:34:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:34:59: #2 number of paired peaks: 83082 INFO @ Fri, 05 Jul 2019 11:34:59: start model_add_line... INFO @ Fri, 05 Jul 2019 11:35:00: start X-correlation... INFO @ Fri, 05 Jul 2019 11:35:00: end of X-cor INFO @ Fri, 05 Jul 2019 11:35:00: #2 finished! INFO @ Fri, 05 Jul 2019 11:35:00: #2 predicted fragment length is 264 bps INFO @ Fri, 05 Jul 2019 11:35:00: #2 alternative fragment length(s) may be 264 bps INFO @ Fri, 05 Jul 2019 11:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.20_model.r INFO @ Fri, 05 Jul 2019 11:35:00: #2 number of paired peaks: 83082 INFO @ Fri, 05 Jul 2019 11:35:00: start model_add_line... INFO @ Fri, 05 Jul 2019 11:35:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:35:00: start X-correlation... INFO @ Fri, 05 Jul 2019 11:35:00: end of X-cor INFO @ Fri, 05 Jul 2019 11:35:00: #2 finished! INFO @ Fri, 05 Jul 2019 11:35:00: #2 predicted fragment length is 264 bps INFO @ Fri, 05 Jul 2019 11:35:00: #2 alternative fragment length(s) may be 264 bps INFO @ Fri, 05 Jul 2019 11:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.10_model.r INFO @ Fri, 05 Jul 2019 11:35:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:36:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:36:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:36:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:36:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:36:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.05_summits.bed INFO @ Fri, 05 Jul 2019 11:36:57: Done! pass1 - making usageList (77 chroms): 7 millis pass2 - checking and writing primary data (14244 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.20_summits.bed INFO @ Fri, 05 Jul 2019 11:37:02: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (322 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 11:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX1120746/ERX1120746.10_summits.bed INFO @ Fri, 05 Jul 2019 11:37:03: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (1602 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。